US20080166747A1 - Biosensor - Google Patents

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US20080166747A1
US20080166747A1 US11/785,591 US78559107A US2008166747A1 US 20080166747 A1 US20080166747 A1 US 20080166747A1 US 78559107 A US78559107 A US 78559107A US 2008166747 A1 US2008166747 A1 US 2008166747A1
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biosensor
ligand
sample
glucose
binding
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Homme W. Hellinga
Loren L. Looger
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Duke University
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    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/001—Enzyme electrodes
    • 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
    • G01N33/536—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase
    • G01N33/542—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
    • 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
    • G01N33/566—Immunoassay; Biospecific binding assay; Materials therefor using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/195—Assays involving biological materials from specific organisms or of a specific nature from bacteria

Definitions

  • the present invention relates to biosensors and to methods of making and using same.
  • Biosensors are analytical tools that can be used to measure the presence of a single molecular species in a complex mixture by combining the extraordinary molecular recognition properties of biological macromolecules with signal transduction mechanisms that couple ligand binding to readily detectable physical changes (Hall, Biosenisors , Prentice-Hall, Englewood Cliffs, N.J.; Scheller et al., Curr. Op. Biotech. 12:35-40, 2001).
  • a biosensor is reagentless and, in contrast to enzyme-based assays or competitive immunoassays, does not change composition as a consequence of making the measurement (Hellinga & Marvin, Trends Biotech. 16:183-189, 1998).
  • biosensors combine a naturally occurring macromolecule such as an enzyme or an antibody, with the identification of a suitable physical signal particular to the molecule in question, and the construction of a detector specific to that system (Meadows, Adv. Drug Deliv. Rev. 21:177-189, 1996). Recently, molecular engineering techniques have been explored to develop macromolecules that combine a wide range of binding specificities and affinities with a common signal transduction mechanism, to construct a generic detection system for many different analytes (Hellinga & Marvin, Trends Biotech. 16:183-189, 1998).
  • Escherichia coli periplasmic binding proteins are members of a protein superfamily (bacterial periplasmic binding proteins, bPBPs) (Tam & Saier, Microbiol. Rev. 57:320-346, 1993) that has been shown to be well suited for the engineering of biosensors (U.S. Pat. No. 6,277,627). These proteins comprise two domains linked by a hinge region (Quiocho & Ledvina, Molec. Microbiol. 20:17-25, 1996). The ligand-binding site is located at the interface between the two domains.
  • the proteins typically adopt two conformations: a ligand-free open form, and a ligand-bound closed form, which interconvert via a hinge-bending mechanism upon ligand binding.
  • This global, ligand-mediated conformational change has been exploited to couple ligand binding to changes in fluorescence intensity by positioning single, environmentally sensitive fluorophores in locations that undergo local conformational changes in concert with the global change (Brune et al., Biochemistry 33:8262-8271, 1994; Gilardi et al., Prot. Eng. 10:479-486, 1997; Gilardi et al., Anal. Chem. 66:3840-3847, 1994; Marvin et al., Proc. Natl. Acad. Sci.
  • Conformational coupling mechanisms can also be devised to alter the flow of current between the surface of an electrode derivatized with the engineered bPBP containing a covalently attached redox cofactor (Benson et al., Science 293: 1641-1644, 2001).
  • the present invention provides a method of utilizing bPBPs to generate biosensors for a variety of chemical classes including sugars, amino acids, dipeptides, cations, and anions. These biosensors have widespread utility including in clinical, industrial, and environmental settings.
  • the present invention relates to biosensors, making them from mutant or wildtype members of the bacterial periplasmic binding protein (bPBP) superfamily, and using them to assay for (i.e., detect and/or quantitate) ligand.
  • the tertiary structure of bPBPs is comprised of two domains linked by a hinge region with a ligand-binding pocket located at an interface between the two domains. They typically adopt two conformations: a ligand-free open form and a ligand-bound closed form, which interconvert via a hinge-bending mechanism which depends on whether ligand is bound or not at the site.
  • Biosensors are made by covalently or non-covalently attaching at least one reporter group to one or more specific positions of a bPBP. Upon binding of ligand to the biosensor, there is a change in the signal transduced by the reporter group which can be analyzed by assessing any of its observable properties (e.g., optical or electrochemical properties). Biosensors are classified according to the relationship between the attachment site of the reporter group and the binding site(s) of the ligand (i.e., allosteric, endosteric, or peristeric) or distance between those sites (i.e., distal or proximal).
  • the event of ligand binding to biosensor changes the local environment of the position-specific attached reporter group.
  • the signal of the reporter group may be generated by one or more fluorophores and/or redox cofactors.
  • the biosensor may be operated under physiological conditions without additional reagents.
  • FIG. 1 shows the 3-D structures of eleven bPBPs indicating locations of allosteric, endosteric, and peristeric sites used. Each protein is shown in the closed form, with bound ligand indicated by ball-and-stick structures. The two domains of each bPBP are oriented vertically with the first (containing the N-terminus) above the second (containing the C-terminus). A hinge segment connects the domains. The structure of histidine BP is used to represent the as yet unsolved structure of glutamate/aspartate BP.
  • Residues mutated to cysteine are indicated by differently shaded spheres, and differentiated as allosteric (heavy shading), endosteric (medium shading, in GBP only), or peristeric (light shading). Structures are grouped by cluster as defined by Tam & Saier (Microbiol. Rev. 57:320-346, 1993) according to sequence-based relationships.
