US20070023643A1 - Differentially encoded biological analyzer planar array apparatus and methods - Google Patents

Abstract

A method of probing a plurality of analyzer molecules distributed about a detection platform is disclosed. 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. A molecule detection platform including a substrate and a plurality of targets positioned about the substrate is also disclosed. 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. A method including providing a substrate for supporting biological analyzer molecules the substrate including at least one scanning pathway is also disclosed. The scanning pathway includes a plurality of scanning targets. Specific biological analyzer molecules adapted to detect a specific target analyte are distributed 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.

Description

CROSS REFERENCE
• This application 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 Feb. 1, 2005 and the same is expressly incorporated herein by reference.
• This invention was made with government support under grant reference number NSF ECS-0200424 awarded by the National Science Foundation. The Government has certain rights in the invention.
TECHNICAL FIELD
• The present invention generally relates to apparatus, methods and systems for detecting the presence of one or more target analytes or specific biological materials in a sample, and more particularly to a laser compact disc system for detecting the presence of biological materials and/or analyte molecules bound to target receptors on a disc by sensing changes in the optical characteristics of a probe beam reflected, transmitted, or diffracted by the disc caused by the materials 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, pathogens, 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: Ekins, R., F. Chu, and E. Biggart,Development of microspot multi-analyte ratiometric immunoassay using dual flourescent-labelled antibodies. Anal. Chim. Acta, 1989, Vol. 227, p. 73-96; Ekins, R. and F. W. Chu,Multianalyte microspot immunoassay—Microanalytical “compact Disk” of the future.Clin. Chem., 1991, Vol. 37(11), p. 1955-1967; Ekins, R.,Ligand assays: from electrophoresis to miniaturized microarrays.Clin. Chem., 1998, Vol. 44(9), p. 2015-2030]. Conventional fluorescence detection is employed to sense the presence in the microarray 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., AGaAs/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; Dübendorfer, 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 range 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 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 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.
• 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.
• Additional embodiments, aspects, and advantages of the present invention will be apparent from the following description.
BRIEF DESCRIPTION OF THE DRAWINGS
• FIG. 1 shows a graph of noise power density versus frequency according to an embodiment of the present invention;
• FIG. 2 shows a graph of power spectrum versus frequency according to an embodiment of the present invention;
• FIG. 3 shows a distribution of elements according to an embodiment of the present invention;
• FIG. 4 shows a distribution of elements according to an embodiment of the present invention;
• FIG. 5 shows scanning of an element according to an embodiment of the present invention;
• FIG. 6 shows a distribution of elements according to an embodiment of the present invention;
• FIG. 7 shows a distribution of elements according to an embodiment of the present invention;
• FIG. 8 shows a bio-CD according to an embodiment of the present invention;
• FIG. 9A shows a bio-CD according to an embodiment of the present invention;
• FIG. 9B shows a bio-CD according to an embodiment of the present invention;
• FIG. 10A shows a bio-CD according to an embodiment of the present invention;
• FIG. 10B shows a bio-CD according to an embodiment of the present invention;
• FIG. 11 shows a bio-CD according to an embodiment of the present invention;
• FIG. 12 shows scanning of elements according to an embodiment of the present invention;
• FIG. 13 shows a detection system according to an embodiment of the present invention;
• FIG. 14 shows a graph of time domain results of scanning a differentially encoded MD-class calibration disk;
• FIG. 15 shows a graph of frequency domain results of scanning a differentially encoded MD-class calibration disk;
• FIG. 16 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;
• FIG. 17 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;
• FIG. 18 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;
• FIG. 19 shows a graph of frequency domain results of scanning a differentially encoded MD-class disk;
• FIG. 20 shows a portion of an MD-class disk;
• FIG. 21 shows a graph of time domain results of scanning the disk ofFIG. 20;
• FIG. 22 shows a graph of frequency domain results of scanning the disk ofFIG. 20;
• FIG. 23 shows a graph of time domain results of scanning a PC-class disk;
• FIG. 24 shows a portion of a PC-class disk;
• FIG. 25 shows a magnified view of a portion ofFIG. 24;
• FIG. 26 shows Fourier domain results of scanning the disk ofFIG. 24;
