WO2006083915A1

WO2006083915A1 - Multiplexed and differentially encoded biological analyzer planar array apparatus and methods

Info

Publication number: WO2006083915A1
Application number: PCT/US2006/003475
Authority: WO
Inventors: David D. Nolte; Manoj Varma; Leilei Peng; Fred E. Regnier; Ming Zhao
Original assignee: Purdue Research Foundation
Priority date: 2005-02-01
Filing date: 2006-02-01
Publication date: 2006-08-10

Abstract

A planar array for example, a bioCD, having plurality of biological recognition molecules including a first type of biological recognition molecules distributed about a substrate according to a first frequency, and a second type of biological recognition molecules distributed about the substrate according to a second frequency is disclosed. An apparatus including a surface normal interferometry platform including a scanning pathway and a plurality of analyzer molecules adapted to detect the presence or absence of a plurality of target analytes is also disclosed.

Description

MULTIPLEXED AND DIFFERENTIALLY ENCODED BIOLOGICAL ANALYZERPLANAR ARRAYAPPARATUS AND METHODS

Cross Reference

This application claims the benefit of U.S. Provisional Patent Application Serial No. 60/649,043, entitled "MULTI-PLEXED LASER SCANNING INTEREEROMETRIC BIOCHIPS AND BIODISKS," filed on February 1, 2005, and claims the benefit of U.S. Provisional Patent Application Serial No. 60/648,724, entitled "METHOD FOR CONDUCTING CARRIER-WAVE SIDE-BAND OPTICAL

ASSAYS FOR MOLECULAR RECOGNITION," filed on February 1, 2005, and the same are expressly incorporated herein by reference.

Technical Field

The present invention generally relates to a device for detecting the presence of specific biological material in a sample, and more particularly to a laser compact disc system for detecting the presence of biological pathogens and/or analyte molecules bound to target receptors on the disc by sensing changes in the optical characteristics of a probe beam reflected from the disc caused by the pathogens and/or analytes.

Background

In many chemical, biological, medical, and diagnostic applications, it is desirable to detect the presence of specific molecular structures in a sample. Many molecular structures such as cells, viruses, bacteria, toxins, peptides, DNA fragments, and antibodies are recognized by particular receptors. Biochemical technologies including gene chips, immunological chips, and DNA arrays for detecting gene expression patterns in cancer cells, exploit the interaction between these molecular structures and the receptors. [For examples see the descriptions in the following articles: Sanders, G.H.W. and A. Manz, Chip-based microsystems for genomic and proteomic analysis. Trends in Anal. Chem., 2000, Vol. 19(6), p. 364-378. Wang, J., From DNA biosensors to gene chips. Nucl. Acids Res., 2000, Vol. 28(16), p. 3011- 3016; Hagman, M., Doing immunology on a chip. Science, 2000, Vol. 290, p. 82-83; Marx, J., DNA Arrays reveal cancer in its many forms. Science, 2000, Vol. 289, p. 1670-1672], These technologies generally employ a stationary chip prepared to include the desired receptors (those which interact with the target analyte or molecular structure under test). Since the receptor areas can be quite small, chips may be produced which test for a plurality of analytes. Ideally, many thousand binding receptors are provided to provide a complete assay. When the receptors are exposed to a biological sample, only a few may bind a specific protein or pathogen. Ideally, these receptor sites are identified in as short a time as possible.

One such technology for screening for a plurality of molecular structures is the so-called immunological compact disk, which simply includes an antibody microarray. [For examples see the descriptions in the following articles: Eldns, R., F. Chu, and E. Biggart, Development of microspot multi-analyte ratiometric immunoassay using dual flourescent-Jabelled antibodies. Anal. Chim. Acta, 1989, Vol. 227, p. 73-96; Eldns, R. and F. W. Chu, Multianalyte microspot immunoassay - Microanalytical "compact Disk" of the future. Clin. Chem., 1991, Vol. 37(11), p. 1955-1967; Eldns, R., Ligand assays: from electrophoresis to miniaturized microarray s. Clin. Chem., 1998, Vol. 44(9), p. 2015-2030]. Conventional fluorescence detection is employed to sense the presence in the miciOarray of the molecular structures under test. Other approaches to immunological assays employ traditional Mach-Zender interferometers that include waveguides and grating couplers. [For examples see the descriptions in the following articles: Gao, H., et al., Immunosensing with photo-immobilized immunoreagents on planar optical wave guides. Biosensors and Bioelectronics, 1995, Vol. 10, p. 317-328; Maisenholder, B., et al., A GaAs/AlGaAs-based refractometer platform for integrated optical sensing applications. Sensors and Actuators B, 1997, Vol. 38-39, p. 324-329; Kunz, R.E., Miniature integrated optical modules for chemical and biochemical sensing. Sensors and Actuators B, 1997, Vol. 38-39, p. 13-28; Dϋbendorfer, J. and R.E. Kunz, Reference pads for miniature integrated optical sensors. Sensors and Actuators B, 1997 Vol. 38-39, p. 116-121; Brecht, A. and G. Gauglitz, recent developments in optical transducers for chemical or biochemical applications. Sensors and Actuators B, 1997, Vol. 38-39, p. 1-7]. Interferometric optical biosensors have the intrinsic advantage of interferometric sensitivity, but are often characterized by large surface areas per element, long interaction lengths, or complicated resonance structures. They also can be susceptible to phase drift from thermal and mechanical effects. Current practice is to perform long time integrations (as in fluorescence detection) to achieve a significant signal. However, the long integration times place the measurement firmly in the l'ange of 1/f noise (frequency = 1/τ, where τ is the measurement time). Likewise, SPR measurement approaches (for example systems from Biacore) or resonant mirror approaches (for example systems from SRU Biosystems) are angle resolved or wavelength resolved, requiring detailed measurements that take long integration times. While the abovementioned techniques have proven useful for producing and reading assay information within the chemical, biological, medical and diagnostic application industries, developing improved fabrication and reading techniques for planar arrays with significant improvement in performance over existing planar array technology is desirable.

Summary

One embodiment according to the present invention includes a planar array having plurality of biological recognition molecules including at least two types of biological recognition molecules distributed about a substrate. A first type of biological recognition molecules is distributed according to a first frequency and a second type of biological recognition molecules is distributed according to a second frequency. In another embodiment according to the present invention the substrate is an optically readable disk and the first type of biological recognition molecules is adapted to selectively bind a first type of antibody or antigen. In a further embodiment according to the present invention the substrate is a micro diffraction bio-CD, a phase contrast bio- CD, or an adaptive optics bio-CD. In an additional embodiment according to the present invention the plurality of biological recognition molecules includes molecules for binding cells, viruses, bacteria, toxins, peptides, DNA fragments, or antibodies. Another embodiment according to the present invention includes a planar array having plurality of biological recognition molecules including at least two kinds of biological recognition molecules distributed about a substrate. A first kind of biological recognition molecules is distributed at a first height or depth relative to a surface of the substrate and a second kind of biological recognition molecules is distributed at a second height or depth relative to the surface. In a further embodiment according to the present invention the first ldnd of biological recognition molecules is adapted to selectively bind a first ldnd of antibody or antigen and the second ldnd of biological recognition molecules is adapted to selectively bind a second ldnd of antibody or antigen. In another embodiment according to the present invention the first ldnd of biological recognition molecules is adapted to bind an antibody or antigen and the second ldnd of biological recognition molecule is adapted to bind a cDNA or DNA fragment.

A further embodiment according to the present invention includes an apparatus including a surface normal interferometry platform including a scanning pathway and a plurality of analyzer molecules adapted to detect the presence or absence of a plurality of target analytes. The plurality of analyzer molecules are distributed about the scanning pathway according to a multiplexing scheme. In an additional embodiment according to the present invention the platform is a micro diffraction bio-CD, a phase contrast bio-CD, or an adaptive optics bio-CD. In a further embodiment according to the present invention the plurality of analyzer molecules includes first analyzer molecules for detecting the presence or absence of a first antibody or antigen and second analyzer molecules for detecting the presence or absence of a second antibody or antigen. In another embodiment according tot the present invention the multiplexing scheme includes frequency-domain multiplexing, space-domain multiplexing, wavelength-domain multiplexing, or code-division multiplexing. In a further embodiment according to the present invention the pathway is substantially ring shaped and the surface-normal interferometry platform is a self referencing phase quadrature interferometry platform. A further embodiment according to the present invention further includes a plurality of ring shaped pathways each including a plurality of analyzer molecules distributed thereabout according to a multiplexing scheme.

Another embodiment of the present invention includes a method including multiplexing a plurality of lands of capture molecules about a detection pathway, contacting a biological sample to the array, detecting the presence or absence of binding of the plurality of lands of capture molecules and a plurality of target analytes using interferometry. In another embodiment according to the present invention the multiplexing includes distributing a first kind of capture molecule at first spatial frequency, distributing a second kind of capture molecule at a second spatial frequency, and distributing a third kind of capture molecule at a third spatial frequency. In a further embodiment according to the present invention the detecting further comprises detecting a first binding using a first wavelength of laser light and a second binding using a second wavelength of laser light. In an additional embodiment according to the present invention the detection pathway is defined along a surface of a bio-optical disk. A further embodiment according to the present invention further includes rotating the pathway in connection with the detecting. In another embodiment according to the present invention the detecting uses self-referencing phase quadrature interferometry. An additional embodiment according to the present invention further includes demultiplexing information of a particular capture molecule and a particular target analyte in connection with the detecting. A further embodiment according to the present invention includes a method of probing a plurality of analyzer molecules distributed about a detection platform. The method includes contacting a test sample to the plurality of analyzer molecules, scanning the plurality of analyzer molecules at a rate relating to a carrier frequency signal, and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially at a sideband of the carrier frequency signal. Another embodiment according to the present invention further includes prescanning the plurality of analyzer molecules before the contacting and improving the detecting based upon a difference between the scanning and the prescanning. In an additional embodiment according to the present invention the sideband is substantially free from overlap with the carrier frequency signal. In another embodiment according to the present invention the detecting utilizes self referencing phase quadrature interferometric detection. In a further embodiment according to the present invention the detection platform is a bio-CD. Another embodiment according to the present invention further includes suppressing the carrier frequency signal. In another embodiment according to the present invention the detecting utilizes interferometry and the scanning utilizes a laser beam. Another embodiment according to the present invention further includes detecting the presence or absence of a second biological molecule based at least in part upon the presence or absence of a second signal substantially at a second sideband of the carrier frequency signal. In an additional embodiment according to the present invention the detecting includes detecting a harmonic signal closest to zero frequency. In another embodiment according to the present invention the detecting includes detecting a harmonic signal at a frequency greater than that of a harmonic signal closest to zero frequency. In a further embodiment according to the present invention the detecting includes detecting a signal at or about a fundamental carrier frequency. In an additional embodiment according to the present invention the detecting utilizes fluorescence detection.