  • Cluster 2 arabinose BP (ABP), glucose BP (GBP), and ribose BP (RBP).
  • Cluster 5 dipeptide BP (DPP).
  • Cluster 3 glutamine BP (QBP), histidine BP (HBP), and glutamate/aspartate BP (EBP).
  • Cluster 6 phosphate BP (PBP) and sulfate BP (SBP).
  • Cluster 1 maltose BP (MBP) and Fe(III) BP (FeBP).
  • MBP maltose BP
  • FeBP Fe(III) BP
  • FIG. 2 shows alignment of sequences of E. coli YBEJ (putative glutamate/aspartate BP), glutamine BP, and histidine BP using clustalW (Thompson et al., Nucl. Acids Res. 22:4673-4680, 1994). Numbering begins from the putative initiation codon of the open reading frame for YBEJ, including its leader sequence. The underlined methionine is the initiation codon for expression of YBEJ used in the study. Residues in each protein that were mutated to cysteine for fluorophore conjugation are in bold font. The letters “a” and “p” beneath these residues indicate their classification as allosteric or peristeric, respectively.
  • FIG. 3 shows structural formulae of thiol-reactive fluorophores. Approximate wavelengths of maximal fluorescence excitation and emission, respectively, of the protein-bound fluorophores are (in nm): pyrene (340, 390); acrylodan (390, 500); fluorescein (485, 520); NBD (490, 540); NBDE (490, 530); JPW4039 (485, 590); JPW4042 (470, 640); and JPW4045 (470, 640).
  • FIGS. 4A and 4B show a definition of fluorimetric parameters.
  • FIG. 4A shows parameters ⁇ std , I 1 and I 2 used to determine the standard intensity change ⁇ I std .
  • FIG. 4B shows parameters A 1 , A 2 , 0 A, and ⁇ A used to determine ⁇ R. Each of the areas ⁇ A encompasses the respective area 0 A.
  • FIGS. 5A and 5B show fluorimetric titration of glucose BP and glutamate/aspartate BP conjugates.
  • FIG. 5A shows titration of glucose BP W183C-acrylodan with glucose.
  • FIG. 5B Titration of glutamate/aspartate BP T129C-NBD with amino acids. Data points: ⁇ glutamic acid; + aspartic acid; ⁇ asparagine; x glutamine.
  • the lines shown are the best fit binding isotherms.
  • FIGS. 6A-6C shows occurrence of fluorimetric parameters in the set of 320 fluorescent conjugates.
  • FIG. 6A shows distribution of the shift in wavelength of maximum fluorescent intensity ( max ⁇ saturated ⁇ max ⁇ apo ).
  • FIG. 6B shows distribution of the intensity change parameter ⁇ I std .
  • FIG. 6C shows distribution of the ratiometric change parameter ⁇ R max . For each parameter, the upper bound of each interval is indicated.
  • FIG. 7 shows occurrence of changes in ligand affinity among the three classes of fluorophore attachment site.
  • endosteric sites filled bars; peristeric sites, hatched bars; allosteric sites, open bars.
  • wt K d is that of the C64A mutant, in which all conjugates were made.
  • Data for dipeptide BP and Fe(III) BP are not included.
  • the K d for Gly-Leu dipeptide in the wild-type has not been reported.
  • Fe(III) BP the K d of the unconjugated mutant E57D was not determined.
  • the upper bound is indicated.
  • the interval labeled “0” contains values of log( mut K d / wt K d )> ⁇ 1 and ⁇ 0.
  • FIGS. 8A and 8B show ratiometric titration of bPBP fluorophore conjugates using different pairs of emission wavelength bands.
  • FIG. 8A shows glucose BP-W183C conjugated to acrylodan, titrated with glucose at the following ratios of fluorescence emission (wavelengths in nm): ⁇ , F 450-459 /F 550-559 ( app K d ⁇ 5.0 mM); ⁇ , F 450-459 /F 486-495 ( app K d ⁇ 10.4 mM); ⁇ , F 472-481 /F 450-459 ( app K d ⁇ 17.4 mM). Lines show fit to equation 4.
  • FIG. 8B shows ribose BP-T135C conjugated to acrylodan, titrated with ribose at the following ratios of fluorescence emission (wavelengths in nm): ⁇ , F 501-510 /F 450-459 ( app K d ⁇ 41 ⁇ M); ⁇ , F 450-459 /F 501-510 ( app K d ⁇ 254 ⁇ M); ⁇ , F 450-459 /F 547-556 ( app K d ⁇ 461 ⁇ M).
  • the present invention relates to biosensors constructed using engineered bPBPs, for example, E. coli bPBPs.
  • conjugates are constructed that can be used to monitor binding of ligands to bPBPs.
  • Conjugates can be produced by introducing mutations into a bPBP at one or more specific positions in the protein structure where covalently attached reporter groups (e.g., fluorophores or redox cofactors) respond to a conformational change of the bPBP which occurs upon ligand binding.
  • reporter groups e.g., fluorophores or redox cofactors
  • Other methods for covalently or non-covalently attaching at least one reporter group to one or more amino acid residue positions in the primary amino acid sequence of a mutant or wildtype bPBP include: addition or substitution of any activatable crosslinkers, use of designer or non-natural tRNAs, introduction of coordination sites, etc.
  • the ligand-binding pocket may be engineered to bind ligands which are not bound by the wild-type bPBP.