• FIG. 27 shows a demodulated image of the of the Fourier domain results ofFIG. 26;
• FIG. 28 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 toFIG. 1 there is showngraph1000 with frequency increasing along its x axis as indicated byx axis arrow1020 and noise power density increasing along its y axis as indicated by itsy axis arrow1010. Frequency can be either temporal frequency (Hz) or spatial frequency (1/cm).Graph1000 illustrates noise power density versus frequency in the absence of a carrier frequency.Curve1030 illustrates the noise power density of total noise as it varies with frequency.Curve1040 illustrates the noise power density of 1/f noise as it varies with frequency. A bandwidth betweenfrequencies1060 and1070 is indicated by arrows BW. The total noise for this bandwidth is given by the area undercurve1030 labeled1080 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 byline1050 and represents the frequency above which a signal may be detected over noise.
• With reference toFIG. 2 there is showngraph2000 with frequency increasing along its x axis as indicated byx axis arrow2020 and power spectrum increasing along its y axis as indicated byy axis arrow2010. The power level of 1/f noise is illustrated bycurve2030. ADC sideband signal2040 having DCsideband center frequency2041, acarrier signal2060 havingcarrier center frequency2061, andcarrier sidebands2050 and2070 having carriersideband center frequencies2051 and2071, respectively, are also shown.
• Graph2000 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 carrier 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 ingraph2000, carrier sideband signals2050 and2070 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:$i\left(t\right)=\frac{1}{2}\left(1+\cos {\omega }_{c}t\right)\left(1+A\cos {\omega }_{m}t\right)$
  Equation 1 has a harmonic decomposition described by Equation 2:$\begin{array}{c}i\left(t\right)=\frac{1}{2}+\frac{1}{2}\cos {\omega }_{c}t+\frac{A}{2}\cos {\omega }_{m}t+\frac{A}{4}\cos \left({\omega }_c+{\omega }_m\right)t+\\ \frac{A}{4}\cos \left({\omega }_c-{\omega }_m\right)t\end{array}$
  Equation 2 describes a DC sideband at ω_m, a carrier band at ω_c, and two carrier sidebands at ω_c−ω_mand ω_c+ω_mwhich correspond toDC sideband2040, acarrier2060, andsidebands2050 and2070 as shown ingraph2000. InEquations 1 and 2, t is time, i(t) is detector output current as a function of time, ω_cis carrier angular frequency, ω_mthe 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 toFIG. 3 there is shown a distribution ofelements3000 includingelements3010 and3020.Elements3010 and3020 are distributed about readingpathway3004 which is defined on a substrate. As shown by dashedlines3030,3040,3050,3060, and3070,elements3010 and3020 are arranged in alternating groups of four. As shown byellipses3006 and3008 this pattern can continue beyond the segment illustrated inFIG. 3 with the groups of four elements alternating as described above. A unit cell includes a group of fourelements3010 and a group of fourelements3020 as is indicated by arrow UC between dashedlines3030 and3050. Scanning footprint SF travels along readingpathway3004 to scan the distribution ofelements3000. Additional embodiments include alternating groups of different numbers, for example, one, two, three, five or more, and corresponding different sizes of unit cells.
• Elements3010 include specific analyzer molecules which selectively bind with a target analyte andelements3020 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,elements3010 include specific antibodies immobilized about their surfaces, for example, as a monolayer, fractional monolayer, partial monolayer, or near monolayer, andelements3020 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 whichcase elements3020 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 ofelements3000 is one example of differential encoding or envelope modulation of bimolecular information. According to a preferred embodiment of the present invention, distribution ofelements3000 is on a bio-CD whereelements3010 and3020 are interferometric microstructures formed on a surface of the bio-CD, andreading pathway3004 is one of a number of a substantially concentric circular tracks. As described above,elements3010 on the track are active (carrying a specific biological analyzer molecule) andelements3020 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 ofelements3010 and3020, 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 kHz and the detection frequency is approximately 12.5 kHz. 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 carrier frequency, and the back end referenced to the unit cell can be used to scan a bio-CD having distribution ofelements3000 with a laser. Differential encoding of distribution ofelements3000, 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. Pat. 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 Ser. No. 10/726,772 filed on Dec. 3, 2003 entitled “Adaptive Interferometric Multi-Analyte High-Speed Biosensor” (published on Aug. 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 Feb. 1, 2005, entitled “Phase-Contrast Quadrature For Spinning Disk Interferometry And Immunological Assay”, U.S. Provisional Patent Application No. 60/755,177, filed Dec. 