MOLECULAR BIOSENSORS CAPABLE OF SIGNAL AMPLIFICATION
20180011087 · 2018-01-11
Assignee
Inventors
Cpc classification
C12Q1/6818
CHEMISTRY; METALLURGY
C12Q2565/519
CHEMISTRY; METALLURGY
C12Q2565/519
CHEMISTRY; METALLURGY
G01N33/542
PHYSICS
C12Q1/6818
CHEMISTRY; METALLURGY
G01N33/54353
PHYSICS
International classification
Abstract
The present invention provides molecular biosensors capable of signal amplification, and methods of using the molecular biosensors to detect the presence of a target molecule.
Claims
1. A molecular biosensor comprising two constructs, the constructs comprising:
R.sup.1—R.sup.2—R.sup.3; and
R.sup.4—R.sup.5—R.sup.6; (I) wherein: R.sup.1 is an epitope-binding agent that binds to a first epitope on a target molecule; R.sup.2 is a flexible linker attaching R.sup.1 to R.sup.3; R.sup.3 is a single stranded nucleotide sequence comprising R.sup.7 and R.sup.8; R.sup.7 is a nucleotide sequence comprising at least one restriction endonuclease recognition site; R.sup.8 is a nucleotide sequence complementary to R.sup.9; R.sup.6 is a single stranded nucleotide sequence comprising R.sup.9; R.sup.9 is a nucleotide sequence complementary to R.sup.8, such that when R.sup.8 and R.sup.9 associate to form an annealed complex in the presence of a polymerase, R.sup.8 and R.sup.9 are extended by the polymerase to form a nucleotide sequence complementary to R.sup.7, forming at least one double-stranded endonuclease recognition site; R.sup.5 is a flexible linker attaching R.sup.4 to R.sup.6; R.sup.4 is an epitope-binding agent that binds to a second epitope on a target molecule.
2. The molecular biosensor of claim 1, wherein the free energy for association of R.sup.3 and R.sup.6 are from about −5.5 kcal/mole to about −8.0 kcal/mole at a temperature from about 21° C. to about 40° C., and a salt concentration from about 1 mM to about 100 mM.
3. The molecular biosensor of claim 1, wherein R.sup.3 and R.sup.6 are independently from about 2 to about 40 nucleotides in length.
4. The molecular biosensor of claim 1, wherein R.sup.3 comprises at least one restriction endonuclease recognition site.
5. The molecular biosensor of claim 1, wherein R.sup.3 comprises at least two restriction endonuclease recognition sites.
6. The molecular biosensor of claim 5, wherein R.sup.3 comprises at least two restriction endonuclease recognition sites distal to each other.
7. The molecular biosensor of claim 5, wherein R.sup.3 comprises at least two restriction endonuclease recognition sites proximal to each other.
8. The molecular biosensor of claim 1, wherein R.sup.6 comprises at least one restriction endonuclease recognition site.
9. The molecular biosensor of claim 1, wherein R.sup.6 comprises at least two restriction endonuclease recognition sites.
10. The molecular biosensor of claim 9, wherein R.sup.6 comprises at least two restriction endonuclease recognition sites distal to each other.
11. The molecular biosensor of claim 9, wherein R.sup.6 comprises at least two restriction endonuclease recognition sites proximal to each other.
12. A method for determining the presence of a target molecule in a sample, the method comprising: a) combining a molecular biosensor of claim 1 with a target molecule; b) extending R.sup.8 and R.sup.9 to form a nucleotide sequence complementary to R.sup.7; c) contacting the molecular biosensor with a restriction endonuclease that recognizes R.sup.7; d) repeating steps b and c to amplify the displaced single-stranded nucleotide sequence. e) measuring the release of the displaced single-stranded nucleotide sequence, wherein an increase in signal indicates the presence of a target molecule.
Description
BRIEF DESCRIPTION OF THE FIGURES
[0005] The application file contains at least one photograph executed in color. Copies of this patent application publication with color photographs will be provided by the Office upon request and payment of the necessary fee.
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DETAILED DESCRIPTION OF THE INVENTION
[0020] The present invention encompasses a molecular biosensor capable of signal amplification. Such a biosensor may be used to detect a target molecule. In one embodiment, the biosensor is comprised of two components, which comprise two epitope-binding agent constructs. Alternatively, in another embodiment, the biosensor is comprised of three components, which comprise two epitope-binding agent constructs and an oligonucleotide construct comprising a restriction enzyme recognition site. Each of these embodiments is discussed in more detail below.
[0021] Advantageously, a molecular biosensor of the invention, irrespective of the embodiment, is capable of signal amplification and provides a rapid homogeneous means to detect a variety of target molecules, including but not limited to proteins, carbohydrates, nucleic acids, macromolecules, and analytes.