  • the ligand-binding site is located at the interface between the bPBP's two domains. Mutating amino acid residues at that interface which are near (i.e., in or around) the binding site of wild-type bPBP may generate new contacts with ligand (e.g., Zn ++ for MBP) and destroy or alter binding with cognate ligand (e.g., maltose for MBP). This can be used to change the specificity of the ligand-binding pocket.
  • ligand e.g., Zn ++ for MBP
  • cognate ligand e.g., maltose for MBP
  • maltose binding protein has been mutated to specifically bind to noncognate ligand: e.g., metal Zn ++ ion, trinitrotoluene, L-lactate, and serotonin (Marvin & Hellinga, Proc. Natl. Acad. Sci. USA 98:4955-4960, 2001; Looger et al., Nature 423:185-190, 2003; Dwyer et al., Proc. Natl. Acad. Sci. USA 100:11255-11260, 2003).
  • noncognate ligand e.g., metal Zn ++ ion, trinitrotoluene, L-lactate, and serotonin
  • biosensors which bind noncognate ligand can be made by mutating amino acid residues at the interface of the two bPBP domains to generate a new ligand-binding pocket; ligand bound by such biosensors may not bind to wild-type bPBP.
  • mutations in the bPBP may be made to affect function of the biosensor: e.g., mutations may increase or decrease binding affinity or specificity; enhance or reduce signal transduction; add a new functionality by fusion with another carbohydrate, lipid, or protein domain; improve thermostability or thermolability; introduce a catalytic activity; shorten or lengthen operational life; widen or narrow the conditions for operation; or any combination thereof.
  • mutating amino acid residues at positions of the bPBP where a reporting group is not attached e.g., at least one missense mutation which is not a cysteine conjugated through a thiol bond to a fluorophore).
  • the present invention relates to a method of constructing a reagentless fluorescent biosensor.
  • the method comprises identifying sites on a bPBP that undergo a local conformational change in concert with a ligand-mediated hinge-bending motion. Cysteine residues can be introduced at one or more such sites and a fluorophore coupled thereto so that fluorescence intensity of the fluorophore changes upon ligand binding.
  • bPBPs suitable for use in the present method can be selected or designed.
  • the bPBP superfamily is well suited for the redesign of ligand-binding specificities either by computational methods or by other means or both based on the ligand to be detected (see, for example, analytes referenced in Table 1).
  • Sites on the bPBP appropriate for attachment of one or more reporters include allosteric sites, peristeric sites, and endosteric sites (a reporter can also be present at a non-signaling site for use, for example, as a reference).
  • the reporter e.g., fluorophore
  • the reporter can be placed at one or more locations distant from the ligand-binding site (i.e., distal from the ligand-binding pocket) that undergo local conformational changes upon ligand binding.
  • the reporter e.g., fluorophore
  • the reporter can be positioned on the “rim” of the binding site but not such that it directly interacts with the ligand.
  • the reporter e.g., fluorophore
  • the reporter can be present in the binding site so that it interacts directly with the ligand. The latter two examples show attachment proximal to the ligand-binding pocket.
  • Allosteric, peristeric, and endosteric sites can be designed in at least two different ways, as detailed in the Example that follows.
  • a structure-based design approach can be used in which the structures of the open and closed states (for allosteric designs) or the closed state only (for peristeric and endosteric designs) are examined.
  • a sequence-based design approach can be used wherein homology relationships can be exploited to predict the location of cysteine mutations in proteins the three-dimensional structures of which have not been determined, provided that such mutations have been characterized in proteins of known structure.
  • reporters suitable for use in the invention include, but are not limited to, fluorophores and redox cofactors.
  • fluorophores the choice is dependent, at least in part, on the nature of the location within the particular protein. While one fluorophore may function better in a certain location than another, one skilled in the art can readily select the preferred fluorophore for a particular application (see, for example, U.S. Pat. No. 6,277,627).
  • eight different fluorophores are used in the design of fluorescent sensors for:
  • ABSP Arabinose Arabinose binding protein
  • DPP Dipeptides Dipeptide binding protein Glutamate and asparate Glu/Asp binding protein
  • EBP Glutamine Glutamine binding protein
  • QBP Fe(III) Iron binding protein
  • FeBP Iron binding protein
  • HBP Maltose Maltose binding protein
  • MBP Glucose Glucose binding protein
  • GBP Phosphate Phosphate binding protein
  • SBP Sulfate Sulfate binding protein
  • Redox reporters for use in the invention can be a redox-active metal center or a redox-active organic molecule. It can be a natural organic cofactor such as NAD, NADP, FAD or a natural metal center such as Blue Copper, iron-sulfur clusters, or heme, or a synthetic center such as an organometallic compound such as a ruthenium complex, organic ligand such as a quinone, or an engineered metal center introduced into the protein or engineered organic cofactor binding site. Cofactor-binding sites can be engineered using rational design or directed evolution techniques.
  • the redox reporter can be covalently or non-covalently attached to the protein, either by site-specific or adventitious interactions between the cofactor and protein.
  • the redox reporter can be, for example, bound (e.g., covalently) at a position where the amino acid residue is on the protein's surface.
  • the redox reporter can be a metal-containing group (e.g., a transition metal-containing group) that is capable of reversibly or semi-reversibly transferring one or more electrons.
  • a metal-containing group e.g., a transition metal-containing group
  • the reporter group has a redox potential in the potential window below that subject to interference by molecular oxygen and has a functional group suitable for covalent conjugation to the protein (e.g., thiol-reactive functionalities such as maleimides or iodoacetamide for coupling to unique cysteine residues in the protein).
