Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
  • G01N33/54366—Apparatus specially adapted for solid-phase testing
  • G01N33/54373—Apparatus specially adapted for solid-phase testing involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B82—NANOTECHNOLOGY
  • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
  • B82Y15/00—Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B82—NANOTECHNOLOGY
  • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
  • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites

Definitions

• the present invention relates to methods of using evanescent field sensing to detect or evaluate unlabeled, unpurified analytes of interest.
• the present invention features the use of evanescent field sensing techniques for detection or evaluation of unpurified, unlabeled analytes of interest.
• Capture molecules capable of binding to the analytes of interest can be immobilized to a sensing surface of an evanescent field sensor. Binding of the unpurified, unlabeled analytes to the capture molecules alters the refractive index at the sensing surface, thereby producing a detectable signal in the reflected light from the surface.
• the present invention provides methods of using evanescent field sensing for evaluating or monitoring interactions between an unpurified analyte and a capture molecule.
• These methods comprise the steps of: contacting a raw sample with a sensing surface of an evanescent field sensor, where the raw sample comprises the analyte, and the sensing surface is coated with the capture molecule; and detecting a change in the refractive index at the sensing surface.
• the change in the refractive index indicates whether the analyte is capable of interacting with the capture molecule.
• the evanescent field sensors employed in the present invention are grating-coupled waveguides, such as those described in U.S. Patent No. 4,815,843 or U.S. Patent Application "Substrate Index Modification for Increasing the Sensitivity of Grating-Coupled Waveguides" (Attorney Dockey No. SP03-081 (WJT003-0036)).
• a grating-coupled waveguide typically involves: directing a light beam (e.g., a laser beam) into the waveguide to produce an evanescent tail that extends beyond a sensing surface coated with capture molecules; and receiving a reflected light beam from the waveguide to detect a resonant condition that indicates whether an analyte in the sample binds to the immobilized capture molecules.
• a light beam e.g., a laser beam
• Raw samples amenable to the present invention include, but are not limited to, cell lysates, supernatants of cultured cells, bodily fluids, tissue extracts, food or beverage samples, pharmaceutical samples, clinical samples, or other samples that have not been subject to substantial purification.
• the raw sample being analyzed is a lysate or supernatant of cultured cells
• the analyte of interest is a recombinant protein expressed by the cultured cells.
• control samples are used to determine baseline refractive index changes at the sensing surface.
• the desired signals such as refractive index changes caused by the binding of an analyte of interest to the sensing surface, can be extracted by comparing the refractive index changes produced by the raw sample of interest to the baseline refractive index changes.
• a control samples is prepared from the same source as the raw sample being analyzed, but does not include the analyte of interest.
• Other types of control samples such as blocking buffers containing bovine serum albumin or other proteins, can also be used.
• the present invention features methods for evaluating or monitoring molecular interactions in multi-sample formats.
• These methods comprise the steps of: contacting a plurality of raw samples with respective sensing surfaces of an evanescent field sensor, where each raw sample comprises an analyte of interest, and each sensing surface is coated with a capture molecule; and detecting a change in the refractive index at each sensing surface.
• the change in the refractive index at each sensing surface indicates whether the captures molecules immobilized at that surface interact with the analyte of interest in the corresponding raw sample.
• the evanescent field sensor comprises a microplate which includes a plurality of wells. Each well comprises or incorporates a grating- coupled waveguide that includes a sensing surface coated with capture molecules.
• the present invention also features methods for detecting the presence or absence of an analyte of interest in raw samples. These methods comprise the steps: contacting a raw sample with a sensing surface of an evanescent field sensor, where the sensing surface is coated with capture molecules capable of binding to the analyte of interest; and detecting a change in the refractive index at the sensing surface. The change in the refractive index is indicative of the presence or absence of the analyte of interest in the raw sample.
• the raw sample is a bodily fluid sample (e.g., blood, serum, sputum, tears, sweat, semen or urine) or a tissue extract (e.g., a brain or lung extract), and the analyte of interest is an antibody specific to an epitope of a pathogen (such as a virus or bacterium).