Another embodiment according to the present invention includes a molecule detection platform including a substrate and a plurality of targets positioned about the substrate. Specific analyzer molecules adapted to bind a specific analyte are immobilized about a first set of the targets. Nonspecific analyzer molecules are immobilized about a second set of the targets. The targets positioned about the substrate along at least a segment of a scanning pathway alternate between at least one of the first set and at least one of the second set. In another embodiment according to the present invention the targets positioned about the substrate alternate along the first segment of the scanning pathway between at least four of the first set and at least four of the second set. In a further embodiment according to the present invention the platform is a micro diffraction bio-CD, a phase contrast bio-CD, or an adaptive optics bio-CD. In an additional embodiment according to the present invention the nonspecific analyzer molecules exhibit nonspecific background binding at least substantially similar to the specific analyzer molecules. In another embodiment according to the present invention the targets are interferometric microstructures. In a further embodiment according to the present invention the targets positioned about the substrate along at least a second segment of the scanning pathway adjacent the first segment alternate between at least one of the second set and at least one of the first set in the opposite order as the alternation of the first segment. In an additional embodiment according to the present invention the targets are substantially contiguous along the segment of a scanning pathway. A further embodiment according to the present invention includes a method including providing a substrate for supporting biological analyzer molecules. The substrate includes at least one scanning pathway. The scanning pathway including a plurality of scanning targets. The method further includes distributing specific biological analyzer molecules adapted to detect a specific target analyte about a first set of the targets which alternate in groups of at least one with a second set of the targets. The second set of the targets does not include the specific biological analyzer molecules. Another embodiment according to the present invention further includes distributing nonspecific analyzer molecules about the second set of the targets. In a further embodiment according to the present invention the first set of the targets alternate in groups of at least four with the second set of the targets. Another embodiment according to the present invention further includes contacting a test sample to the molecules, scanning the plurality of targets at a rate, and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially about a frequency offset from a frequency defined by the distribution of the targets and the scanning rate. In an additional embodiment according to the present invention the detecting utilizes fluorescence. In another embodiment according to the present invention the substrate is a surface of a bio-CD, and the detecting utilizes phase quadrature interferometric detection

Additional embodiments, aspects, and advantages of the present invention will be apparent from the following description. Brief Description of the Drawings

Fig. 1 is a top schematic view of a distribution of elements including multiple analyzer molecules according to one embodiment of the present invention. Fig. 2 is a graph illustrating harmonic signals indicating the detection of analytes by the analyzer molecules of Fig. 1.

Fig. 3 is a top schematic view of a bio-CD according to one embodiment of the present invention.

Fig. 4 is a side sectional schematic view of a biosensor platform according to one embodiment of the present invention.

Fig. 5 is a side sectional schematic view of a biosensor platform according to one embodiment of the present invention.

Fig. 6 is a top schematic view of a distribution of elements including multiple analyzer molecules according to one embodiment of the present invention. Fig. 7 is a view of orthogonal bit sequences relating to the distribution of elements of Fig. 6;

Fig. 8 shows a graph of noise power density versus frequency according to an embodiment of the present invention;

Fig. 9 shows a graph of power spectrum versus frequency according to an embodiment of the present invention;

Fig. 10 shows a distribution of elements according to an embodiment of the present invention;

Fig. 11 shows a distribution of elements according to an embodiment of the present invention; Fig. 12 shows scanning of an element according to an embodiment of the present invention;

Fig. 13 shows a distribution of elements according to an embodiment of the present invention;

Fig. 14 shows a distribution of elements according to an embodiment of the present invention;

Fig. 15 shows a bio-CD according to an embodiment of the present invention; Fig. 16A shows a bio-CD according to an embodiment of the present invention;

Fig. 16B shows a bio-CD according to an embodiment of the present invention;

Fig. 17A shows a bio-CD according to an embodiment of the present invention;

Fig. 17B shows a bio-CD according to an embodiment of the present invention; Fig. 18 shows a bio-CD according to an embodiment of the present invention;

Fig. 19 shows scanning of elements according to an embodiment of the present invention;

Fig. 20 shows a detection system according to an embodiment of the present invention; Fig. 21 shows a graph of time domain results of scanning a differentially encoded MD-class calibration disk;

Fig. 22 shows a graph of frequency domain results of scanning a differentially encoded MD-class calibration disk;

Fig. 23 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;

Fig. 24 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;

Fig. 25 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk; Fig. 26 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;

Fig. 27 shows a portion of an MD-class disk;

Fig. 28 shows a graph of time domain results of scanning the disk of Fig. 20;

Fig. 29 shows a graph of frequency domain results of scanning the disk of Fig. 20;

Fig. 30 shows a graph of time domain results of scanning a PC-class disk;

Fig. 31 shows a portion of a PC-class disk;

Fig. 32 shows a magnified view of a portion of Fig. 24;

Fig. 33 shows Fourier domain results of scanning the disk of Fig. 24; Fig. 34 shows a demodulated image of the of the Fourier domain results of Fig.

26;

Fig. 35 shows a graph of a comparison of prescan subtraction without demodulation and prescan subtraction with demodulation. Detailed Description

For the purposes of promoting an understanding of the principles of the invention, reference will now be made to the embodiments illustrated in the drawings and specific language will be used to describe the same. It will nevertheless be understood that no limitation of the scope of the invention is thereby intended, such alterations and further modifications in the illustrated device, and such further applications of the principles of the invention as illustrated therein being contemplated as would normally occur to one skilled in the art to which the invention relates. With reference to Fig. 1 there is shown a distribution of elements 100 according to one embodiment of the present invention. The distribution of elements 100 includes at least three types of analyzer molecules 110, 120 and 130 distributed about scanning pathway 104 at three frequencies. Analyzer molecules 110 are distributed at a frequency of every other element of distribution 100. Analyzer molecules 120 are distributed at a frequency of every fourth element of distribution 100. Analyzer molecules 130 are distributed at a frequency of every eighth element of distribution 100. Distribution 100 also includes elements 150 which do not include analyzer molecules 110, 120, or 130. Additional types of analyzer molecules could be present at elements 150 and could, for example, be distributed at different frequencies such as every 16 elements, every 32 elements, or at other frequencies. Elements 150 could also not include analyzer molecules. As indicated by ellipses 106 and 108, elements 100 and reading pathway 104 can extend beyond the segment illustrated in Fig. 1 with the distribution of various analyzer molecules occurring at various frequencies as described above. Scanning footprint 102 travels over the distribution of elements 100 along scanning pathway 104 in the direction indicated by arrow R. In a preferred embodiment of the present invention, the distribution of elements 100 can be about a bio-CD which is scanned with a laser beam to detect the presence or absence of analytes bound to the analyzer molecules. In one embodiment the bio-CD is preferably scanned using surface normal self referencing phase quadrature interferometry techniques. In this embodiment elements 100 might, for example, be microstructures such as radial spokes formed on the surface of the bio-CD, and analyzer molecules 110, 120, and 130 may be immobilized, for example, as monolayers, fractional monolayers, partial monolayers, or near monolayers on surfaces of the microstructures. Furthermore, scanning pathway 104 can be one of multiple substantially concentric tracks which may be scanned with a laser, for example, using interferometry techniques such as phase quadrature interferometric detection techniques. Examples of phase quadrature interferometric techniques include the micro-diffraction quadrature class ("MD-class") and adaptive optic quadrature class ("AO-class") as described in U.S. Application Serial No.

10/726,772 filed on December 3, 2003 entitled "Adaptive Interferometric Multi-Analyte High-Speed Biosensor" (published on August 26, 2004 as U.S. Pub. No. 2004/0166593), the contents of which are incorporated herein by reference. Other examples of phase quadrature interferometric techniques include the phase-contrast quadrature class ("PC-class") as described in U.S. Provisional Patent Application No. 60/649,070, filed February 1, 2005, entitled "Phase-Contrast Quadrature For Spinning Disk Interferometry And Immunological Assay", U.S. Provisional Patent Application No. 60/755,177, filed December 30, 2005, entitled "Phase-Contrast BioCD: High-Speed Immunoassays at Sub-Picogram Detection Levels", and U.S. Application Serial No. ??/???,??? being filed the same day as the present application that claims priority to these two provisional applications and entitled "Method And Apparatus For Phase Contrast Quadrature Interferometric Detection Of An Immunoassay". The disclosures of the utility application entitled "Method And Apparatus For Phase Contrast Quadrature Interferometric Detection Of An Immunoassay" is incorporated herein by reference. In these embodiments, the scanning pathway is preferably a ring shaped track of a bio-CD. During scanning the bio-CD is rotated at a scanning rate, for example, 223 revolutions per minute, to successively pass elements through the footprint of the laser beam. Under these conditions, the spatial frequency of the distribution of elements 100 corresponds to a temporal frequency. Distribution of elements 100 is one exemplary embodiment of frequency- domain multiplexing in which different analyzer molecules are distributed at different spatial frequencies. Frequency-domain multiplexing can be used to test for many different analytes along a scanning pathway without requiring spatial separation of analyzer molecules used to detect particular analytes into sectors. In embodiments utilizing a rotating disk as a detection platform, systematics that depend on theta, the angular position about the disk, are substantially averaged out using this technique.