  • the metal of the reporter group should be substitutionally inert in either reduced or oxidized state (i.e., advantageously, exogenous groups do not form adventitious bonds with the reporter group).
  • the reporter group can be capable of undergoing an amperometric or potentiometric change in response to ligand binding.
  • the reporter group is water soluble, is capable of site-specific coupling to a protein (e.g., via a thiol-reactive functional group on the reporter group that reacts with a unique cysteine in the protein), and undergoes a potentiometric response upon ligand binding.
  • Suitable transition metals for use in the invention include, but are not limited to, copper (Cu), cobalt (Co), palladium (Pd), iron (Fe), ruthenium (Ru), rhodium (Rh), osmium (Os), rhenium (Re), platinum (Pt), scandium (Sc), titanium (Ti), vanadium (V), chromium (Cr), manganese (Mn), nickel (Ni), molybdenum (Mo), technetium (Tc), tungsten (W), and iridium (Ir).
  • the first series of transition metals the platinum metals (Ru, Rh, Pd, Os, Ir, and Pt), along with Fe, Re, W, Mo, and Tc, are preferred.
  • Particularly preferred are metals that do not change the number of coordination sites upon a change in oxidation state, including ruthenium, osmium, iron, platinum and palladium, with ruthenium being especially preferred.
  • the reporter group can be present in the biosensor as a covalent conjugate with the protein or it can be a metal center that forms part of the protein matrix (for instance, a redox center such as iron-sulfur clusters, heme, Blue copper, the electrochemical properties of which are sensitive to its local environment).
  • the reporter group can be present as a fusion between the protein and a metal binding domain (for instance, a small redox-active protein such as a cytochrome).
  • the reporter group is covalently conjugated to the protein via a maleimide functional group bound to a cysteine (thiol) on the protein.
  • the reporter group is attached to the protein so that it is located between the protein and the electrode.
  • Engineered proteins of the invention can be produced by site-specifically introducing a reporter group(s) by total synthesis, semi-synthesis, or gene fusions (see, for example, Adams et al., Nature 39:694-697, 1991; Brune et al., Biochemistry 33:8262-8271, 1994; Gilardi et al., Anal. Chem. 66:3840-3847, 1994; Godwin et al., J. Am. Chem. Soc. 118:6514-6515, 1996; Marvin et al., Proc. Natl. Acad. Sci. U.S.A. 94:4366-4371, 1997; Post et al., J. Biol. Chem.
  • Assays for ligand may be performed with the biosensor.
  • a sample is contacted with the biosensor under appropriate assay conditions.
  • Ligand present in the sample if any, may be detected by binding to the biosensor and measuring the signal transduced by ligand-bound biosensor in the assay.
  • binding does not need to be quantitative because a simple determination of whether the ligand is present or absent (within detection limits) needs to be performed. Otherwise, comparison to a series of control samples (e.g., known quantities of ligand) may be required to quantitate the amount or concentration of ligand in the sample. Given the volume of the sample, the amount (i.e., mass) of ligand and the concentration of ligand are interconvertible.
  • a blank sample containing no ligand may be used to determine background signal.
  • Standards may be used to construct a standard curve (e.g., hyperbolic) used to quantitate unknown samples.
  • homogeneous assay formats i.e., those requiring no separation of bound and non-bound ligand
  • separation in a heterogeneous assay format may be required if substances which significantly interfere with signal transduction and/or measurement are present in the sample.
  • Signal transduction preferably does not require the addition of exotic reagents so assays of body fluids may be performed with minimal sample preparation and under physiological conditions. They may even be performed in vivo if the biosensor is adapted to an implantable medical device. Alternatively, a biosensor in contact with the skin may assay interstitial fluid or perspiration. Lavage may be used to sample mucosal tissues.
  • the sample can be obtained in a laboratory setting (e.g., clinic or research institution); from an environmental source (e.g., air, aquafers and other bodies of water, animal or plant products grown on the land, soil); from an industrial source (e.g., the food, biopharmaceutical, chemical, or other manufacturing industries).
  • the analyte to be assayed is identical to the ligand, comprised of multiple copies of the ligand, chemically related to the ligand such that it is identified by a change in signal transduction (e.g., a related chemical structure is more strongly or more weakly bound by the biosensor as compared to its “correct” ligand), or any combination thereof.
  • the change in signal transduction may be correlated to the change in chemical structure such that the non-identical analyte is identified (see below description of integrative assays).
  • ligands which may be detected or quantitated include: amino acids; carbohydrates; bioactive solid and gaseous compounds which are soluble in an aqueous sample; contraband or controlled substances (i.e., substances which are illegal to use or possess, or which are highly regulated); environmental pollutants (e.g., phosphates, sulfates); explosives (e.g., TNT); food contaminants and byproducts (e.g., carcinogens, plant toxins, teratogens); lipids; metal ions (e.g., divalent cations, ferric ions); microbial toxins (e.g., toxic products of viruses, bacteria, or protozoa); neurotransmitters (e.g., serotonin); nucleosides or nucleotides (e.g., NAD, NADP, FAD
  • One or more biosensors may be covalently or noncovalently attached to a solid or porous substrate.
  • the substrate may be flat and planar (e.g., filter membrane, glass slide, semiconductor chip); cylindrical (e.g., optical fiber, plastic rod); spherical (e.g., crosslinked polymer or glass bead); or formed as a container (e.g., cell or cuvette, multiwell plate).