• the immobilized capture molecules comprise the epitope of the pathogen and, therefore, are recognizable by the analyte of interest.
• the analyte of interest is a cancer cell marker, and the immobilized capture molecules are antibodies specific to the cancer cell marker.
• FIG 1 diagrammatically illustrates the layout of a source plate and a label-dependent detection (LID) test plate employed in the present invention.
• LID label-dependent detection
• Figure 2 shows LID interrogation of interactions between purified streptavidin and immobilized biotin.
• Figure 3 is a corrected LID response curve indicating the bulk index shift due to interactions between purified streptavidin and immobilized biotin.
• Figure 4 demonstrates LID interrogation of interactions between streptavidin in cell lysate and immobilized biotin.
• Figure 5 is a corrected LID response curve indicating the bulk index shift due to interactions between streptavidin in cell lysate and immobilized biotin.
• the present invention features the use of evanescent field sensing for detecting or evaluating unpurified, unlabeled analytes in raw samples.
• Capture molecules capable of binding to an analyte of interest can be immobilized at a sensing surface of an evanescent field sensor.
• the interaction between the analyte of interest in a raw sample and the immobilized capture molecules alters the refractive index at the sensing surface, which in turn produces a detectable signal in the reflected light from the surface.
• Raw samples amenable to the present invention include, but are not limited to, cell lysates, tissue extracts, bodily fluid, or other biologically-derived samples.
• Microbial samples, food/beverage samples, or other crude samples that have not been subject to substantial purification can also be analyzed according to the present invention.
• the ability to detect unlabeled analytes in raw samples by evanescent field sensing is unexpected due to the sensitivity of an evanescent field sensing surface to non-specific bindings. Therefore, the present invention represents a significant advance in the field of label-independent detection.
• Evanescent field sensing enables label-independent optical monitoring of biological events.
• the associated electromagnetic field penetrates a small distance (typically about 100- 1 ,000 nm) away from the surface to create a so-called evanescent electromagnetic field.
• This field can interact with molecules attached to the surface.
• the interaction of the evanescent electromagnetic field with the surface-attached molecules can be used to detect refractive index changes on the surface which occur when analytes in a sample bind to the molecules immobilized to the surface.
• the evanescent field sensors employed in the present invention are grating-coupled waveguides.
• grating- coupled waveguides include those described in U.S. Patent No. 4,815,843 and U.S. Patent Application "Substrate Index Modification for Increasing the Sensitivity of Grating-Coupled Waveguides" (Attorney Dockey No. SP03-081 (WJT003-0036)), both of which are incorporated herein by reference in their entireties.
• a grating-coupled waveguide typically includes a substrate, a diffraction grating, and a waveguide film. The diffraction grating can be directly fabricated into the waveguide film or the substrate.
• the diffraction grating can also be located in optical proximity to the waveguide film, or even constitutes the waveguide film itself.
• a light beam e.g., a coherent laser beam
• Light reflected from the waveguide is received and analyzed to detect resonant conditions that are indicative of the presence or absence of an analyte of interest in the sensing region above the waveguide film.
• Patent Application "Substrate Index Modification for Increasing the Sensitivity of Grating-Coupled Waveguides" are used for the detection of unlabeled analytes in raw samples.
• These grating-couple waveguide include a substrate with an index of refraction of no greater than 1.5 and a waveguide film having a higher index of refraction than the substrate.
• the low-index substrate effectively increases the field strength of the evanescent tail extending from the sensing surface and therefore significantly improves the detection sensitivity of the waveguide.
• Suitable materials for making low-index substrates include, but are not limited to, thermoplastic materials, such as polyvinylidene fluoride, polymethylpentene, blends of polyvinylidene fluoride/polymethylmethacrylate, or fluoropolymers (e.g., fluoroacrylate).
• thermoplastic materials such as polyvinylidene fluoride, polymethylpentene, blends of polyvinylidene fluoride/polymethylmethacrylate, or fluoropolymers (e.g., fluoroacrylate).
• Materials having a refractive index of greater than 1.5 can also be used to prepare the substrate of a grating-coupled waveguide employed in the present invention.