In addition to the embodiments described above, a variety of additional exemplary embodiments are also contemplated. For example, elements and analytes might be distributed in a variety of shapes such as substantially circular, oval, ellipsoid, square, polygonal, or other shapes. A variety of scanning pathway configurations might be utilized, including substantially linear or circular pathways, open pathways, closed pathways, curvilinear pathways, or spiral pathways, for example. A variety of frequency distributions of analyzer molecules can be used in addition to or instead of those described above. A variety of spacing of elements or analyzer molecules may also be used, for example, successive elements or analyzer molecules may be adjacent or adjoining, or may be spaced at intervals differing from those shown in connection with Fig. 1, or may overlap or occupy the same position. A variety of substrates and platforms may also be used including disks or chips supporting planar arrays including, for example, those described herein. Additionally, the variations and additional embodiments described elsewhere herein may apply to the present embodiment.

With reference to Fig. 2 there is shown graph 200 illustrating an example of detection of target analytes using the distribution of elements 100 illustrated and described in connection with Fig. 1. The x axis of graph 200 is frequency which increases from origin 206 in the direction indicated by x axis arrow 204. The y axis of graph 200 is harmonic signal intensity which increases from origin 206 in the direction indicated by y axis arrow 202.

As shown in Fig. 2, the results of a scanning of the distribution of elements 100 can be represented in the frequency domain. Harmonic signals 210, 220 and 230 indicate detection of binding of target analytes to analyzer molecules 110, 120, and 130, respectively. Signal 230 has center frequency 231, signal 220 has center frequency 221, and signal 210 has center frequency 211. Center frequencies 231, 221, and 211 correspond to the spatial frequencies of analyzer molecules 130, 120, and 110, respectively, and the rate of scanning. Since the spatial frequency of analyzer molecules 110 is 16 times that of analyzer molecules 130 and 4 times that of analyzer molecules 120, the harmonic signal 210 has a center frequency 211 sixteen times that of the center frequency 231 of harmonic signal 231 and four times that of center frequency 221 of harmonic signal 220. Detection of signals at a variety of different frequencies corresponding to spatial frequencies of analyzer molecules is possible. Furthermore, time domain detection techniques can be utilized.

With reference to Fig. 3 there is shown a bio-CD 300 according to another embodiment of the present invention. Bio-CD 300 includes sectors 310, 320, 330, 340, 350, 360, 370, 380 and 390. A substantially circular scanning pathway 302 is defined about the read surface of Bio-CD 300 and scanning footprint 304 follows pathway 302 when bio-CD 300 is rotated. Bio-CD 300 may also include multiple other scanning pathways substantially concentric with pathway 302 located inside the outer perimeter 306 of bio-CD 300. Additionally, bio-CD 300 may include an aperture located at its center for receiving a device used to rotate bio-CD 300. Each of sectors 310, 320, 330, 340, 350, 360, 370, 380 and 390 could include a different type of analyzer molecule to test for a different analyte in a single sample, or could include the same type of analyzer molecule and test different samples for the same analyte. Combinations of these two examples are also possible, for example, the eight sectors shown in Fig. 3 could be used to test two samples for four different analytes, four samples for two different analytes, two samples for one analyte and two samples for three analytes, one sample for one analyte another sample for two analytes and another sample for five analytes, or various other combinations using all or some of the sectors for various other combinations of analyzer molecule(s) and test sample(s). In a preferred embodiment according to the present invention, a bio-CD including a plurality of tracks as reading pathways provides a platform that can be divided into sectors as described above and used in a surface normal self referencing phase quadrature interfero metric detection system. One such embodiment preferably includes 1024 interferometric elements per track and is divided into sixteen sectors for receiving sixteen samples. The total number of assays in this case is sixteen times the number of tracks. At 1000 tracks this allows 16,000 assays. Another such preferred embodiment includes 8192 interferometric elements per track and is divided into 128 sectors for receiving 128 samples. The total number of assays in this case is 128 times the number of tracks. For 1000 tracks, this is 128,000 assays. Thus, very high numbers of assays may be conducted in the time required to scan a bio-CD, which can be as little as about twenty minutes or less.

With reference to Fig. 4 there is shown a multi-layer biosensor platform 400 according to one embodiment of the present invention. Platform may be a disk or chip including, for example, those described herein. Platform 400 includes an upper surface 404 and scanning levels 410, 412, and 414 which are positioned at different distances from surface 404. Scanning levels 410, 412, and 414 include interferometric elements 420A, 420B, and 420C, respectively. For simplicity, only a few interferometric elements are labeled, but additional interferometric elements are present as indicated by ellipses 421A, 421B, and 421C. Analyzer molecules may be provided on scanning surfaces of interferometric elements 420A, 420B, and 420C, and may be exposed to test samples via microfluidic channels internal to platform 400. Confocal microscope optics can be used to direct a laser beam 402 to scan interferometric elements 420A, 420B, and 420C. As shown in Fig. 4 laser beam 402 is scanning elements 420B of level 412. Thus, it is possible to isolate a signal from a specific scanning level of platform 400. In a preferred embodiment of the present invention platform 400 is a multi-level bio-CD. In this embodiment, the interferometric elements can be transparent or partially transparent elements, placed in a stack at different levels in a fashion similar to that of a high-density DVD. To focus at a different level, the disk is moved to or away from the objective, or else the optical train is moved toward or away from the disk or chip.

The embodiments described above in connection with Figs. 3 and 4 are examples of space domain multiplexing in which spatially separate segments of a biosensor platform cany different analytes. Additionally, the variations and additional embodiments described elsewhere herein may apply to the present embodiment. With reference to Fig. 5 there is shown a biosensor platform 500 according to one embodiment of the present invention. Platform 500 includes substrate 504 having upper surface 505. Microstructures 510, 520 and 530 are disposed on surface 505 and have a variety of heights. Microstructures 510, 520 and 530 and are scanned by laser beam 502. Laser beam 502 preferably includes a plurality of wavelengths of laser light represented by arrows LA, LB, and LC. The height of microstructure 510 shown by arrows HA is 1/8 wavelength LA, the height of microstructure 520 shown by arrows HB is 1/8 wavelength LB, and the height of microstructure 530 shown by arrows HC is 1/8 wavelength LC. Thus, microstructures 510, 520, and 530 are individually tuned to produce a phase quadrature condition for the different wavelengths LA, LB, and LC, respectively. As described above, each of microstructures 510, 520, and 530 could include a different analyzer molecule immobilized to its surface for detecting a different analyte. It is also contemplated that additional or fewer microstructure heights and/or light wavelengths could be used.

The embodiments shown and described above in connection with Fig. 5 is one example of wavelength-domain multiplexing which includes having multiple types of microslructures on a single track that are individually tuned to different wavelengths. A variety of additional embodiments and variations are also contemplated. In a preferred embodiment according to the present invention biosensor platform 500 is a bio-CD and the scanning of elements is accomplished by rotating the bio-CD to pass the interferometric microstructures through the footprint of the laser beam. In this embodiment microstructures can be radial spokes formed at different heights. The heights can be selected so that a microstructure is in quadrature for one wavelength, but null for a different wavelength. Furthermore, the distribution of analyzer molecules about the microstructures can be according to frequency-domain multiplexing, space- domain multiplexing or code-domain multiplexing schemes including those described above and below.

In other embodiments according to the present invention different height microstructures are not required, rather a laser probe contains a continuum of wavelengths, and readout in the far field can use an imaging spectrometer to separate theta and wavelength, for example, or readout can use interferometry techniques. In one preferred embodiment according to the present invention a phase contrast bio-CD provides an interferometry platform including a multiplexed distribution of analyzer molecules without different height microstructures. This phase contrast platform can be scanned with a plurality of wavelengths to define quadrature conditions and quadrature angles. Different wavelengths interact differently with this phase contrast platform and can be separated during detection to extract independent information from the wavelengths, for example, using interferometry. Multiple discrete wavelengths can be utilized or one or more wavelength continuums can be utilized. Other exemplary platforms not including different height microstructures include surface plasmon resonance platforms including a multiplexed distribution of analyzer molecules. Scanning of such platforms with multiple wavelengths can be read out as angular shifts or as frequency shifts.

Wavelength-domain multiplexing techniques allow probing at many different wavelengths, bringing spectroscopic molecular specificity to bear on the laser-scanning interferometry. There can be significant information contained in the spectral absorption of biomolecules. This information can be used in detecting target analytes in a sample. Additionally, the variations and additional embodiments described elsewhere herein may apply to the present embodiment. With reference to Fig. 6 there is shown a distribution of elements 600 according to another embodiment of the present invention. The distribution of elements 600 includes three types of analyzer molecules 610, 620 and 630 distributed about scanning pathway 604 according to a pseudorandom sequence or a random sequence. As indicated by ellipses 606 and 608, elements 600 and reading pathway 604 can extend beyond the segment illustrated in Fig. 6 with the distribution of various analyzer molecules occurring pseudorandomly or randomly as described above.

Scanning footprint 602 travels over the distribution of elements 600 along scanning pathway 604 in the direction indicated by arrow RR. In a preferred embodiment of the present invention, the distribution of elements 600 can be on a bio- CD which is scanned with a laser beam to detect the presence or absence of analytes bound to the analyzer molecules preferably using surface normal self referencing phase quadrature interferometry techniques. In this embodiment elements 600 may be microstructures such as radial spokes formed on the surface of the bio-CD and analyzer molecules 610, 620, and 630 may be immobilized as monolayers, fractional monolayers, partial monolayers, or near monolayers on surfaces of the microstructures. Alternatively, in this and other embodiments, the elements may be defined regions on a substrate without microstructures. Furthermore, scanning pathway 604 can be one of multiple substantially concentric tracks which may be scanned with a laser, for example, as described above. In this embodiment, the scanning pathway is preferably a substantially ring shaped track of a bio-CD.