  • the substrate may be fabricated for analysis by instruments which measure the signal transduced by the reporter group (e.g., microscope, photometer, spectrometer).
  • biosensors may be coded by an attached marker (e.g., bar code, radio frequency or RFID, or biopolymer) which can be decoded by a reader (e.g., scanner of light-and-dark patterns, radio receiver, specific binding probe or automated sequencer) or separated by a sorter in accordance with their marker.
  • the code identifying each biosensor may be used in parallel analysis by rapidly assaying a sample for a plurality of ligands. Multiple biosensors with different ligand-binding specificities are used in the same assay to detect and/or quantitate multiple ligands at the same time. Alternatively, attaching different biosensors at particular spots on the substrate may be used to identify their ligand-binding specificities by where the signals are being produced.
  • Signals may be authenticated by repeating the assay, using multiple biosensors with the same specificity for redundant assays, or correlating the results from multiple biosensors with overlapping specificities for integrative assays. In the latter, particular reactivity patterns of the biosensors are correlated with the identity of the analyte bound by them. Analytes that are more closely related in their chemical structure to the ligand will bind more strongly to the cognate biosensor. Signals from a plurality of biosensors with overlapping, known ligand-binding specificities are integrated to deduce the identity of the analyte.
  • the invention relates, in further embodiments, to biosensors constructed using the above-described methods and to the use thereof in analyte detection in, for example, clinical, industrial, and environmental settings. Particular utilities are described in the specific Example that follows. Provided is a description of a number of sites that can be used for optical glucose sensors based on GBP (W183C conjugated to acrylodan has been used successfully in fiber-optic prototypes of a glucose sensor).
  • biosensors constructed in accordance with the present approach may be present in the public domain (e.g., may be disclosed in Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997 or in U.S. Pat. No. 6,277,627), such biosensors are not within the scope of the present invention.
  • PCR was used to amplify wild-type genes for bPBPs from genomic DNA of E. coli strain CSH100 (arabinose, dipeptide, histidine, ribose, sulfate, and glutamate/aspartate BP); strain W1485 (glucose and glutamine BP) and strain RU1012 (phosphate BP), or of H. influenzae strain Rd (Fe(III) BP). Amplified products were cloned into one of the protein expression vectors pAED4 (Doering, “Functional and structural studies of a small f-actin binding domain” in Ph.D.
  • N-terminal oligonucleotide primers were designed to clone only the processed periplasmic form, deleting the signal sequence.
  • Two tandem stop codons (TAATGA) follow the last His codon.
  • Maltose BP mutants were made in and expressed from plasmid pMAL-c2X (New England BioLabs). E. coli strains XL1-BLUE (Stratagene) and DH5 ⁇ (Hanahan, J. Mol. Biol. 166:557-580, 1983) were used for plasmid construction. Single amino acid substitutions were generated by overlapping PCR mutagenesis (Ho et al., Gene 77:51-59, 1989). All clones and mutations were confirmed by nucleotide sequencing.
  • Plasmids were transformed into E. coli strain BL21-DE3, grown in nutrient broth overnight at 37° C., then diluted 100-fold into fresh medium and grown further at 37° C. or 25° C. Expression was induced by the addition of isopropyl ⁇ -D-1-thiogalactopyranoside to 1 mM when the optical density of the culture at 600 nm reached 0.4. After 2 to 4 hours, cells were harvested by centrifugation, resuspended in 20 mM 3-morpholinopropanesulfonic acid (MOPS), 100 mM NaCl, pH 6.9 and stored frozen or lysed immediately for protein purification.
  • MOPS 3-morpholinopropanesulfonic acid
  • Protein was eluted with loading buffer containing 400 mM imidazole, and was collected in fractions and assessed for purity by gel electrophoresis. All preparations were at least 95% pure by this criterion. Protein-containing fractions were dialyzed exhaustively against buffer (20 mM MOPS, 100 mM NaCl, pH 6.9, or 20 mM NaH 2 PO 4 , 100 mM NaCl, pH 6.9) or desalted by gel filtration to remove bound ligand.
  • Fluorophore conjugation to cysteine-substituted bPBPs Fluorophore conjugation to cysteine-substituted bPBPs.
  • Thiol-reactive fluorophores obtained from Molecular Probes (Eugene, Oreg.) were 5-iodoacetamidofluorescein (fluorescein); N-(1-pyrene) iodoacetamide (pyrene); N,N′-dimethyl-N-(iodoacetyl)-N′-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylenediamide (NBD); N-((2-(iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-1,3-diazole (NBDE); and 6-acryloyl-2-dimethylaminonaphthalene (acrylodan).
  • the styryl and naphthyl dyes JPW4039, JPW4042, and JPW4045 ( FIG. 3 ) were synthesized at the University of Connecticut. All fluorophore conjugation steps were typically carried out at room temperature. To protein at a concentration of 100 ⁇ M was added tris-(2-carboxyethyl)phosphine HCl to a five-fold molar excess to reduce intermolecular disulfide bonds. A thiol-reactive fluorophore (20 to 25 mM in acetonitrile or dimethyl sulfoxide) was added in small aliquots to a five-fold molar excess over protein.
  • Conjugation proceeded in the dark at room temperature for 4 hours, or overnight at 4° C. Separation of protein from unreacted fluorophore was achieved by exhaustive dialysis or by size-exclusion chromatography. The efficiency of reporter group attachment was assessed by determination of unreacted thiol with Ellman's reagent (Ellman, Arch. Biochem. Biophys. 74:443-450, 1958) or by measuring the ratio of fluorophore to protein from absorbance spectra of the purified conjugate.