• glass SiO 2 , quartz, polycarbonate (PC), poly(methyl methacrylate) (PMMA), polyimide (PI), polystyrene (PS), polyethylene (PE), polyethylene terephthalate (PET), polyurethane (PU), or other materials can be used to prepare the substrate of a grating-coupled waveguide.
• an array of grating-coupled waveguides (such as in a multi-cell format) is used to detect unlabeled analytes in raw samples.
• Many methods are available for making grating-coupled waveguides in a multi-well format. See, for example, U.S. Patent Application "Substrate Index Modification for Increasing the Sensitivity of Grating-Coupled Waveguides" (Attorney Docket No. SP03-081 (WJT003-0036)).
• a grating-coupled waveguide is incorporated into a well of a microplate by first preparing diffraction grates in a low-index ultraviolet- curable material and then transferring the low-index material into the well, followed by exposing the well to ultraviolet light to form a low-index substrate.
• the low-index substrate can be subsequently coated with a waveguide film.
• SPR surface plasmon resonance
• SPW surface plasmon wave
• the change in the index of refraction at the surface alters the angle at which the resonance occurs.
• the surface can be pre-coated with an immobilized layer of capture molecules that have strong affinities for the analyte of interest. These capture molecules cause the analyte of interest to bind to the surface, thereby modifying the index of refraction at the surface and producing a detectable shift in the SPR curve or the output light intensity.
• the present invention contemplates detection or evaluation of any type of analytes, such as proteins, lipids, polysaccharides, nucleic acids, or other chemical compounds of interest.
• analytes that are amenable to the present invention include, but are not limited to, antigens (such as bacterial or viral antigens), antibodies (such as those induced in response to infection or allergic reactions), cancer markers, growth factors, kinases, phosphatases, proteases, metabolic enzymes, enzyme co factors, G protein coupled receptors, phospholipases, hormone receptors, G-protein regulators, growth factor receptors, cytokines, trophic factors, signaling effectors, neurotransmitters, ion channels, steroids, hormones, cholesterols, lipoproteins, peptide inhibitors, peptide mimics, therapeutic compounds, illicit drugs, toxins, chelating reagents, mRNA, cDNA, cRNA, genomic sequence fragments, oligonucleotides, expressed sequence tags, cell
• the molecule weight of an analyte of interest can be in any range.
• the analytes being detected have a molecular weight of at least 10 kDa, 20 kDa, 30 kDa, 40 kDa, 50 kDa, 60 kDa, 70 kDa, 80 kDa, 90 kDa, 100 kDa, or more.
• Analytes having a molecular weight of less than 10 kDa can also be evaluated according to the present invention.
• an analyte of interest is a viral or bacterial antigen, or an antibody thereto.
• viral antigens include those derived from human immunodeficiency viruses (e.g., HIV-I and HIV-2), influenza viruses (e.g., influenza A, B and C viruses), coronaviruses (e.g., human respiratory coronavirus), hepatitis viruses (e.g., hepatitis viruses A to G), or herpesviruses (e.g., HSV 1-9).
• Non-limiting examples of bacterial antigens include those derived from Bacillus (e.g., Bacillus anthracis or Bacillus cereus), Escherichia (e.g., Escherichia coli), Haemophilus (e.g., Haemophilus influenza or Haemophilus parainfluenzae), Listeria (e.g., Listeria monocytogenes), Neisseria (e.g., Neisseria gonorrhoeae or Neisseria meninigitidis), Nocardia (e.g., Nocardia asteroides), Salmonella (e.g., Salmonella typhi or Salmonella typhimurium), Staphylococcus (e.g., Staphylococcus aureus, Staphylococcus saprophyticus or Staphylococcus epidermis), or Streptococcus (e.g., Streptococcus pyogenes or Streptococc
• a viral or bacterial antigen can be, for example, a protein, a lipid, a polysaccharide, or a nucleic acid.
• an analyte of interest is a cancer marker. Many genes are over-expressed in cancer cells. The expression products of these genes can therefore be used as biomarkers for the diagnosis of the corresponding cancers.