Scanning of distribution of elements 600 can yield a multiplexed bit sequence which can be processed using known orthogonal bit sequence, for example with matched gating techniques, to produce bit sequences corresponding to each analyzer molecule. Fig. 7 shows a group of mutually orthogonal bit sequences 702 corresponding to the occurrences of analyzer molecules 610, 620, and 630 shown and described above in connection with Fig. 6. Orthogonal bit sequence 710 corresponds to the occurrences of molecules 610, orthogonal bit sequence 720 corresponds to the occurrences of molecules 620, and orthogonal bit sequence 730 corresponds to the occurrences of molecules 630.

Distribution of elements 600 is one exemplary embodiment of code-division multiplexing in which different analyzer molecules are distributed according to a known pseudorandom or random sequence. A variety of additional exemplary embodiments are also contemplated. For example, greater numbers of analyzer molecules could be used. Additionally, the variations and additional embodiments described above and below may also apply to the present embodiment.

With reference to Fig. 8 there is shown graph 1000 with frequency increasing along its x axis as indicated by x axis arrow 1020 and noise power density increasing along its y axis as indicated by its y axis arrow 1010. Frequency can be either temporal frequency (Hz) or spatial frequency (I/cm). Graph 1000 illustrates noise power density versus frequency in the absence of a carrier frequency. Curve 1030 illustrates the noise power density of total noise as it varies with frequency. Curve 1040 illustrates the noise power density of 1/f noise as it varies with frequency. A bandwidth between frequencies 1060 and 1070 is indicated by arrows BW. The total noise for this bandwidth is given by the area under curve 1030 labeled 1080 which represents detected noise power for a measurement taken at bandwidth BW. The frequency range where only static is detectable is illustrated by arrows ST. The frequency value of the 1/f noise knee is illustrated by line 1050 and represents the frequency above which a signal may be detected over noise.

With reference to Fig. 9 there is shown graph 2000 with frequency increasing along its x axis as indicated by x axis arrow 2020 and power spectrum increasing along its y axis as indicated by y axis arrow 2010. The power level of 1/f noise is illustrated by curve 2030. A DC sideband signal 2040 having DC sideband center frequency 2041, a carrier signal 2060 having carrier center frequency 2061, and earner sidebands 2050 and 2070 having earner sideband center frequencies 2051 and 2071, respectively, are also shown.

Graph 2000 illustrates one example of frequency domain detection of the molecular, cellular, or particulate content of a liquid or air sample in which an analyte binds on or in a support material to produce a periodic, quasi-periodic or harmonic modulation of phase or amplitude of an electromagnetic wave that probes the support material. The periodic or quasi-periodic modulation can be in time or space, leading to a time-domain carrier frequency or a space-domain earner frequency, by relative motion of the probe beam and support. The presence of the bound analyte appears as a modulation sideband of the carrier frequency. As shown in graph 2000, carrier sideband signals 2050 and 2070 indicate the presence of one or more target analytes bound to analyzer molecules distributed about a support material which is probed with an electromagnetic wave in a detection system. The detection system preferably includes a photodetector, or another detector responsive to electromagnetic waves, that outputs a current as described below by Equation 1:

ϊ^'(t) * —{1 + COSCOj)(I + Acosω_mt) Equation 1 has a harmonic decomposition described by Equation 2:

i ( t) =« — •+ — cos ω_c t + — cos ω_m t + — cos {u)_c -t ω_m ) I + — cos (ω_c - ω_m ) t

2 _*ϊ 2 A- 4

Equation 2 describes a DC sideband at ω_m, a carrier band at ω_c, and two carrier sidebands at ω_c - ω_m and ω_c + ω_m which correspond to DC sideband 2040, a carrier 2060, and sidebands 2050 and 2070 as shown in graph 2000. In Equations 1 and 2, t is time, i(t) is detector output current as a function of time, ω_c is carrier angular frequency, ω_m the modulation angular frequency, and A is the envelope amplitude. In further embodiments detector output could be a voltage, another electrical signal, an optical signal, or a magnetic signal, for example, or some combination of these and/or other outputs.

With reference to Fig. 10 there is shown a distribution of elements 3000 including elements 3010 and 3020. Elements 3010 and 3020 are distributed about reading pathway 3004 which is defined on a substrate. As shown by dashed lines 3030, 3040, 3050, 3060, and 3070, elements 3010 and 3020 are arranged in alternating groups of four. As shown by ellipses 3006 and 3008 this pattern can continue beyond the segment illustrated in Fig. 10 with the groups of four elements alternating as described above. A unit cell includes a group of four elements 3010 and a group of four elements 3020 as is indicated by arrow UC between dashed lines 3030 and 3050. Scanning footprint SF travels along reading pathway 3004 to scan the distribution of elements 3000. Additional embodiments include alternating groups of different numbers, for example, one, two, three, five or more, and corresponding different sizes of unit cells. Elements 3010 include specific analyzer molecules which selectively bind with a target analyte and elements 3020 include nonspecific analyzer molecules which do not selectively bind with a target analyte but may exhibit similar binding properties with respect to other molecules. In a preferred embodiment according to the present invention, elements 3010 include specific antibodies immobilized about their surfaces, for example, as a monolayer, fractional monolayer, partial monolayer, or near monolayer, and elements 3020 include similarly immobilized nonspecific antibodies. For example, if an assay is to be conducted to identify a particular mouse protein the specific antibody could be goat anti-mouse IgG (the antibody to the mouse protein produced by a goat) and the nonspecific antibody could be goat anti-rat IgG (the antibody to an analogous rat protein produced by a goat), The goat anti-mouse IgG will selectively bind the mouse protein while the goat anti-rat IgG will not bind with it or will have a substantially lesser binding affinity, however, both IgGs exhibit similar nonspecific background binding with molecules other than the target analyte. In additional embodiments the non-specific protein could be a non-IgG, for example, casein or bovine serum albumin (BSA). These proteins could be used to test general protein-protein background, and could be used to test for systematics that are common to both groups of immobilized molecules. In further embodiments the specific analyzer molecules could be a cDNA that is complimentary to the target DNA, and the non- specific group could be a statistically similar, but not identical, cDNA. Additional embodiments cal include specific and non-specific aptamers. A variety of other specific and nonspecific antibody pairs may also be used, including those exhibiting varying degrees of similarity in nonspecific background binding and those not exhibiting similar nonspecific background binding. Furthermore, combinations of specific and nonspecific analyzer molecules other than antibodies may also be used. Additionally, nonspecific analyzer molecules may be omitted entirely in which case elements 3020 would not include immobilized molecules. These alternative exemplary embodiments and others can be used in connection with the present embodiment and also in connection with the other embodiments including those described elsewhere herein. Distribution of elements 3000 is one example of differential encoding or envelope modulation of bimolecular information. According to a preferred embodiment of the present invention, distribution of elements 3000 is on a bio-CD where elements 3010 and 3020 are interferometric microstructures formed on a surface of the bio-CD, and reading pathway 3004 is one of a number of a substantially concentric circular tracks. As described above, elements 3010 on the track are active (carrying a specific biological analyzer molecule) and elements 3020 are inactive (carrying nonspecific molecules, no molecules, or inert molecules that may be comparable in size with the analyzer molecule). In this 4 on / 4 off format, the carrier frequency corresponds to the positioning of each individual one of elements 3010 and 3020, and the detection frequency corresponds to the repeat period of the unit cell UC which is every eight elements. Thus, the detection frequency is equal to one-eighth of the carrier frequency. At disk rotation speeds of 6000 rpm (100 Hz) and 1024 elements per track, the carrier frequency is approximately 100 IcHz and the detection frequency is approximately 12.5 IcHz. A wide variety of other bimolecular platforms, scanning rates, and element distributions including, for example, those described herein, are contemplated and can result in a variety of other carrier frequencies and detection frequencies.

According to a preferred embodiment of the present invention, an optical detection system including two phase-locked loops in series, with the front end referenced to the earner frequency, and the back end referenced to the unit cell can be used to scan a bio-CD having distribution of elements 3000 with a laser. Differential encoding of distribution of elements 3000, for example as described above and elsewhere herein, can preferably reduce susceptibility to laser intensity drift or disk wobble by subtracting out these and other system drifts and biases, and can preferably directly subtract non-specific background binding, for example if the off region is printed with nonspecific antibody. One example of a detection system according to a preferred embodiment of the present invention can be found in U.S. Patent No. 6,685,885 which is hereby incorporated by reference. This detection system could also be any other detection system responsive to electromagnetic waves including for example those described elsewhere herein.