  • Phosphate BP solutions and buffer (20 mM MOPS, 100 mM NaCl, pH 6.9) were depleted of phosphate by addition of 7-methylguanosine to 1 mM and dialyzed against bacterial nucleoside phosphorylase (1 unit ml ⁇ 1 ) (Sigma-Aldrich) partitioned in a separate dialysis tube (Brune et al., Biochem. 33:8262-8271, 1994).
  • Fluorimetry All measurements were conducted with an SLM Aminco-Bowman series 2 fluorimeter, with sample stirring at 25° C. Fluorescence emission spectra were acquired with excitation and emission slit widths of 4 and 8 nm, respectively. Photomultiplier tube potential was maintained between 400 and 800 volts. Protein concentrations were in the range of 50 to 1000 nM.
  • Fluorophore-specific excitation was at the following approximate wavelengths: tryptophan, 290 nm; acrylodan, 390 nm; fluorescein, 485 nm; pyrene, 340 nm; NBD and NBDE, 490 nm; JPW4039, 485 nm; JPW4042, 470 nm; JPW4045, 470 nm.
  • Fe(III) BP has a dissociation constant for Fe(III) on the order of 10 ⁇ 21 M (Adhikari et al., J. Biol. Chem. 270:25142-25149, 1995), hindering accurate fluorescence-based measurements of affinity at nanomolar protein concentrations.
  • Fe(III) citrate (logK ⁇ 10.25) (Martell and Smith, Critical Stability Constants , Plenum Press, New York, 1977) as the ligand in a competition assay.
  • bPBP monosaccharides
  • maltose BP maltose BP
  • three bind amino acids glutamine BP
  • one binds di- and tripeptides dipeptide BP
  • two bind oxyanions phosphate and sulfate BP
  • Most of these bPBPs bind at most two or three related ligands with high affinity (micromolar or better).
  • phosphate BP binds phosphate and arsenate but not other oxyanions (Luecke & Quiocho, Nature 347:402-406, 1990), while glucose BP binds glucose and galactose but not other monosaccharides (Anraku, J. Biol. Chem. 243:3116-3122, 1968).
  • Dipeptide BP is an exception in that it binds a wide variety of di- and tripeptides (Smith et al., Microbiology 145:2891-2901, 1999). Measured ligand dissociation constants in these proteins are typically in the range of 0.1 to 1 ⁇ M.
  • Fe(III) BP where the K d for Fe(III) (aq) is estimated to be 10 ⁇ 21 M in competition assays with Fe(III) chelates (Adhikari et al., J. Biol. Chem. 270:25142-25149, 1995).
  • Coupling between ligand binding and a change in the fluorescent signal of a covalently attached, environmentally sensitive fluorophore can be established if the local environment of the fluorophore changes as a result of formation of the complex and a linked conformational change.
  • Two mechanisms can be distinguished to establish such structural linkage relationships.
  • Direct linkage involves formation of a non-bonded contact between the bound ligand and the conjugated fluorophore.
  • Indirect linkage involves changes in the local protein structure in the immediate vicinity of the attached fluorophore, and relies on ligand-mediated conformational changes such as the hinge-bending motion observed in the bPBPs.
  • Direct linkage relationships are readily designed by replacing a residue known to form a ligand contact with a cysteine to which the fluorophore is attached (“endosteric” attachment site).
  • Indirect linkage relationships can be established in two ways. The most straightforward method relies on visual inspection of the ligand complex structure, and identifying residues that are located in the vicinity of the binding site, but do not interact directly with the ligand, and that are likely to be involved in conformational changes. In the case of the bPBPs, such are residues located at the perimeter of the inter-domain cleft that forms the ligand binding site. The environment of these “peristeric” sites changes significantly upon formation of the closed state. These are examples of positions which are proximal to the ligand-binding pocket.
  • the second approach identifies sites in the protein structure that are located some distance away from the ligand-binding site (i.e., distal to the ligand-binding pocket), and undergo a local conformational change in concert with ligand binding. If the structures of both the open and closed states are known, then such “allosteric” sites can be identified using a computational method that analyzes the conformational change (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). Alternatively, once allosteric sites have been identified in one bPBP, modeling and structural homology arguments can be invoked to identify such sites in other bPBPs in which only one state has been characterized (Marvin & Hellinga, J. Am. Chem. Soc. 120:7-11, 1998). Table 3 summarizes the designs of all three classes of sites in each of the receptors used in this study. The locations of these sites in the eleven bPBPs are shown in FIG. 1 .
  • Ligand-binding can then be determined by direct experimentation, or be inferred either by structural relationships to bPBPs of known function, or by establishing genetic linkage to other genes of known function (Pellegrini et al., Proc. Natl. Acad. Sci. USA 96:4285-4288, 1999). Subsequently sites within the homolog that undergo local conformational change, and to which reporter functions can be attached, must be identified. The selection of sites for attaching reporter functions relies on homology to bPBPs of known structure.
  • a glutamate biosensor was constructed starting from genome sequence data only.
  • the genome of E. coli K12 contains the locus ybeJ encoding a protein identified as a putative bPBP based on amino acid sequence homology with glutamine and histidine BPs (26% and 23% sequence identity; 41% and 43% sequence similarity, respectively) (Blattner et al., Science 277:1453-1474, 1997).