• cancer markers include, but are not limited to, CA 125 (ovarian cancer), CA 15-3 and 27-29 (breast cancer), CA 19-9 (pancreas, colon, stomach cancer), carcinoembryonic antigen (ovarian, lung, breast, pancreas, and gastrointestinal tract cancers), alpha-fetoprotein (liver and testicular cancer), beta HCG (testicular cancer), calcitonin or thyroglobulin (thyroid cancer), and PSA (prostate cancer).
• an analyte of interest is a component of a signal transduction pathway, or a binding partner thereof (e.g., inhibitors, stimulators, agonists, or antagonists).
• Non-limiting examples of signal transduction pathways include apoptosis pathways (such as caspase cascade, the p53 signaling pathway, ATM/p53 signaling pathway, or Fas signaling pathway), pathways involving cytokines, growth factors or hormones (such as EGF receptor signal transduction pathway, TNF signaling pathway, insulin pathway, or glucocorticoid receptor signaling), the JAK/STAT signaling pathway, STAT3 signaling pathway, PPAR signaling pathway, T cell receptor signaling, B cell receptor signaling, signaling by inositol phospholipids, ubiquitin-proteasome pathway, Akt signaling, mitogen-activated protein kinase cascades, oxidative stress pathway, lipid-mediated cell signaling, and noradrenergic, dopaminergic or serotonergic pathways.
• apoptosis pathways such as caspase cascade, the p53 signaling pathway, ATM/p53 signaling pathway, or Fas signaling pathway
• a raw sample refers to a sample which has not been subject to substantial purification.
• samples include, but are not limited to, blood, serum, saliva, sputum, tears, sweat, semen, urine, feces, cerebrospinal fluid, interstitial fluid, cellular extracts, tissue extracts, or other secreted, excremental or biologically-derived fluids or samples.
• Microbial samples, food/beverage samples, pharmaceutical samples, clinical samples, soil samples, or other naturally-occurring or artificially-produced samples that have complex compositions can also be analyzed according to the present invention.
• analytes in partially purified samples can be detected according to the present invention, hi many cases, the amount of the analyte being investigated in a raw sample is insignificant as compared to other organic components in the sample (e.g., by weight percentage or mole percentage).
• the analyte being investigated is a protein (or a nucleic acid) which constitutes less than 1%, 0.5%, 0.1%, or 0.01% by weight of the total protein content (or nucleic acid content) of the sample.
• the raw or partially purified sample comprises a significant amount of other proteins, nucleic acids, polysaccharides or lipids, which prevent the detection of the analyte of interest by conventional gel electrophoresis or chromatography (e.g., SDS-PAGE for protein, agarose gels for DNA/RNA, and thin layer chromatography for lipid or polysaccharide).
• gel electrophoresis or chromatography e.g., SDS-PAGE for protein, agarose gels for DNA/RNA, and thin layer chromatography for lipid or polysaccharide.
• the raw sample is a lysate or supernatant of cultured cells
• the analyte being investigated is a recombinant protein expressed by the cultured cells.
• Host cells suitable for this purpose include eukaryotic cells (e.g., mammalian cells, insect cells or yeast) or prokaryotic cells (e.g., bacteria).
• eukaryotic cells e.g., mammalian cells, insect cells or yeast
• prokaryotic cells e.g., bacteria
• suitable eukaryotic host cells include Chinese hamster ovary cells (CHO), HeLa cells, COS cells, 293 cells, or CV-I cells.
• suitable prokaryotic host cells include E. coli (e.g., HBlOl, MC1O61) or B. subtilis.
• the analyte being investigated is expressed as a cytoplasmic or membrane protein in the host cells.
• the lysate of the host cells is directly applied to an evanescent field sensing surface to detect interactions between the analyte and the capture molecules immobilized on the surface.
• the analyte being investigated is expressed as a secreted protein, and the supernatant of the host cells is applied to the sensing surface to detect interactions between the secreted analyte and the immobilized capture molecules.
• capture molecules can be immobilized to an evanescent field sensing surface.
• capture molecules include antibodies, antibody mimics, high affinity binders, antigens, peptides, proteins, lipids, polysaccharides, oligonucleotides, nucleic acids (e.g., cDNA, cRNA, mRNA), protein- binding ligands, receptors, small molecules, chemical compounds, cell fragments, cellular substructures, synapses, cell organelles, cancer cells, tissue samples, viruses, bacteria, or other microbes.