According to a preferred embodiment of the present invention the detection system can utilize phase quadrature interferometric techniques. Examples of phase quadrature interferometric techniques include the micro-diffraction quadrature class ("MD-class") and adaptive optic quadrature class ("AO-class") as described in U.S. Application Serial No. 10/726,772 filed on December 3, 2003 entitled "Adaptive Interferometric MuI ti -Anal yte High-Speed Biosensor" (published on August 26, 2004 as U.S. Pub. No. 2004/0166593), the contents of which are incorporated herein by reference. Other examples of phase quadrature interferometric techniques include the phase-contrast quadrature class ("PC-class") as described in U.S. Provisional Patent Application No. 60/649,070, filed February 1, 2005, entitled "Phase-Contrast Quadrature For Spinning Disk Interferometry And Immunological Assay", U.S. Provisional Patent Application No. 60/755,177, filed December 30, 2005, entitled "Phase-Contrast BioCD: High-Speed Immunoassays at Sub-Picogram Detection Levels", and U.S. Application Serial No. ??/???,??? being filed the same day as the present application that claims priority to these two provisional applications and entitled "Method And Apparatus For Phase Contrast Quadrature Interferometric Detection Of An Immunoassay." The disclosure of the utility application being filed on the same day as the present application is incorporated herein by reference. Additionally, further embodiments of the present invention include detection systems adapted to utilize surface plasmon resonance or SPR, fluorescence, resonance and other techniques in which high frequency modulation in time or space originates from analyte bound to a solid support with a spatial frequency that is scanned to produce a sideband indicating the presence of the analyte. Still other preferred embodiments of the present invention include detection platforms for use in these and other detection systems which include distributions of targets including analyzer molecules which produce sideband signals that depend upon modulation indicative of the presence of an analyte. With reference to Fig. 11 there is shown a biosensor platform 4000 including a substrate 4030 having an upper surface 4010 and lower surface 4020. Interferometric elements 4040, 4050, 4060, and 4070 are formed on the upper surface 4010 of substrate 4030. Platform 4000 may also include additional interferometric elements in addition to those shown in the portion of platform 4000 illustrated in Fig. 11. A laser beam 4002 having wavelength λ scans the interferometric elements 4040, 4050, 4060, and 4070 in the direction indicated by arrow DM. Elements 4040 and 4050 include specific analyzer molecules immobilized about their scanned surfaces and elements 4060 and 4070 include nonspecific analyzer molecules immobilized about their scanned surfaces. These specific and nonspecific analyzer molecules can be, for example, the same or similar to those described above in connection with Fig. 10 and elsewhere herein. This configuration of specific and nonspecific analyzer molecules of biosensor platform 4000 is another example of differential encoding according to a preferred embodiment of the present invention. In one preferred embodiment of the present invention platform 4000 is a micro-diffraction bio-CD and elements 4040, 4050, 4060, and 4070 are radial spokes distributed about the surface of the bio-CD. Platform 4000 can also be any of various other biosensor platforms including, for example, those described herein.

Biosensor platform 4000 is one example of carrier suppression according to a preferred embodiment of the present invention. Elements 4060 and 4040 have a height illustrated by arrows HA and elements 4050 and 4070 have a height illustrated by arrows HB. Height HA is about λ/8 and height HB is about 3λ/8. Successive scanning of elements alternating between height HA and HB flips the phase quadratures detected for successive elements. This results in a modulation at about twice the amplitude as compared to a platform having interferometric elements with substantially uniform element heights. The carrier is suppressed by an approximately π phase difference between phase quadrature signals detected for successive elements. Carrier suppression may be useful in a variety of circumstances. In one example, where earner side bands are weak relative to the carrier, earner noise can impact detection. In another example where carrier sidebands overlap with the carrier, carrier noise can also impact detection. Carrier wave suppression can preferably increase the ratio of signal to noise. Complete earner suppression or double sideband detection may be used to improve the signal to noise ratio of detection in these and other situations. Partial carrier suppression may also improve the signal to noise ratio of detection in these and other situations. Carrier wave suppression can also be accomplished in other manners, for example, fabrication of disk structures and reflectivities relative to beam width, through use of a clipper circuit that clips the high signal detected from a land of a detection platform, or through use of a filter, for example a band stop filter.

With reference to Fig. 12 there is shown an example of a scanning 5000 during which footprint 5020 passes over element 5010. Areas 5021 are the areas of the scanning footprint not over element 5010 and area 5011 is the area in which scanning footprint 5020 overlaps element 5010. According to a preferred embodiment element 5010 is a gold microdiffraction element placed on a partially reflecting substrate. This embodiment allows earner suppression by the total power reflected from the element being equal to the total power reflected under the condition of quadrature which removes the large modulation caused by the approximately 50% amplitude modulation of a micro diffraction bio-CD. This effect can be illustrated through the following equations. The total electrical (far) field is given by Equation 3:

The total reflected intensity is given by Equation 4:

I₇ -

Under the condition of Land: Φ = 0, A_L= A and A,- = 0. Thus, intensity reflected by land is given by Equation 5:

I ₁- T D Under the condition of Quadrature: Φ = π/2. Thus, the reflected intensity under a condition of quadrature is given by Equation 6:

-/,[* iβl 4- R_ra *

where &_\ is the area fraction, and a_t, + a_r= 1. Conditions of balanced operation are given by Equations 7 and 8:

The solution of which are given in Equations 9 and 10:

1 + a_L B₁,

For Equations 3-10, 1₁- is the total reflected intensity, I_L is the intensity reflected by land, Io is the incident reflected intensity, I_Q is the reflected intensity under a condition of quadrature, E₀ is the reflected field, A is the total area, A_L is area 5021, A,- is area 5011, aL is AL divided by the area of the beam footprint, a_R is A_L divided by the area of the element 5010 intersecting element 5020, RL is |Γ_L|², R₁- is |r,|² and Φ is the phase difference between reflected components of the laser. Thus, if the partially reflective substrate is silicon, for example, which has RL = 32% and R₁. = 98%, then a_L = 51% and a_r = 49%.

With reference to Fig. 13 there is shown a biosensor platform 6000 including substrate 6030 having an upper surface 6010 and a lower surface 6020. Upper surface 6010 includes analyzer molecules 6040, 6050, 6060, 6070, 6080 and 6090 immobilized about surface 6010. Analyzer molecules 6040, 6060, and 6080 are specific analyzer molecules for selectively binding a particular analyte and analyzer molecules 6050, 6070 and 6090 are nonspecific analyzer molecules. The specific and nonspecific analyzer molecules can be, for example, the same or similar to those described elsewhere herein. Fig. 13 shows one example of an alternating pattern of specific and nonspecific analyzer molecules. Laser beam 6002 scans the analyzer molecules in the direction indicated by the arrow DM which is preferably accomplished by rotating the platform 6000 but could also be accomplished by other movement of platform 6000 or by movement of beam 6002. According to a preferred embodiment of the present invention platform 6000 is a phase contrast bio-CD or an adaptive optical bio-CD and analyzer molecules 6040, 6050, 6060, 6070, 6080 and 6090 are radial spokes or other patterns of analyzer molecules, however, platform 6000 could also be another kind of bio-CD or other platform including, for example, those described elsewhere herein.

During scanning of platform 6000 by laser beam 6002 signal phase modulation depends only upon the binding differences between the specific and nonspecific analyzer molecules. For example, nonspecific binding that is common to both the types of analyzer molecules is not imparted onto the signal beam or has minimal impact on the signal beam. The detected signal is therefore independent of nonspecific binding. In this embodiment there is no signal detected at or about the carrier frequency and only the modulation caused by binding of the specific analyte and the specific analyzer molecule is detected. This is one example of differential encoding including earner wave suppression and double sideband detection.

With reference to Fig. 14 there is shown a biological analyzer platform 7000 including substrate 7030 including upper surface 7010 and lower surface 7020. Interferometric elements 7070 are distributed about upper surface 7010 and are spaced apart by gaps 7060. Interferometric elements 7070 include specific biological analyzer molecules 7040 and nonspecific biological analyzer molecules 7050 immobilized about their surfaces which can be the same or similar to those described elsewhere herein. Groups of the interferometric elements and analyzer molecules 7090 and 7091 are also shown. Groups 7090 and 7091 have patterns of specific and nonspecific analyzer molecules that are at spatial frequencies with a π phase difference, that is, the positions of specific and nonspecific analyzer molecules are flipped between groups 7090 and 7091. Platform 7000 is preferably an adaptive optical bio-CD, however, platform 6000 could also be any other type of biosensor platform or another type of bio-CD including, for example, those described elsewhere herein.

During scanning of platform 7000 by a laser beam the phase of the carrier is periodically flipped by π for successive groups 7090 and 7091. The effect of the phase flipping of the carrier is that the carrier is suppressed in the power spectrum and the modulation due to binding of a specific analyzer molecule to the specific antibodies is detectable at earner sidebands. This is one example of differential encoding including earner wave suppression and double sideband detection.

According to a preferred embodiment modulated signals are detected within a detection bandwidth Δfj. Narrow bandwidths reject more noise, but the detection bandwidth should preferably not be smaller than the signal bandwidth, otherwise a part of the signal is rejected with the noise. The signal bandwidth is determined by the relationship described by Equation 11:

ACU_XAT ** 1 where Δω_s = 2πΔf_s, Δf_s is the signal bandwidth, and Δτ is the duration of either a contiguous part of the signal, or the duration of the signal detection measurement. In preferred embodiments utilizing bio-CDs, the earner frequency, f_caπϊe_r> is set by the rotation frequency of the bio-CD, f^_k, and by the number of spokes, targets, or interferometric elements, N, around a specified circumference as described by Equation 12:

Scurf for ^** ΛΛftffc

The signal bandwidth Δ/_s is described by Equation 13:

The relative signal bandwidth Δ/_reι is described by Equation 14:

For a single continuous track around a circumference, the relative bandwidth Δ/_re| is described by Equation 14:

If a circumference is divided into S equal arcs of M spokes, the relative bandwidth increases by a factor of S as described by Equation 15:

Thus, for example, if N = 1024, and S = 16, the relative bandwidth is 0.25%. If /_di_sk = 100 Hz, then/_v = 100 kHz, Δ/_Λ. = 16 Hz and Δ/_{s re}i = 256 Hz. These relations suggest that S up to 128 segments or more is clearly a possible scenario for homogeneous bandwidths for which Δ/_s = 2IcHz and Δ/_{s re}ι = 2%.