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 toFIG. 4 there is shown abiosensor platform4000 including asubstrate4030 having anupper surface4010 andlower surface4020.Interferometric elements4040,4050,4060, and4070 are formed on theupper surface4010 ofsubstrate4030.Platform4000 may also include additional interferometric elements in addition to those shown in the portion ofplatform4000 illustrated inFIG. 4. Alaser beam4002 having wavelength λ scans theinterferometric elements4040,4050,4060, and4070 in the direction indicated by arrow DM.Elements4040 and4050 include specific analyzer molecules immobilized about their scanned surfaces andelements4060 and4070 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 withFIG. 3 and elsewhere herein. This configuration of specific and nonspecific analyzer molecules ofbiosensor platform4000 is another example of differential encoding according to a preferred embodiment of the present invention. In one preferred embodiment of thepresent invention platform4000 is a micro-diffraction bio-CD andelements4040,4050,4060, and4070 are radial spokes distributed about the surface of the bio-CD.Platform4000 can also be any of various other biosensor platforms including, for example, those described herein.
• Biosensor platform4000 is one example of carrier suppression according to a preferred embodiment of the present invention.Elements4060 and4040 have a height illustrated by arrows HA andelements4050 and4070 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 carrier side bands are weak relative to the carrier, carrier 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 carrier 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 toFIG. 5 there is shown an example of ascanning5000 during whichfootprint5020 passes overelement5010.Areas5021 are the areas of the scanning footprint not overelement5010 andarea5011 is the area in whichscanning footprint5020 overlapselement5010. According to apreferred embodiment element5010 is a gold microdiffraction element placed on a partially reflecting substrate. This embodiment allows carrier 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:$E_T=\frac{E_0}{\sqrt{A}}\left[r_L{A}_L+r_r{A}_r{e}^{i\Phi }\right]$
  The total reflected intensity is given by Equation 4:$I_T=\frac{{\mathrm{<figure-callout\; label="E"\; filenames="US20070023643A1-20070201-D00016.png,US20070023643A1-20070201-D00025.png"\; state="\{\{state\}\}">E</figure-callout>}}_0^2}{A}\left[R_L{\mathrm{<figure-callout\; label="A\; L"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">A</figure-callout>}}_L^{}+R_r{A}_{\mathrm{<figure-callout\; label="r"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">r</figure-callout>}}^2+2r_L{r}_r{A}_L{A}_r\cos \varphi \right]$
  Under the condition of Land: Φ=0, A_L=A and A_r=0. Thus, intensity reflected by land is given by Equation 5:
  I_L=I₀R_L
  Under the condition of Quadrature: Φ=π/2. Thus, the reflected intensity under a condition of quadrature is given by Equation 6:$\begin{array}{c}{I}_Q=\frac{{\mathrm{<figure-callout\; label="E"\; filenames="US20070023643A1-20070201-D00016.png,US20070023643A1-20070201-D00025.png"\; state="\{\{state\}\}">E</figure-callout>}}_0^2}{A}\left[R_L{\mathrm{<figure-callout\; label="A\; L"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">A</figure-callout>}}_L^{}+R_r{A}_r^2\right]\\ =I_0\left[R_L{a}_{\mathrm{<figure-callout\; label="L"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">L</figure-callout>}}^2+R_r{a}_r^2\right]\end{array}$
  where a_iis the area fraction, and a_L+a_r=1. Conditions of balanced operation are given by Equations 7 and 8:
  I_Q=_L
  R_Lα_L²+R_rα_r²=R_L
  The solution of which are given in Equations 9 and 10:$\frac{1-a_{\mathrm{<figure-callout\; label="L"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">L</figure-callout>}}}{1+a_L}=\frac{R_L}{R_r}$$a_L=\frac{1-\frac{R_{\mathrm{<figure-callout\; label="L\; R\; r"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">L</figure-callout>}}}{R_r}}{1+\frac{R_L}{R_r}}$
  For Equations 3-10, I_ris the total reflected intensity, I_Lis the intensity reflected by land, I_Ois the incident reflected intensity, I_Qis the reflected intensity under a condition of quadrature, E_ois the reflected field, A is the total area, A_Lisarea5021, A_risarea5011, a_Lis A_Ldivided by the area of the beam footprint, a_Ris A_Ldivided by the area of theelement5010intersecting element5020, R_Lis |r_L|², R_ris |r_r|²and Φ is the phase difference between reflected components of the laser. Thus, if the partially reflective substrate is silicon, for example, which has R_L=32% and R_r=98%, then a_L=51% and a_r=49%.