• antibodies antibody mimics, high affinity binders, antigens, peptides, proteins, lipids, polysaccharides, oligonucleotides, nucleic acids (e.g., cDNA, cRNA, mRNA), protein- binding ligands, receptors, small molecules, chemical compounds, cell fragments, cellular substructures, synapses, cell organelles, cancer cells, tissue samples, viruses, bacteria, or other microbe
• Antibodies suitable for the present invention include, but are not limited to, polyclonal antibodies, monoclonal antibodies, chimeric antibodies, single chain antibodies, synthetic antibodies, Fab fragments, or fragments produced by Fab expression libraries. Methods for preparing antibodies that are specific to an analyte of interest are well known in the art. In many embodiments, the binding affinity of an immobilized capture molecule to the respective analyte is at least 10 4 M "1 , 10 5 M- 1 , 10 6 M "1 , 10 7 M- 1 , 10 8 M "1 , or stronger.
• capture molecules are attached to the sensing surface through an adhesion promoting layer.
• adhesion promoting layer There are several ways in which this layer can be formed. One way is to silanize the sensing surface to form a layer of silane molecules and another way is to use a self-assembled monolayer (SAM).
• SAM self-assembled monolayer
• the sensing surface is silanized with compounds such as
• Proteins e.g., antibodies
• Nucleic acids or other capture molecules can be modified with amino groups, permitting immobilization of these molecules to a silanized surface.
• the sensing surface is coated with avidin, and the capture molecules are conjugated with a biotin moiety.
• the high-affinity binding between biotin and avidin allows stable attachment of the capture molecules to the sensing surface.
• An adhesion promoting layer can be further chemically modified to alter the surface properties.
• a silanized surface can be reacted with functionalized saturated or unsaturated organic/hetero-organic/inorganic molecules or derivatives to manipulate hydrophobic/hydrophilic balance of the surface.
• ionic or potentially ionic compounds can be used to create positive or negative charges at the surface.
• 3-amino-l-propanol is used to modify the characteristics of a silanized surface.
• the nitrogen (amine group) introduced at the surface is quaternized by protons and, therefore, provides positive charges for interactions with negatively charged molecules, such as DNA, RNA or other types of nucleic acid molecules.
• polyethyleneglycol (PEG) or derivatives thereof are used to render the sensing surface hydrophilic, which can prevent nonspecific absorption of proteins to the surface.
• Reactive or photoreactive groups can also be attached to an evanescent field sensing surface. These groups can serve as anchor groups for stable coupling of capture molecules to the surface, hi one example, a silanized sensing surface is coated with PEG derivatized with ethylenediamine groups. The ethylenediamine groups react with the thiol groups in oxidized proteins (e.g., antibodies), allowing covalent coupling of the proteins to the silanized surface.
• oxidized proteins e.g., antibodies
• a SAM can be obtained, for example, by treating the sensing surface with amphiphilic alkylphosphates (e.g. stearyl phosphate).
• amphiphilic alkylphosphates e.g. stearyl phosphate
• the phosphate headgroup reacts with the hydroxy groups at the surface and leads to the formation of an ordered monolayer of the amphiphilic alkylphoshates.
• the hydrophophic alkyl chains render the surface hydrophobic and thus enable the physisorption of antibodies or other proteins.
• a SAM can also be used for immobilization of other capture molecules, e.g., DNA, RNA or PNA. In such a case, amphiphilic phosphates, or phosphates modified with amine or epoxy groups, can be used.
• An adhesion promoting layer can also include multiple layers in order to produce desired surface characteristics, e.g. desired hydrophobicity, contact angle or charge density.
• desired surface characteristics e.g. desired hydrophobicity, contact angle or charge density.
• chemical linker molecules or photochemical linker molecules can also be considered as an intermediate adhesion promoting layer. This controlled combination of layers or molecules with different functionalities can create a supramolecular structure which provides a functionality that differs from that of individual molecules.