  • the assignment of YBEJ as an amino-acid binding protein was strengthened by the presence of conserved residues found to be associated with binding to the ⁇ -amino and ⁇ -carboxylate groups of the ligand in all bPBP amino-acid binding proteins of known structure identified in E. coli (Table 4).
  • ybeJ is located adjacent to three tandem genes (gltJ, gltK, gltL) postulated to be involved in the glutamate/aspartate transport system (Lum & Wallace, GenBank Accession Number U10981, 1995), suggesting that ybeJ encodes a glutamate/aspartate BP.
  • Putative allosteric, endosteric, and peristeric sites were identified from a structure-based sequence alignment of YBEJ with glutamine BP and histidine BP ( FIG. 2 ).
  • the protein was produced by over-expression of the processed form in the cytoplasm with an initiation methionine placed just before the N-terminus of the processed protein, under the control of a strong inducible promoter in the pAED4 (Doering, “Functional and structural studies of a small f-actin binding domain” in Ph.D. thesis, Massachusetts Institute of Technology, 1992); pET-21a (Studier et al., Meth. Enzymol. 185:60-89, 1990) (Novagen); or pKK223-3 (Blattner et al., Science 277:1453-1474, 1997) plasmids.
  • oligohistidine tag was fused to the carboxy terminus of the cloned receptor to permit facile purification by immobilized metal affinity chromatography (Hochuli et al., J. Chromatogr. A 411:177-184, 1987). In all cases, the receptors expressed well (at least 50 mg of pure protein per liter of fermentation). The molecular masses estimated by gel electrophoresis corresponded to the predicted mass of the expressed reading frame.
  • Cysteine point mutations were introduced by the PCR overlap method (Ho et al., Gene 77:51-59, 1989). Mutant proteins typically expressed as well as the wild type protein. All cysteine substitutions in arabinose BP were constructed in the C64A background to prevent interference from this endogenous cysteine (Miller et al., J. Biol. Chem. 254:7521-7528, 1979). In the case of Fe(III) BP, all mutations were constructed in the E57D background. In the crystal structure of Fe(III) BP, this glutamate is coordinated to the iron (Bruns et al., Nat. Struct. Biol. 4:919-924, 1997).
  • ⁇ I std is defined as the normalized intensity change relative to the average intensity, determined at the wavelength mid-point between the two emission maxima:
  • ⁇ ⁇ ⁇ I std ⁇ 2 ⁇ ( I 1 ⁇ ( ⁇ std ) - I 2 ⁇ ( ⁇ std ) ) I 1 ⁇ ( ⁇ std ) + I 2 ⁇ ( ⁇ std ) ⁇ ( 1 )
  • ⁇ std ( ⁇ max, unbound + ⁇ max, saturated )/2 and I 1 , I 2 are the fluorescence intensities at ⁇ std of each spectrum respectively ( FIG. 4A ).
  • ⁇ R is defined in terms of two emission bands, A 1 ([ ⁇ 1 , ⁇ 2 ]) and A 2 ([ ⁇ 3 , ⁇ 4 ]) ( FIG. 4B ):
  • ⁇ ⁇ ⁇ R ⁇ A 1 0 A 2 0 - A 1 ⁇ A 2 ⁇ ⁇ ( 2 )
  • F fluorescence at ligand concentration [S]
  • K d is the dissociation constant
  • F F , F B are the fluorescence intensities of the ligand-free and ligand-saturated states, respectively.
  • Examples of binding isotherms are shown in FIG. 5 for glucose BP and glutamate/aspartate BP.
  • eq. 3 has to be modified to account for differentially weighted contributions of the two emission bands (Lakowicz, Principles of Fluorescence Spectroscopy, 2 nd Ed. Kluwer Academic Press, New York, p. 698, 1999):
  • R is ratio A 1 /A 2
  • R B ⁇ A 1 / ⁇ A 2
  • R F 0 A 1 / 0 A 1
  • app K d is an apparent dissociation constant
  • K d app A 2 0 A 2 ⁇ ⁇ K d ( 5 )
  • the success of the fluorescent biosensor design strategy was evaluated by determining the probability of encountering an effectively responding fluorescent conjugate, and assessing how the ligand-binding affinities are affected by the fluorophore conjugate.
  • Fe(III) citrate was added to conjugates of other bPBPs and the effect on emission intensity was monitored. It was found that Fe(III) citrate quenched fluorescence in all cases, but only at concentrations much higher than those that led to the effect in Fe(III) BP.
  • the decrease in fluorescence intensity observed in all conjugates of Fe(III) BP is therefore due to a binding-specific process, and may involve relaxation of the excited state via a metal-mediated redox mechanism (Lakowicz, Principles of Fluorescence Spectroscopy, 2 nd Ed. Kluwer Academic Press, New York, p. 698, 1999).
  • the probability of encountering a conjugate that responds with a particular intensity declines with increasing magnitude of ⁇ I std ( FIG. 6B ).
  • the ratiometric response behaves similarly ( FIG. 6C ).
  • the two criteria of greatest utility for optical sensing are ⁇ I std and ⁇ R max .
  • the collection of bPBP conjugates was categorized by class of steric site, fluorophore, and protein scaffold, then, for each category, quantified according to the fraction with ⁇ I std >0.25 and with ⁇ R max >1.25.
  • the results (Tables 6 to 8) give an indication of the overall success rate for finding potentially useful fluorescent biosensor conjugates.