The foregoing example describes the case of homogeneous signal bandwidth. Signal bandwidths in practice are generally larger than the homogeneous bandwidths. These arise, for example, from frequency instability, which in the bio-CDs is from inhomogeneities in the fabricated or printed spokes. If the placement of the spokes is only accurate to 10 microns, then the bandwidth of the repetitive spoke pattern is approximately 4 kHz with a relative bandwidth of 4%. This inhomogeneous signal bandwidth sets the correct detection bandwidth for the bio-CDs. The number of segments can be increased to increase the homogeneous bandwidth until it is equal to the inhomogeneous bandwidth to the relationships described by Equations 16 and 17:

For detection bandwidth BW, this sets the maximum segment number according to Equation 18:

which for BW = 3 IcHz and f_caπ.j_er = 100 IcHz for N = 1024, this sets the maximum S = 136.

The ability to support segments suggests a disk array layout that segments the printed antibodies into wells. For N wells on a disk or S segments, the size of a well and its radial thickness are given by Equations 19 and 20: a «■ rdθdr » Λ /Λ^?

where a is the area of a well, r is radius, dr is radial thickness of a well, θ is angular position, dθ is well arclength, A is the area of the annular region between radii R₂ and R₁, N is number of wells, S is the number of segments, Ri is the inner radius, and R₂ is the outer radius.

With reference to Fig. 15 there is shown a bio-CD 8000 according to one embodiment of the present invention. Bio-CD 8000 is a 100 mm diameter disk or silicon wafer, however, any other dimension disk, wafer chip or other substrate or platform could also be used. Bio-CD 8000 includes sectors 8001, 8002, 8003, 8004, 8005, 8006, 8007, 8008, 8009, 8010, 8011, 8012, 8013, 8014, 8015, and 8016. Bio-CD 8000 further includes substantially concentric tracks of wells 8021, 8022, 8023, 8024, 8025, 8026, 8027, and 8028. Bio-CD 8000 has S = 16 sectors, N = 128 then T = 8 (tracks) and the inner track radius and radial thicknesses are given in Table I:

Bio-CD 8000 is one example of an equal area well layout according to the present invention. Other layouts are also contemplated, for example, a 512 well layout with S = 16, T = 32, and any other combination of sectors and tracks. According to a preferred embodiment layouts are used which bring the aspect ratio of arclength and radial thickness closer to unity which simplifies fabrication. Fabrication of this and other embodiments of the present invention can include particular features for various classes of bio-CDs. For example, a micro-diffraction bio-CD can have radial spokes fabricated from gold across the entire disk, and wells defined by hydrophobic dams. A pin plotter or ink-jet printer modified from biochip array printers can be used to deposit an equal amount of analyzer molecules into each well. Different antibodies can be deposited which then self-immobilize on thiolated gold. In another example gel printing can be used. In another example, for adaptive optical bio-CDs and phase constant bio-CDs, spokes can be printed as inert protein, dams can be put into place and antibody deposited into the wells by pin array plotters or protein spotters.

With reference to Figs. 16A, 16B, 17A, 17B and 18 there are shown bio-CDs 9000A, 9000B, 10000A, 10000B, and 11000 according to embodiments of the present invention where the wells are of equal area. In these embodiments, dr is held constant among the tracks, and ds = rdθ is also held constant. This leads to a varying dθ across the disk. In the preferred embodiment where well areas remain are equal, the radial width of each well is constant which simplifies design of the protein plotter, and optimal use of real-estate is made. This embodiment requires a carrier spoke number C to vary with radius, also causing the carrier frequency to vary with radius (for constant angular velocity). The relation of the spoke number is given by Equation 21: c ^2m

Λ where A is the spatial period, usually A = 2w, where w is the beam waist. For a beam waist of 20 microns and A = 40 microns, this gives the number of spokes as a function of radius C = 3000 at r = 20 mm and C = 8000 at r = 50 mm. The carrier frequencies are 300 IcHz and 800 kHz, respectively.

For N wells, the area of each well is given by Equation 22: a ** rdθdr ∞ AtN

The aspect ratio a_r is set by the Equation 23: rdθ ™ a_rdr The radial widths and angular widths are given by Equation 24:

Fig. 16A shows a 96 well disk with an aspect ratio of 1 and dr = 7.5 mm, a = 61mm², T = 4, Sj = 15, and S₀ = 33. Fig. 16B shown a 96 well disk with an aspect ratio of 4 and dr = 4.3 mm, a = 64mm², T = 7, Si = 8, and S₀ = 19. The well in Figs. 16A and 16B areas are approximately 0.6 cm². Fig. 17A shows a 512 well disk with an aspect ratio of 4, dr = 1.76 mm, a = 12.7 mm², T = 17, Sj = 17, and S₀ = 42, Fig. 17B shows a 1000 well disk with an aspect ratio of 4, dr = 1.25 mm, a = 6.4 mm², T = 24, S; = 24, and S₀ = 59. Fig. 18 shows an 8000 well disk with an aspect ratio of 4, dr = 0.45 mm, a = 0.82 mm², T = 66, Sj = 69, and S₀ = 172. A variety of other disks with equal area wells and unequal well areas are also contemplated. In general, larger aspect ratios have narrower detection bandwidth, but more tracks with smaller track pitches.

With reference to Fig. 19 there are shown examples of scanning targets 12000. Targets 12000 are a periodically alternating pattern of targets including specific antibodies 12010 and targets including nonspecific antibodies or not including antibodies 12020. Specific and nonspecific antibodies are being immobilized about a substrate, for example, as described herein. After exposure to a sample including a specific target analyte, targets 12010 have the analyte bound to their analyzer molecules while targets 12020 exhibit little or no binding of the specific analyte. The period of the alternating pattern is shown by arrows LL, and the spatial frequency of the pattern is inversely proportional to its period as shown by Equation 25:

V" Έ= — 1 —

JX where Λ is the spatial periodicity and V_spatiai is the spatial frequency.

During scanning targets 12000 are illuminated by a scanning footprint such as a laser spot. The scanning footprint could be, for example, focused laser spot vv which has a width W₀ less than spatial periodicity Λ (preferably W₀ « Λ) and moves relative to the targets 12000 with a velocity in the direction indicated by arrow v. Under these scanning conditions the spatial frequency v_Spaiiai is converted into temporal frequency on the transmitted or reflected beam as described by Equation 26:

where/is the carrier frequency of phase or amplitude modulation. The scanning footprint could also be, for example, broad area laser spot z which has a width W₀ greater than spatial periodicity A (preferably W₀ » A) and can be stationary or can move relative to the targets 12000 with a velocity V in the direction indicated by arrow v. When laser spot z is stationary and broadly illuminates the spatial frequency, then the spatial frequency leads to diffraction at specific angles as described by Equation 27:

where λ is the illumination wavelength, and Λ is the spatial period. When laser spot z moves over to targets 12000, or targets 12000 move with velocity V, then the diffracted orders acquire a phase modulation that is time-periodic.

The foregoing examples illustrate how spatial frequencies on a scanning platform, for example a chip or disk, can be converted into temporal frequencies in a laser scanning system, and how the two types of frequencies can be combined when a laser probes more than one target on the platform.

With reference to Fig. 20 there is shown detection system 13000 which includes detector 13010 and detector 13020. Detectors 13010 and 13020 could be any detectors for detecting electromagnetic waves, for example optical detectors. System 13000 further includes probe beam 13030 which can be a focused probe beam or a broad area probe beam. Probe beam 13030 scans targets 13040 which move relative to beam 13030 with a relative velocity in the direction indicated by arrow RV. The scanning targets 13040 by beam 13030 results in a transmitted or reflected mode 13012 and a diffracted mode 13022. Mode 13012 is directed to detector 13010 and mode 13022 is directed to detector 13020. Reference beam 13023 is directed to detector 13010 and reference beam 13023 is directed to detector 13020. Reference beam 13023 is preferably maintained in a condition of phase quadrature relative to the transmitted mode 13012. Reference beam 13033 is preferably maintained in a condition of phase quadrature relative to diffracted mode 13022. System 13000 also includes beam splitters 13011 and 13021 which could also be adaptive optical beam combiners. Having a reference wave that is in phase quadrature with detected signal allows a small shift in the phase modulation of the signal to linearly proportional change in detected intensity allowing signal modulation per bound analyte molecule to be maximized. Reference beams 13033 and 13023 can be added before photodetectors or can be combined adaptively with signals. Reference beams 13033 and 13023 can arise from a diffracted spatial mode, for example, in the case of wavefront splitting, from free space, or from partial reflections, for example, in the case of amplitude splitting. It is also contemplated that detection system 13000 could include only one or the other of detectors 13010 and 13020 and their related beams and modes. Experimental demonstrations of several exemplary embodiments including earner side band detection according to the present invention will now be described in connection with Figs. 21-35. With reference to Fig. 21, there is shown graph 14000 with time increasing along its x axis as indicated by x axis arrow 1420 and signal intensity (voltage) increasing along its y axis as indicated by y axis arrow 14010. Graph 14000 further shows signal 14030 which is a voltage signal that varies with time. Signal 14030 results from the scanning of an MD-class calibration disk which was fabricated with 1024 gold spokes deposited radially on a dielectric substrate. The average (mean) spoke height was 80 nm. Of the 1024 spokes, 512 spokes were below the average height, 512 spokes were above the average height, and the spokes alternated between those above the average height and those below the average height.

Scanning the MD-class calibration disk produced signal 14030 which includes a series of alternating local minima 14031 and 14032 corresponding to and indicating the two spoke heights. The signal intensity difference between the alternating local minima 14031 and 14032 is illustrated by arrow 14040 and corresponds to a height difference of about 30 nm between alternating spokes. This height difference is representative of the height difference cause by certain target analytes to analyzer molecules. The signal level corresponding to the average spoke height of about 80 nm is indicated by dashed line 14050. The MD-class calibration disk thus provides a simulation of a differential encoding scheme whereby every other alternating spoke includes analyzer molecules that bind a target analyte and can be compared to a reference spoke. The fast relative comparison between the two types of spokes allows for significant noise reduction.