• With reference toFIG. 6 there is shown abiosensor platform6000 includingsubstrate6030 having anupper surface6010 and alower surface6020.Upper surface6010 includesanalyzer molecules6040,6050,6060,6070,6080 and6090 immobilized aboutsurface6010.Analyzer molecules6040,6060, and6080 are specific analyzer molecules for selectively binding a particular analyte andanalyzer molecules6050,6070 and6090 are nonspecific analyzer molecules. The specific and nonspecific analyzer molecules can be, for example, the same or similar to those described elsewhere herein.FIG. 6 shows one example of an alternating pattern of specific and nonspecific analyzer molecules.Laser beam6002 scans the analyzer molecules in the direction indicated by the arrow DM which is preferably accomplished by rotating theplatform6000 but could also be accomplished by other movement ofplatform6000 or by movement ofbeam6002. According to a preferred embodiment of thepresent invention platform6000 is a phase contrast bio-CD or an adaptive optical bio-CD andanalyzer molecules6040,6050,6060,6070,6080 and6090 are radial spokes or other patterns of analyzer molecules, however,platform6000 could also be another kind of bio-CD or other platform including, for example, those described elsewhere herein.
• During scanning ofplatform6000 bylaser beam6002 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 carrier wave suppression and double sideband detection.
• With reference toFIG. 7 there is shown abiological analyzer platform7000 includingsubstrate7030 includingupper surface7010 andlower surface7020.Interferometric elements7070 are distributed aboutupper surface7010 and are spaced apart bygaps7060.Interferometric elements7070 include specificbiological analyzer molecules7040 and nonspecificbiological analyzer molecules7050 immobilized about their surfaces which can be the same or similar to those described elsewhere herein. Groups of the interferometric elements andanalyzer molecules7090 and7091 are also shown.Groups7090 and7091 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 betweengroups7090 and7091.Platform7000 is preferably an adaptive optical bio-CD, however,platform6000 could also be any other type of biosensor platform or another type of bio-CD including, for example, those described elsewhere herein.
• During scanning ofplatform7000 by a laser beam the phase of the carrier is periodically flipped by π forsuccessive groups7090 and7091. 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 carrier sidebands. This is one example of differential encoding including carrier wave suppression and double sideband detection.
• According to a preferred embodiment modulated signals are detected within a detection bandwidth Δf_d. 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:
  Δω₈Δτ=1
  where Δω_s=2πΔf_s, Δf_sis 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 carrier frequency, f_carrier, is set by the rotation frequency of the bio-CD, f_disk, and by the number of spokes, targets, or interferometric elements, N, around a specified circumference as described by Equation 12:
  ƒ_carrierNƒ_disk
  The signal bandwidth Δƒ_sis described by Equation 13:$\Delta f_s=\frac{{\mathrm{<figure-callout\; label="f\; disk"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">f</figure-callout>}}_{\mathrm{disk}}}{2\pi }$
  The relative signal bandwidth Δƒ_relis described by Equation 14:$\Delta f_{\mathrm{rel}}=\frac{\Delta f}{f_{\mathrm{carrier}}}$
  For a single continuous track around a circumference, the relative bandwidth Δƒ_relis described by Equation 14:$\Delta f_{\mathrm{rel}}=\frac{1}{2\mathrm{\pi \Delta \tau }{f}_{\mathrm{carrier}}}=\frac{{\mathrm{<figure-callout\; label="f\; disk"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">f</figure-callout>}}_{\mathrm{disk}}}{2\pi {\mathrm{Nf}}_{\mathrm{disk}}}=\frac{1}{2\pi N}$
  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:$\Delta f_{\mathrm{rel}}^S=\frac{N}{M}\Delta f_{\mathrm{rel}}=S\Delta f_{\mathrm{rel}}$
  Thus, for example, if N=1024, and S=16, the relative bandwidth is 0.25%. If ƒ_disk=100 Hz, then ƒ_s=100 kHz, Δƒ_s=16 Hz and Δƒ_{s rel}=256 Hz. These relations suggest that S up to 128 segments or more is clearly a possible scenario for homogeneous bandwidths for which Δƒ_s=2 kHz and Δƒ_{s rel}=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 byEquations 16 and 17:
  Δƒ^S=Δƒ_{in hom}
  BW=√{square root over (2)}ƒ_{in hom}
  For detection bandwidth BW, this sets the maximum segment number according to Equation 18:$S=\sqrt{2}\pi N\left(\frac{\mathrm{BW}}{f_{\mathrm{carrier}}}\right)$
  which for BW=3 kHz and f_carrier=100 kHz 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=rd\theta \mathrm{dr}=r\frac{2\pi }{S}\mathrm{dr}=A/N$$\mathrm{dr}=\frac{\mathrm{AS}}{2\pi \mathrm{rN}}=\frac{\left({\mathrm{<figure-callout\; label="R"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">R</figure-callout>}}_2^2-{\mathrm{<figure-callout\; label="R"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">R</figure-callout>}}_1^2\right)\mathrm{<figure-callout\; label="S"\; filenames="US20070023643A1-20070201-D00019.png,US20070023643A1-20070201-D00022.png"\; state="\{\{state\}\}">S</figure-callout>}}{2\mathrm{rN}}$
  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 R₂and R₁, N is number of wells, S is the number of segments, R₁is the inner radius, and R₂is the outer radius.
• With reference toFIG. 8 there is shown a bio-CD8000 according to one embodiment of the present invention.Bio-CD8000 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-CD8000 includessectors8001,8002,8003,8004,8005,8006,8007,8008,8009,8010,8011,8012,8013,8014,8015, and8016. Bio-CD8000 further includes substantially concentric tracks ofwells8021,8022,8023,8024,8025,8026,8027, and8028.Bio-CD8000 has S=16 sectors, N=128 then T=8 (tracks) and the inner track radius and radial thicknesses are given in Table I:

  	Inner Track Radius	Radial Thickness dr
  Track Number	(millimeters)	(millimeters)

  8028	20	6.56
  8027	26.56	4.94
  8026	31.50	3.60
  8025	35.10	3.39
  8024	38.50	3.13
  8023	41.63	2.93
  8022	44.56	2.76
  8021	47.33	2.62

  
  Bio-CD8000 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 toFIGS. 9A, 9B,10A,10B and11 there are shown bio-CDs9000A,9000B,10000A,10000B, and11000 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:$C=\frac{2\pi r}{\Lambda }$
  where Λ is the spatial period, usually Λ=2w, where w is the beam waist. For a beam waist of 20 microns and Λ=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 kHz and 800 kHz, respectively.
• For N wells, the area of each well is given by Equation 22:
  α=rdθdr=A/N
  The aspect ratio a_ris set by the Equation 23:
  rdθ=α_rdr
  The radial widths and angular widths are given by Equation 24:$\mathrm{dr}=\sqrt{\frac{A}{a_{r}N}}\mathrm{and}$$d\theta =\frac{1}{r}\sqrt{\frac{a_{r}A}{N}}$
  FIG. 9A shows a 96 well disk with an aspect ratio of 1 and dr=7.5 mm, a=61 mm², T=4, S_i=15, and S_o=33.FIG. 9B shown a 96 well disk with an aspect ratio of 4 and dr=4.3 mm, a=64 mm², T=7, S_i=8, and S_o=19. The well inFIGS. 9A and 9B areas are approximately 0.6 cm².FIG. 10A shows a 512 well disk with an aspect ratio of 4, dr=1.76 mm, a=12.7 mm², T=17, S_i=17, and S_o=42,FIG. 10B shows a 1000 well disk with an aspect ratio of 4, dr=1.25 mm, a=6.4 mm², T=24, S_i=24, and S_o=59.FIG. 11 shows an 8000 well disk with an aspect ratio of 4, dr=0.45 mm, a=0.82 mm², T=66, S_i=69, and S_o=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 toFIG. 12 there are shown examples of scanning targets12000.Targets12000 are a periodically alternating pattern of targets includingspecific antibodies12010 and targets including nonspecific antibodies or not includingantibodies12020. 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,targets12010 have the analyte bound to their analyzer molecules whiletargets12020 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:$v_{\mathrm{spatial}}=\frac{1}{\Lambda }$
  where Λ is the spatial periodicity and ν_spatialis the spatial frequency.
• During scanningtargets12000 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 w_oless than spatial periodicity Λ (preferably w_o<<Λ) and moves relative to thetargets12000 with a velocity in the direction indicated by arrow v. Under these scanning conditions the spatial frequency ν_spatialis converted into temporal frequency on the transmitted or reflected beam as described by Equation 26:
  ƒ=V·v
  where ƒ 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 w_ogreater than spatial periodicity Λ (preferably w_o>>Λ) and can be stationary or can move relative to thetargets12000 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:$\theta ={\sin }^{-1}\left(\frac{\lambda }{\Lambda }\right)$
  where λ is the illumination wavelength, and Λ is the spatial period. When laser spot z moves over totargets12000, ortargets12000 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 toFIG. 13 there is showndetection system13000 which includesdetector13010 anddetector13020.Detectors13010 and13020 could be any detectors for detecting electromagnetic waves, for example optical detectors.System13000 further includesprobe beam13030 which can be a focused probe beam or a broad area probe beam.Probe beam13030scans targets13040 which move relative tobeam13030 with a relative velocity in the direction indicated by arrow RV. The scanning targets13040 bybeam13030 results in a transmitted or reflectedmode13012 and a diffractedmode13022.Mode13012 is directed todetector13010 andmode13022 is directed todetector13020. Reference beam13023 is directed todetector13010 and reference beam13023 is directed todetector13020. Reference beam13023 is preferably maintained in a condition of phase quadrature relative to the transmittedmode13012.Reference beam13033 is preferably maintained in a condition of phase quadrature relative to diffractedmode13022.System13000 also includesbeam splitters13011 and13021 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 beams13033 and13023 can be added before photodetectors or can be combined adaptively with signals. Reference beams13033 and13023 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 thatdetection system13000 could include only one or the other ofdetectors13010 and13020 and their related beams and modes.