  • the scaffolds having the highest success rates for ⁇ I std and ⁇ R max are arabinose BP, glucose BP, ribose BP, and phosphate BP (Table 6).
  • the former three belong to cluster 2, that includes binding proteins for hexoses and pentoses, while phosphate BP, along with sulfate BP, belongs to cluster 6, that includes binding proteins for inorganic polyanions.
  • the scaffolds having the lowest success rate were dipeptide BP (cluster 5, peptide and nickel binding) and the cluster 3 (polar amino-acid binding) proteins glutamine BP, histidine BP, and Glu/Asp BP.
  • dissociation constants are determined not only by the attachment site, but also by the nature of the attached fluorophore, as illustrated for arabinose BP.
  • Dissociation constants for arabinose of the five cysteine-substitution mutants measured by tryptophan fluorescence, are 5.0 ⁇ M (F23C), 3.2 ⁇ M (L253C), 3.4 ⁇ M (D257C), 7.6 ⁇ M (L298C), and 1.6 ⁇ M (K301C).
  • the cysteine substitutions slightly perturbed affinity for arabinose (K d of C64A mutant ⁇ 2.2 ⁇ M).
  • Bioinformatics makes possible the discovery of new biochemical applications without direct experimentation.
  • individual bacterial genomes may encode scores of bPBPs that bind specific molecules to initiate transport or signal transduction (Blattner et al., Science 277:1453-1474, 1997; Quentin et al., J. Mol. Biol. 287:467-484, 1999). Few of these have been characterized, leaving a vast number untapped as scaffolds for potential biosensors. The feasibility of applying genomic information, combined with structural information from homologous proteins, to construct a biosensor of novel specificity has been demonstrated.
  • a glutamate/aspartate BP had been purified from E. coli (Barash & Halpern, Biochim. Biophys. Acta 386:168-180, 1975; Willis & Furlong, J. Biol. Chem. 250:2574-2580, 1975) and characterized.
  • YBEJ corresponds to this protein.
  • glutamate/aspartate BP was isolated from periplasmic extracts, consistent with ybeJ encoding a protein with a putative periplasmic localization signal sequence.
  • the previously determined molecular mass of glutamate/aspartate BP of 32 kDa (Barash & Halpern, Biochim. Biophys.
  • Glucose BP has the largest number of excellent conjugates. These conjugates all involve fluorophores known to be particularly environmentally sensitive (acrylodan, NBD, pyrene, and the styryl dyes). The incidence of excellent sensors is evenly distributed between allosteric and peristeric sites. All endosteric sites give rise to excellent sensors.
  • the dissociation constant of a conjugate determines the operating concentration range over which the sensor can respond accurately.
  • the operating range guaranteed to give less than a 5% error spans concentrations that fall within five-fold of the K d value (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). If the range required for accurate determination is wider than that span, then a composite biosensor can be constructed using receptors of varying affinities, as has been demonstrated for maltose BP (Marvin et al., Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997). There are three factors affecting the dissociation constant: the nature of the conjugate, the choice of emission bands for a ratiometric sensor (eq. 2), and additional mutations. For particular applications, these three factors can be manipulated to construct an appropriate sensor.
  • Glucose sensor Among the analytes applicable to clinical medicine, glucose is one of the most important, particularly with regard to diagnosing and treating diabetes.
  • the normal range of glucose concentration in adult human serum is 4 to 6 mM (Burtis & Ashwood, Teitz Textbook of Clinical Chemistry, 2 nd Ed. W.B. Saunders Co., Philadelphia, Pa., 1994).
  • the ratiometric parameters the observation window is easily extended from 5.0 to 17.4 mM, allowing all clinically relevant ranges to be observed with one sensor ( FIG. 8A ).
  • the neuroexcitatory amino acid glutamate has normal serum concentrations of 20 to 220 ⁇ M (Burtis & Ashwood, Teitz Textbook of Clinical Chemistry, 2 nd Ed. W.B. Saunders Co., Philadelphia, Pa., 1994).
  • Glutamine is often measured in cerebrospinal fluid (Smith & Forman, Clin. Lab. Sci.
  • This biosensor can be used for such a purpose by mutagenesis to adjust the K d , or by sample dilution.
  • Maltose concentration is relevant to a deficiency in acid maltase, with the normal plasma concentration about 2 ⁇ M (Rozaklis et al., Clin. Chem. 48:131-139, 2002).
  • Fluorescent conjugates of maltose BP mutants having affinities in the 2 ⁇ M range have been described by Marvin et al. (Proc. Natl. Acad. Sci. USA 94:4366-4371, 1997).
  • Ratiometric sensing of ribose using a single ribose BP derivative is illustrated by the T135C-acrylodan conjugate ( FIG. 8B ).
  • emission wavelength bands in the fluorescence ratio eqs. 4, 5
  • the app K d for ribose can be adjusted over a range from 41 to 146 ⁇ M ( FIG. 8B ).
  • High concentrations of phosphate are environmentally deleterious, and could be monitored using phosphate BP conjugates, as noted above for clinical applications.
  • Iron concentration limits primary productivity in certain regions of the oceans (Martin, Iron as a Limiting Factor in Primary Productivity and Biogeochemical Cycles in the Sea . Falkowski & Woodhead, eds., pp.
  • Available ferric ion can be determined using a biosensor derived from Fe(III) BP, such as conjugate E203C-acrylodan (K d ⁇ 138 ⁇ M, ⁇ I std 0.4).
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