• adhesion promotion can be achieved by deposition of microporous layers or gels on the evanescent field sensing surfaces.
• the use of microporous layers or gels can enhance the surface attachment of the capture molecules. It can also improve the detection sensitivity for the analytes of interest.
• Materials suitable for making microporous layers include, but are not limited to, polymers, glass, quartz, ceramic, or fused silica.
• the concentration of the capture molecules that are immobilized to a sensing surface can be in any desired range, such as from about 1 to about 10 molecule/cm 2 , from about 10 to about 10 2 molecule/cm 2 , from about 10 2 to about 10 3 molecule/cm 2 , from about 10 3 to about 10 4 molecule/cm 2 , from about 10 4 to about 10 5 molecule/cm 2 , from about 10 5 to about 10 6 molecule/cm 2 , from about 10 6 to about 10 7 molecule/cm 2 , or more.
• the capture molecules can be randomly distributed in the sensing surface, or organized in a predefined pattern (such as a regularly spaced array). Each sensing surface may include only one type of capture molecules. It can also include two or more different types of capture molecules.
• the present invention features the use of evanescent field sensing to detect unlabeled analytes in raw or partially purified samples.
• a raw or partially purified sample can be directly applied to an evanescent field sensing surface.
• the interaction between an analyte in the sample and the immobilized capture molecules alters the refractive index at the surface, which in turn produces a shift in the resonant wavelength or resonant angle.
• These resonant conditions can be interrogated by observing the reflected light in order to determine the corresponding refractive index changes.
• Many methods are available for this purpose. For instance, where a grating- coupled waveguide is used, the refractive index changes can be monitored by either spectral interrogation or angular interrogation.
• spectral interrogation a nominally collimated, broadband light beam is sent into the grating-coupled waveguide and the reflected light is collected and monitored with a spectrometer. By observing the spectral location of the resonant wavelength (peak), one can monitor binding or refractive index changes on or near the evanescent field sensing surface.
• angular interrogation a nominally single wavelength is focused to create a range of illumination angles and directed into the grating-coupled waveguide. The reflected light can be monitored with a CCD camera or other optical detectors. By monitoring the position of the resonant angle reflected by the grating-coupled waveguide, one can also monitor binding or refractive index changes on or near the evanescent field sensing surface.
• the evanescent field sensing allows detection of an unlabeled, unpurified analyte at a concentration of less than 10 "7 M. In certain instances, the evanescent field sensing enables detection of an unlabeled, unpurified analyte at a concentration of less than 10 "8 M, such as less than 10 ⁇ 9 M, 10 "9 M, 10 "10 M, 10 "1 1 M, or 10 "12 M.
• the desired signal for an analyte of interest can be enhanced by removing non-specific signals. This can be achieved by disrupting or reducing weak or non-specific interactions with the sensing surface. Any method known in the art can be used for this purpose, such as by adding detergents, salts, or other additives.
• the sensing surface can also be pre-treated to block non-specific binding sites.
• control samples can be used. The refractive index changes observed in these control samples can be used as the baseline changes and subtracted from the refractive index changes observed in the sample of interest, thereby eliminating or reducing the contributions from non-specific bindings.
• Evanescent filed sensing with raw or partially purified samples can be used in a wide array of applications.
• diagnostics e.g., detection of pathogenic agents, or antibodies thereto, in blood or other bodily fluids
• bioterror detection or prevention e.g., detection of anthrax or smallpox in food or environmental samples
• cancer screening e.g., detection of cancer markers in tissue samples
• molecular interaction e.g., detection of protein-protein, protein-nucleic acid, protein-lipid, protein-carbohydrate, protein-small molecule, nucleic acid-nucleic acid, nucleic acid-small molecule, or lipid-small molecule interactions
• high throughput screening e.g., identification of modulators for kinases, phosphatases, ion channels, G protein coupled receptors, proteases or other drug targets
• toxicoproteomics gene expression, analysis of splicing variants, analysis of single nucleotide polymorphism, or determination of
• the detection of an unpurified, unlabelled analyte can be either qualitative or quantitative.
• samples comprising known concentrations of an analyte of interest can be used as references to determine the concentration-dependent refractive index changes at the sensing surface.