• Experimental demonstrations of several exemplary embodiments including carrier side band detection according to the present invention will now be described in connection withFIGS. 14-28. With reference toFIG. 14, there is showngraph14000 with time increasing along its x axis as indicated by x axis arrow1420 and signal intensity (voltage) increasing along its y axis as indicated byy axis arrow14010.Graph14000 further shows signal14030 which is a voltage signal that varies with time.Signal14030 results from the scanning of an MD-class calibration disk which was fabricated with1024 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 producedsignal14030 which includes a series of alternatinglocal minima14031 and14032 corresponding to and indicating the two spoke heights. The signal intensity difference between the alternatinglocal minima14031 and14032 is illustrated byarrow14040 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 dashedline14050. 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 toFIG. 15 there is showngraph15000 with frequency increasing along its x axis as shown byx axis arrow15020 and power increasing logarithmically along its y axis as shown byy axis arrow15010.Graph15000 shows the frequency domain results of the scanning of the MD-class calibration disk described above in connection withFIG. 14.Graph15000shows carrier signal15030 at 200 kHz,sideband signal15031 at 100 kHz, and sideband signal15032 at 300 kHz. Thus the sideband signals are present at half carrier frequency increments. A strong 1/f noise peak15040 is present at zero frequency, and a significantly suppressed noise floor is present at the frequencies of carrier and sideband signals15030,15031 and15032. 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 toFIG. 16 there is showngraph16000 with frequency increasing along its x axis as shown byx axis arrow16020 and power increasing along its y axis as shown byy axis arrow16010.Graph16000 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 line16060 and the results of scanning a track including the patterned protein are indicated byline16050.
• Graph16000 shows16030 the 1/f noise at DC and two DC sideband signals16031 and16032. A carrier frequency signal (not shown) is present at about 100 kHz. The presence of protein is detected as a 1/64 harmonic of the carrier frequency at about 1.6 kHz as shown bysignal16032 and also bysignal16031 at about −1.6 kHz. A secondharmonic signal16034 and16033 is also present at 1/32 the carrier frequency and is caused by slight asymmetry in the deposition of the proteins. A comparison ofprotein track signal16050 and signal16060 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 byarrow16040.
• With reference toFIG. 17 there is showngraph17000 with frequency increasing along its x axis as shown byx axis arrow17020 and power spectrum increasing logarithmically along its y axis as shown byy axis arrow17010.Graph17000 presents average values for scanning of six tracks of the MD-class disk which is described above in connection withFIG. 16.Graph17000 shows a comparison of 1/64harmonic signal17040 at about 1.6 kHz, which is generated by and indicates the presence of protein, andcarrier signal17030. As illustrated by arrow17050, the protein modulation is about 4.6% of the carrier wave, which is consistent with a monolayer of immobilized protein.
• With reference toFIG. 18 there is showngraph18000 with frequency increasing along its x axis as shown byx axis arrow18020 and power spectrum increasing logarithmically along its y axis as shown byy axis arrow18010. While the side bands off of DC yielded the best signal-to-noise ratio for scanning the MD-class disk described above in connection withFIG. 16, every carrier harmonic includes two side-bands. Thus, as shown ingraph18000 fundamental carrier harmonic18030 which is at about 80 kHz includessidebands18031 and18032.Sidebands18031 and18032 are small peaks above and below theharmonic carrier frequency18030 which indicate the presence of the protein. Every other carrier harmonic also has two associated sidebands.
• With reference toFIG. 19 there is showngraph19000 with frequency increasing along its x axis as shown byx axis arrow19020 and power spectrum increasing logarithmically along its y axis as shown byy axis arrow19010.Graph19000 shows carrier frequency harmonics19030A (which is the first carrier harmonic18030 at about 80 kHz described above in connection withFIG. 18),19030B,19030C,19030D,19030E,19030F, and19030G. Each carrier harmonic includes protein sidebands, though the wide frequency range of the graph1900 makes it difficult to see the protein sidebands for all the harmonics.Graph19000 also demonstrates the noise-floor roll-off for high frequencies associated to the transit time t=w₀/v of a point on the disk across the width of the focused laser spot w_o.Line19050 shows the approximate midpoint of the noise floor roll off.