With reference to Fig. 22 there is shown graph 15000 with frequency increasing along its x axis as shown by x axis arrow 15020 and power increasing logarithmically along its y axis as shown by y axis arrow 15010. Graph 15000 shows the frequency domain results of the scanning of the MD-class calibration disk described above in connection with Fig. 21. Graph 15000 shows earner signal 15030 at 200 kHz, sideband signal 15031 at 100 kHz, and sideband signal 15032 at 300 kHz. Thus the sideband signals are present at half carrier frequency increments. A strong 1/f noise peak 15040 is present at zero frequency, and a significantly suppressed noise floor is present at the frequencies of carrier and sideband signals 15030, 15031 and 15032. The noise suppression by operating at this scanning rate is over 60 dB or 3 orders of magnitude better signal to noise ratio when compared to a static measurement at DC (zero frequency). This is a fundamental advantage to high speed repetitive sampling according to certain embodiments of the present invention.

With reference to Fig. 23 there is shown graph 16000 with frequency increasing along its x axis as shown by x axis arrow 16020 and power increasing along its y axis as shown by y axis arrow 16010. Graph 16000 shows an example of protein side-band detection for an MD-class disk having proteins (in this case antibody IgG molecules) immobilized on a 1024-spoke disk with 64 segments composed of 8 elements with protein and 8 elements without. This created a disk with an alternating pattern of 8 gold spokes carrying protein followed by 8 bare gold spokes. This pattern repeated for a total of 64 segments each with a total of 16 elements divided into 8 with protein and 8 without. The proteins were patterned using a polydimethylsiloxane (PDMS) stencil on the disk. A control track which did not include printed protein was also included on the disk. The results of scanning the control track are indicated by dotted line 16060 and the results of scanning a track including the patterned protein are indicated by line 16050.

Graph 16000 shows 16030 the 1/f noise at DC and two DC sideband signals 16031 and 16032. A earner frequency signal (not shown) is present at about 100 IcHz. The presence of protein is detected as a 1/64 harmonic of the earner frequency at about 1.6 IcHz as shown by signal 16032 and also by signal 16031 at about -1.6 kHz, A second harmonic signal 16034 and 16033 is also present at 1/32 the carrier frequency and is caused by slight asymmetry in the deposition of the proteins. A comparison of protein track signal 16050 and signal 16060 of a control track containing no protein illustrates the strong effect of the protein in producing sideband signals with a 20:1 signal to noise ratio as indicated by arrow 16040.

With reference to Fig. 24 there is shown graph 17000 with frequency increasing along its x axis as shown by x axis arrow 17020 and power spectrum increasing logarithmically along its y axis as shown by y axis arrow 17010. Graph 17000 presents average values for scanning of six tracks of the MD-class disk which is described above in connection with Fig. 23. Graph 17000 shows a comparison of 1/64 harmonic signal 17040 at about 1.6 IcHz, which is generated by and indicates the presence of protein, and carrier signal 17030. As illustrated by arrow 17050, the protein modulation is about 4.6% of the carrier wave, which is consistent with a monolayer of immobilized protein. With reference to Fig. 25 there is shown graph 18000 with frequency increasing along its x axis as shown by x axis arrow 18020 and power spectrum increasing logarithmically along its y axis as shown by y axis arrow 18010. While the side bands off of DC yielded the best signal-to-noise ratio for scanning the MD-class disk described above in connection with Fig. 23, every carrier harmonic includes two sidebands. Thus, as shown in graph 18000 fundamental carrier harmonic 18030 which is at about 80 kHz includes sidebands 18031 and 18032. Sidebands 18031 and 18032 are small peaks above and below the harmonic earner frequency 18030 which indicate the presence of the protein, Every other carrier harmonic also has two associated sidebands.

With reference to Fig. 26 there is shown graph 19000 with frequency increasing along its x axis as shown by x axis arrow 19020 and power spectrum increasing logarithmically along its y axis as shown by y axis arrow 19010. Graph 19000 shows carrier frequency harmonics 19030A (which is the first carrier harmonic 18030 at about 80 IcHz described above in connection with Fig. 25), 19030B, 19030C, 19030D, 19030E, 19030F, and 19030G. Each earner harmonic includes protein sidebands, though the wide frequency range of the graph 1900 makes it difficult to see the protein sidebands for all the harmonics. Graph 19000 also demonstrates the noise-floor roll-off for high frequencies associated to the transit time t = wo/v of a point on the disk across the width of the focused laser spot W₀. Line 19050 shows the approximate midpoint of the noise floor roll off.

With reference to Fig. 27 there is shown a fluorescence microscope image of portion of an MD-class disk 20000 according to one embodiment of the present invention. Disk 20000 is a half-harmonic differentially encoded MD-class disk which was created using photolithography to immobilize protein on every alternating spoke. During this process half the spokes were covered by photo-patterned photoresist while the other half were exposed to protein. The photoresist was then removed to uncover bare gold spokes. This results in a disk where protein is immobilized on every alternating spoke as shown by lines 20010 (indicating deposition of specific antibody) and 20020 (indicating no deposition of antibody, or deposition of a non-specific antibody). The width of each protein deposit is about 20 microns as indicated by arrows SW. This half-harmonic differential encoding in which every alternating spoke carries protein results in the highest signal-to-noise ratio being attained. This provides for the highest-frequency differencing measurements, and also boosts the total protein signal when the zero-frequency upper sideband and the earner frequency lower side-band merge into a single sideband half way between DC and the fundamental earner frequency.

With reference to Fig. 28 there is shown graph 21000 with time increasing along its x axis as shown by x axis arrow 21020 and voltage increasing along its y axis as shown by y axis arrow 21010. When a 512 differential encoded disk is rotated and scanned, the protein modulates the gold spokes with a frequency at half the fundamental carrier frequency. Graph 21000 shows the detected time trace 21030 from a 512 differential encoded disk. Trace 21030 shows an alternating pattern between the bare and protein-carrying spokes as indicated by the minimum points trace 21030 which alternate in amplitude at the rate of a half harmonic signal 21040.

With reference to Fig. 29 there is shown graph 22000 with frequency increasing along its x axis as shown by x axis arrow 22020 and power spectrum increasing logarithmically along its y axis as shown by y axis arrow 22010. Graph 22000 shows the frequency domain side band effect of the disk described above in connection with Fig. 28. The half-frequency harmonic protein signal 22040 is strong and occurs near the frequency of lowest noise between DC signal 22050 and the first earner signal 22030. As shown in graph 22000 the DC sideband and first carrier sidebands have merged at the half-frequency harmonic protein signal 22040. Furthermore, the protein signal 22050 itself has sidebands 22041 and 22042 caused by slight asymmetries in the protein printing. The signal-to-noise ratio is greatest in this situation where the noise floor is lowest. Thus, detection of protein at signal 22040 represents the optimal performance condition for carrier sideband detection on the MD-class disk described above.

With reference to Fig. 30 there is shown graph 23000 with frequency increasing along its x axis as shown by x axis arrow 23020 and power spectrum increasing logarithmically along its y axis as shown by y axis arrow 23010. Graph 23000 shows the power spectrum for an embodiment of a PC-class disk with a periodic pattern of protein on a dielectric disk with no other disk structure. Graph 23000 shows DC signal 23040 and protein signal 23030 which is caused by and indicates the presence of protein. For this PC-class embodiment, the earner frequency is attributable entirely to the protein, without any contribution from microstructures or other physical structures on the disk. The detection of periodic patterns of immobilized protein on a flat surface is one example of carrier-wave suppression that was discussed above. Additional embodiments including, for example, suppressing the carrier of the gold spokes on MD- class disks are also discussed above. Analyzer molecule patterns on PC-class disks offer a embodiment of side-band detection and manipulation that significantly improves the sensitivity of the bio-CD because the periodic protein patterns can themselves be modulated to form larger spatial patterns.

With reference to Fig. 31 there is shown a portion of a patterned protein PC- class disk 24000 according to one embodiment of the present invention. The radial direction is in the vertical direction the angular direction around the disk is in the horizontal direction. As shown in Fig. 31, the portion of disk 24000 is in a checkerboard pattern. Substantially rectangular areas of periodic stripes of protein 24010 are alternated with substantially rectangular areas of bare disk 24020. Each substantially rectangular area has a radial distance of approximately 0.5 mm indicated by arrow RD and an angular distance of approximately 45 degrees indicated by arrow AD. The height of the printed protein stripes is approximately 5 nm. The signal resulting from scanning the PC-class disk is differential, showing only the steps up and down from the protein stripes.

With reference to Fig. 32 there is shown a magnified portion 25000 of the PC- class disk 24000 shown in Fig. 31 individual protein bands 24011 of protein regions 24010 are visible in magnified portion 25000. The rectangular spatial patterns of areas 24010 and 4020 of disk 24000 create sidebands on the protein peak in the power spectrum. The long-range spatial patterns can be detected using a sideband demodulation process conceptually similar to the demodulation of FM radio. The long- range protein patterns constitute an envelope that modulates the carrier wave. By demodulation, the envelope is extracted. Because it is more slowly varying, envelope demodulation makes it possible to perform more accurate prescan subtraction.

An exemplary procedure for sideband detection will now be described with reference to Fig. 33, 34 and 35. Fig. 33 shows an isolated protein peak 26030 in the power spectrum. The horizontal axis 26010 is temporal frequency and the vertical axis 26020 is spatial frequency along the radius of the disk. The sub-peaks 26031 and 26032 represent the long-range envelope pattern. To demodulate the signal and extract the protein envelope, this protein peak is shifted back to DC and then Fourier-transformed back into the space domain. The resulting demodulated image is shown in Fig. 34. Only the long-range checkerboard pattern 27000 corresponding to areas 24010 and 24020 is visible, with the periodicity of the individual protein bands 24011 removed. After demodulation, subtracting a prescan becomes much more accurate.