• concentration of the analyte of interest in a test sample can then be determined by comparing to the reference samples.
• a label-independent detection (LID) system developed by Corning Inc. was used to evaluate interactions between unlabeled streptavidin and immobilized biotin.
• This LID system is comprised of a multi-well optical reader and a disposable microplate (e.g., a 96- or 384-well microplate). Each well of the microplate contains a grating-coupled waveguide for evanescent field sensing.
• the sensing surface has a surface chemistry layer allowing for attachment of molecules that contain primary amine groups (e.g., biotin-amine). As streptavidin or other analytes of interest bind to the sensing surface, the refractive index at the surface is changed.
• An optical mode propagates and senses the refractive index changes close to the sensing surface. Only light that is "resonant” is strongly reflected, and the exact wavelength of the resonance is a sensitive function of the refractive index at the surface of the sensor.
• a baseline read of the microplate is first established. Addition of a binding partner results in a change in refractive index at the sensing surface, which is indicated as picometer (pm) shift from baseline. Each microplate is read on the optical reader before, during, and after the addition of the binding partner. Resonant wavelength shift (“Response (pm)”) is plotted as a function of time.
• Cell lysate was prepared by diluting a 2 mg/ml stock to 100 ⁇ g/ml final concentration.
• a Corning 96-well clear polystyrene non-treated flat bottom plate (Corning catalog # 3370) was used for source plate preparation.
• each well of the source plate contained extra solution.
• a solution of IX phosphate buffered saline (PBS; 1 mM KH 2 PO4, 10 mM Na 2 HPO4, 137 mM NaCl, and 2.7 mM KCl) was used as a first addition step for baseline measure.
• the source plate was set up as follows: PBS was added to wells A-H on columns 1 and 2 on the source plate ( Figure 1). Cell lysate containing streptavidin (STR + lys) was added to wells A, B, and C in columns 7 and 8 of the source plate. Lysate alone (lys) was added to wells C, D and G in columns 7 and 8. Streptavidin alone (STR) was added to wells E and H in columns 7 and 8.
• Biotin-amine was prepared using a solution of 10 ⁇ M (3.7 ⁇ g/ml) biotin-amine (Pierce catalog # 21346) in 150 mM borate buffer (pH 9.2).
• a solution of 200 mM ethanolamine (EA) in 150 mM borate buffer (pH 9.2) was also prepared.
• Immobilization was performed with addition of 75 ⁇ l biotin-amine solution (“BIOTIN”) or 75 ⁇ l ethanolamine solution (“EA”) to the corresponding wells, followed by incubation at room temperature for 30 minutes ( Figure 1).
• FIG. 3 depicts a corrected LID response curve indicating the bulk index shift due to the binding between purified streptavidin and immobilized biotin.
• Response curves F-H in Figure 2 were averaged and then subtracted from the average of response curves A-E.
• the resulting curve ( Figure 3) indicates the bulk index shift due to streptavidin binding to biotin (after point A). Ethanolamine in borate buffer (between points B and C) did not appear to bind to the target area, and post wash (after point C) did not disrupt the binding of streptavidin to biotin.
• Figure 4 shows the testing results using unpurified streptavidin and immobilized biotin.
• HeLa whole-cell lysate containing the same concentration of streptavidin as shown in Figure 2 was added to the LID microplate.
• Response curves A-B were replicates of cell lysate with streptavidin being added to immobilized biotin;
• response curves C-D were replicates of cell lysate without streptavidin being added to immobilized biotin (to determine influence of lysate on signal response);
• response E was purified streptavidin being added to immobilized biotin (as positive control);
• response curve F was lysate with streptavidin on dextran (negative control to determine non-specific binding); and
• response curve G was lysate without streptavidin on dextran (another negative control to determine non-specific binding).
• PBS was added to establish a baseline read (before point A in Figure 4).
• Cell lysate samples or controls were added, producing shifts in the bulk index due to interactions with immobilized biotin (between points A and B in Figure 4).
• Ethanolamine in borate buffer (pH 9) was then added (after point B) and removed by washing with PBS buffer (after point C).

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