• With reference toFIG. 20 there is shown a fluorescence microscope image of portion of an MD-class disk20000 according to one embodiment of the present invention.Disk20000 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 lines20010 (indicating deposition of specific antibody) and20020 (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 carrier frequency lower side-band merge into a single sideband half way between DC and the fundamental carrier frequency.
• With reference toFIG. 21 there is showngraph21000 with time increasing along its x axis as shown byx axis arrow21020 and voltage increasing along its y axis as shown byy axis arrow21010. 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.Graph21000 shows the detectedtime trace21030 from a512 differential encoded disk.Trace21030 shows an alternating pattern between the bare and protein-carrying spokes as indicated by the minimum points trace21030 which alternate in amplitude at the rate of a halfharmonic signal21040.
• With reference toFIG. 22 there is showngraph22000 with frequency increasing along its x axis as shown byx axis arrow22020 and power spectrum increasing logarithmically along its y axis as shown byy axis arrow22010.Graph22000 shows the frequency domain side band effect of the disk described above in connection withFIG. 21. The half-frequencyharmonic protein signal22040 is strong and occurs near the frequency of lowest noise between DC signal22050 and thefirst carrier signal22030. As shown ingraph22000 the DC sideband and first carrier sidebands have merged at the half-frequencyharmonic protein signal22040. Furthermore, theprotein signal22050 itself hassidebands22041 and22042 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 atsignal22040 represents the optimal performance condition for carrier sideband detection on the MD-class disk described above.
• With reference toFIG. 23 there is showngraph23000 with frequency increasing along its x axis as shown byx axis arrow23020 and power spectrum increasing logarithmically along its y axis as shown byy axis arrow23010.Graph23000 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.Graph23000 showsDC signal23040 and protein signal23030 which is caused by and indicates the presence of protein. For this PC-class embodiment, the carrier 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 toFIG. 24 there is shown a portion of a patterned protein PC-class disk24000 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 inFIG. 11, the portion ofdisk24000 is in a checkerboard pattern. Substantially rectangular areas of periodic stripes ofprotein24010 are alternated with substantially rectangular areas ofbare disk24020. 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 toFIG. 25 there is shown a magnifiedportion25000 of the PC-class disk24000 shown inFIG. 24individual protein bands24011 ofprotein regions24010 are visible in magnifiedportion25000. The rectangular spatial patterns ofareas24010 and4020 ofdisk24000 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 toFIGS. 26, 27 and28.FIG. 26 shows anisolated protein peak26030 in the power spectrum. Thehorizontal axis26010 is temporal frequency and the vertical axis26020 is spatial frequency along the radius of the disk. The sub-peaks26031 and26032 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 inFIG. 27. Only the long-range checkerboard pattern27000 corresponding toareas24010 and24020 is visible, with the periodicity of theindividual protein bands24011 removed. After demodulation, subtracting a prescan becomes much more accurate.
• FIG. 28 showsgraph28000 with distribution probability on the vertical axis and height in nm on the horizontal axis.Graph28000 shows the results of subtracting a prescan from a postscan before demodulation asdistribution28010 and performing the same subtraction after demodulation asdistribution28020. The error in height reduces from 75 pm fordistribution28010 to 20 pm fordistribution28020 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 withFIGS. 14-28 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 patents and patent applications. 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 including, for example, those described herein.
• 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 of the foregoing and other types of analyzer molecules known to a person 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 plus or minus about twenty percent 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 aberrations 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 (25)