Fig. 35 shows graph 28000 with distribution probability on the vertical axis and height in nm on the horizontal axis. Graph 28000 shows the results of subtracting a prescan from a postscan before demodulation as distribution 28010 and performing the same subtraction after demodulation as distribution 28020. The error in height reduces from 75 pm for distribution 28010 to 20 pm for distribution 28020 with demodulation. This increased accuracy improves surface mass sensitivity by over a factor of 3 in this example.

While the examples illustrated and described above in connection with Figs. 21- 35 have made reference to particular embodiments, for example, MD-class disks with protein attached using photolithographic techniques and PC-class disks with printed protein, these specific embodiments are merely exemplary and it is contemplated that differential encoding and sideband detection described above could be employed with a variety of other embodiments according to the present invention including those described elsewhere herein.

Various embodiments according to the present invention can include a variety of biosensor platforms including those described above. For example, these platforms include bio-CDs such as micro-diffraction bio-CDs, adaptive-optical bio-CDs, phase- contrast bio-CDs, and others. Details relating to these various classes of bio-CDs can be found, for example, in the aforementioned patent applications incorporated herein by reference. These platforms further include bio-chips, immunological chips, gene chips, DNA arrays, platforms used in connection with fluorescence assays and other platforms and substrates supporting planar arrays including analyzer molecules.

Various embodiments according to the present invention can include a variety of analyzer molecules useful in detecting the presence or absence of a variety of target analytes in a solution to be tested. For example, these analyzer molecules can include antibodies or immunoglobulins, antigens, DNA fragments, cDNA fragments, aptameres, peptides, proteins, and other molecules. Various embodiments according to the present invention can include combinations of one or more the foregoing and other types of analyzer molecules known to those of ordinary skill in the art arranged, for example, in a planar array.

Various embodiments according to the present invention can be used in connection with a variety of scanning and detection techniques. For example, such techniques include interferometry, including surface normal interferometry techniques, and preferably phase quadrature interferometry techniques where one detected optical mode differs in phase from another by about π/2 or an odd integer multiple thereof, and/or self referencing interferometry techniques where a reference wave is generated locally with respect to a signal wave so that the reference and signal waves experience common abeiτations and path length changes and thus maintain a constant relative phase without the need for active stabilization of different light paths, florescence techniques and platforms, resonance techniques and platforms, and other techniques and platforms.

As used herein terms relating to properties such as geometries, shapes, sizes, physical configurations, speeds, rates, frequencies, periods, amplitudes, include properties that are substantially or about the same or equal to the properties described unless explicitly indicated to the contrary. While the invention has been illustrated and described in detail in the drawings and foregoing description, the same is to be considered as illustrative and not restrictive in character, it being understood that only preferred embodiments have been shown and described and that all changes and modifications that come within the spirit of the invention are desired to be protected.

Claims

What is claimed is:

1. A planar array comprising a plurality of biological recognition molecules including at least two types of biological recognition molecules distributed about a substrate wherein a first type of biological recognition molecules is distributed according to a first frequency and a second type of biological recognition molecules is distributed according to a second frequency.

2. The planar array of claim 1 wherein the substrate is an optically readable disk and the first type of biological recognition molecules is adapted to selectively bind a first type of antibody or antigen.

3. The planar array of claim 1 wherein the substrate is a micro diffraction bio-CD, a phase contrast bio-CD, or an adaptive optics bio-CD.

4. The planar array of claim 1 wherein the plurality of biological recognition molecules includes molecules for binding cells, viruses, bacteria, toxins, peptides, DNA fragments, or antibodies.

5. A planar array comprising a plurality of biological recognition molecules including at least two kinds of biological recognition molecules distributed about a substrate wherein a first land of biological recognition molecules is distributed at a first height or depth relative to a surface of the substrate and a second kind of biological recognition molecules is distributed at a second height or depth relative to the surface.

6. The planar array of claim 5 wherein the first land of biological recognition molecules is adapted to selectively bind a first kind of antibody or antigen and the second kind of biological recognition molecules is adapted to selectively bind a second kind of antibody or antigen.

7. The planar array of claim 5 wherein the first kind of biological recognition molecules is adapted to bind an antibody or antigen and the second land of biological recognition molecule is adapted to bind a cDNA or DNA fragment.

8. An apparatus comprising: a surface-normal interferometry platform including a scanning pathway; and a plurality of analyzer molecules adapted to detect the presence or absence of a plurality of target analytes, the plurality of analyzer molecules distributed about the scanning pathway according to a multiplexing scheme.

9. The apparatus of claim 8 wherein the platform is a micro diffraction bio- CD, a phase contrast bio-CD, or an adaptive optics bio-CD.

10. The apparatus of claim 8 wherein the plurality of analyzer molecules includes first analyzer molecules for detecting the presence or absence of a first antibody or antigen and second analyzer molecules for detecting the presence or absence of a second antibody or antigen.

11. The apparatus of claim 8 wherein the multiplexing scheme includes frequency-domain multiplexing, space-domain multiplexing, wavelength-domain multiplexing, or code-division multiplexing.

12. The apparatus of claim 8 wherein the pathway is substantially ring shaped and the surface-normal interferometry platform is a self referencing phase quadrature interferometry platform.

13. The apparatus of claim 12 comprising a plurality of ring shaped pathways each including a plurality of analyzer molecules distributed thereabout according to a multiplexing scheme.

14. A method comprising: multiplexing a plurality of lands of capture molecules about a detection pathway; contacting a biological sample to the array; detecting the presence or absence of binding of the plurality of kinds of capture molecules and a plurality of target analytes using interferometry.

15. The method of claim 14 wherein the multiplexing comprises distributing a first ldnd of capture molecule at first spatial frequency, distributing a second kind of capture molecule at a second spatial frequency, and distributing a third ldnd of capture molecule at a third spatial frequency.

16. The method of claim 14 wherein detecting further comprises detecting a first binding using a first wavelength of laser light and a second binding using a second wavelength of laser light.

17. The method of claim 14 wherein the detection pathway is defined along a surface of a bio-optical disk.

18. The method of claim 14 further comprising rotating the pathway in connection with the detecting.

19. The method of claim 14 wherein the detecting uses self-referencing phase quadrature interferometry.

20. The method of claim 14 further comprising demultiplexing information of a particular capture molecule and a particular target analyte in connection with the detecting.

21. A method of probing a plurality of analyzer molecules distributed about a detection platform comprising: contacting a test sample to the plurality of analyzer molecules; scanning the plurality of analyzer molecules at a rate relating to a carrier frequency signal; and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially at a sideband of the carrier frequency signal.

22. The method of claim 21 further comprising prescanning the plurality of analyzer molecules before the contacting and improving the detecting based upon a difference between the scanning and the prescanning.

23. The method of claim 21 wherein the sideband is substantially free from overlap with the carrier frequency signal.

24. The method of claim 21 wherein the detecting utilizes self referencing phase quadrature interferometric detection.

25. The method of claim 21 wherein the detection platform is a bio-CD.

26. The method of claim 21 further comprising suppressing the carrier frequency signal.

27. The method of claim 21 wherein the detecting utilizes interferometry and the scanning utilizes a laser beam.

28. The method of claim 21 further comprising detecting the presence or absence of a second biological molecule based at least in part upon the presence or absence of a second signal substantially at a second sideband of the carrier frequency signal.

29. The method of claim 21 wherein the detecting includes detecting a harmonic signal closest to zero frequency.

30. The method of claim 21 wherein the detecting includes detecting a harmonic signal at a frequency greater than that of a harmonic signal closest to zero frequency.

31. The method of claim 21 wherein the detecting includes detecting a signal at or about a fundamental earner frequency.

32. The method of claim 21 wherein the detecting utilizes fluorescence detection.

33. A molecule detection platform comprising a substrate and a plurality of targets positioned about the substrate wherein specific analyzer molecules adapted to bind a specific analyle are immobilized about a first set of the targets, and nonspecific analyzer molecules are immobilized about a second set of the targets, and the targets positioned about the substrate along at least a first segment of a scanning pathway alternate between at least one of the first set and at least one of the second set.

34. The platform of claim 33 wherein the targets positioned about the substrate alternate along the first segment of the scanning pathway between at least four of the first set and at least four of the second set.

35. The platform of claim 33 wherein the platform is a micro diffraction bio- CD, a phase contrast bio-CD, or an adaptive optics bio-CD.

36. The platform of claim 33 wherein the nonspecific analyzer molecules exhibit nonspecific background binding at least substantially similar to the specific analyzer molecules.

37. The platform of claim 33 wherein the targets are interferometric microslructures.

38. The platform of claim 33 wherein the targets positioned about the substrate along at least a second segment of the scanning pathway adjacent the first segment alternate between at least one of the second set and at least one of the first set in the opposite order as the alternation of the first segment.

39. The platform of claim 33 wherein the targets are substantially contiguous along the segment of a scanning pathway.

40. A method comprising: providing a substrate for supporting biological analyzer molecules the substrate including at least one scanning pathway, the scanning pathway including a plurality of scanning targets; and distributing specific biological analyzer molecules adapted to detect a specific target analyte about a first set of the targets which alternate in groups of at least one with a second set of the targets, the second set of the targets not including the specific biological analyzer molecules.

41. The method of claim 40 further comprising distributing nonspecific analyzer molecules about the second set of the targets.

42. The method of claim 40 wherein the first set of the targets alternate in groups of at least four with the second set of the targets.

43. The method of claim 40 further comprising: contacting a test sample to the molecules; scanning the plurality of targets at a rate; and detecting the presence or absence of a biological molecule based at least in part upon the presence or absence of a signal substantially about a frequency offset from a frequency defined by the distribution of the targets and the scanning rate.

44. The method of claim wherein the detecting utilizes fluorescence.

45. The method of claim 43 wherein the substrate is a surface of a bio-CD, and the detecting utilizes phase quadrature interferometric detection