1. 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.

2. The method ofclaim 1 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.

3. The method ofclaim 1 wherein the sideband is substantially free from overlap with the carrier frequency signal.

4. The method ofclaim 1 wherein the detecting utilizes self referencing phase quadrature interferometric detection.

5. The method ofclaim 1 wherein the detection platform is a bio-CD.

6. The method ofclaim 1 further comprising suppressing the carrier frequency signal.

7. The method ofclaim 1 wherein the detecting utilizes interferometry and the scanning utilizes a laser beam.

8. The method ofclaim 1 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.

9. The method ofclaim 1 wherein the detecting includes detecting a harmonic signal closest to zero frequency.

10. The method ofclaim 1 wherein the detecting includes detecting a harmonic signal at a frequency greater than that of a harmonic signal closest to zero frequency.

11. The method ofclaim 1 wherein the detecting includes detecting a signal at or about a fundamental carrier frequency.

12. The method ofclaim 1 wherein the detecting utilizes fluorescence detection.

13. 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 analyte 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.

14. The platform ofclaim 13 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.

15. The platform ofclaim 13 wherein the platform is a micro diffraction bio-CD, a phase contrast bio-CD, or an adaptive optics bio-CD.

16. The platform ofclaim 13 wherein the nonspecific analyzer molecules exhibit nonspecific background binding at least substantially similar to the specific analyzer molecules.

17. The platform ofclaim 13 wherein the targets are interferometric microstructures.

18. The platform ofclaim 13 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.

19. The platform ofclaim 13 wherein the targets are substantially contiguous along the segment of a scanning pathway.

20. 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.

21. The method ofclaim 20 further comprising distributing nonspecific analyzer molecules about the second set of the targets.

22. The method ofclaim 20 wherein the first set of the targets alternate in groups of at least four with the second set of the targets.

23. The method ofclaim 20 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.

24. The method ofclaim 23 wherein the detecting utilizes fluorescence.

25. The method ofclaim 23 wherein the substrate is a surface of a bio-CD, and the detecting utilizes phase quadrature interferometric detection

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