I. Two-Component Molecular Biosensors
[0022] One aspect of the invention encompasses a two-component biosensor and methods of use thereof. For a two-component biosensor, detection of a target molecule typically involves target-molecule induced co-association of two epitope-binding agent constructs (R.sup.1—R.sup.2—R.sup.3 and R.sup.4—R.sup.5—R.sup.6) that each recognize distinct epitopes on the target molecule. The epitope-binding agent constructs each comprise a single-stranded nucleotide sequence (R.sup.3 and R.sup.6). Each single-stranded sequence comprises a complementary sequence (R.sup.8 and R.sup.9). Additionally, at least one single-stranded sequence comprises a restriction endonuclease recognition site (R.sup.7). Association of the epitope binding agents (R.sup.1 and R.sup.4) with a target molecule results in annealing of the complementary sequences (R.sup.8 and R.sup.9) of the single-stranded nucleotide sequences, such that when the complementary regions are extended in the presence of a polymerase, a double-stranded endonuclease recognition site is reconstituted. The newly synthesized double-stranded recognition sequence may be nicked by a nicking restriction endonuclease that recognizes the reconstituted restriction enzyme recognition site. A DNA polymerase may then extend a second nucleic acid from the nick, thereby displacing the first nicked strand to form a displaced strand. The second extended strand may then be nicked, repeating the extension and displacement steps such that multiple copies of the displaced strand are produced, thereby amplifying the signal from the biosensor. The displaced strand may then be detected via several different methods.
[0023] The structure of the biosensor and methods of using the biosensor are discussed in more detail below.
(a) Biosensor Structure
[0024] In exemplary embodiments, a two-component molecular biosensor capable of signal amplification comprises two constructs, which together have formula (I):
R.sup.1—R.sup.2—R.sup.3; and
R.sup.4—R.sup.5—R.sup.6; (I)
wherein: [0025] R.sup.1 is an epitope-binding agent that binds to a first epitope on a target molecule; [0026] R.sup.2 is a flexible linker attaching R.sup.1 to R.sup.3; [0027] R.sup.3 is a single stranded nucleotide sequence comprising R.sup.7 and R.sup.8; [0028] R.sup.7 is a nucleotide sequence comprising at least one restriction endonuclease recognition site; [0029] R.sup.8 is a nucleotide sequence complementary to R.sup.9; [0030] R.sup.6 is a single stranded nucleotide sequence comprising R.sup.9; [0031] R.sup.9 is a nucleotide sequence complementary to R.sup.8, such that when R.sup.8 and [0032] R.sup.9 associate to form an annealed complex in the presence of a polymerase, R.sup.8 and R.sup.9 are extended by the polymerase to form a nucleotide sequence complementary to R.sup.7, forming at least one double-stranded endonuclease recognition site; [0033] R.sup.5 is a flexible linker attaching R.sup.4 to R.sup.6; [0034] R.sup.4 is an epitope-binding agent that binds to a second epitope on a target molecule.
[0035] As will be appreciated by those of skill in the art, the choice of epitope binding agents, R.sup.1 and R.sup.4, in molecular biosensors having formula (I) can and will vary depending upon the particular target molecule. By way of example, when the target molecule is a protein, R.sup.1 and R.sup.4 may be an aptamer, or antibody. By way of further example, when R.sup.1 and R.sup.4 are double stranded nucleic acid the target molecule is typically a macromolecule that binds to DNA or a DNA binding protein. In general, suitable choices for R.sup.1 and R.sup.4 will include two agents that each recognize distinct epitopes on the same target molecule. In certain embodiments, however, it is also envisioned that R.sup.1 and R.sup.4 may recognize distinct epitopes on different target molecules. Non-limiting examples of suitable epitope binding agents may include agents selected from the group consisting of an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, modified nucleic acids, nucleic acid mimics (e.g. LNA or PNA), a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, a chemical entity and an ion.
[0036] In one embodiment, R.sup.1 and R.sup.4 are each aptamers having a sequence ranging in length from about 20 to about 110 bases. In another embodiment, R.sup.1 and R.sup.4 are each antibodies or antibody-like binders selected from the group consisting of polyclonal antibodies, ascites, Fab fragments, Fab′ fragments, monoclonal antibodies, humanized antibodies, chimeric antibodies, single chain antibodies, and non-immunoglobulin scaffolds such as Affibodies, Anticalins, designed Ankyrin repeat proteins and others. In an alternative embodiment, R.sup.1 and R.sup.4 are peptides. In an exemplary embodiment, R.sup.1 and R.sup.4 are each monoclonal antibodies. In an additional embodiment, R.sup.1 and R.sup.4 are each double stranded DNA. In a further embodiment, R.sup.1 is a double stranded nucleic acid and R.sup.4 is an aptamer. In an additional embodiment, R.sup.1 is an antibody and R.sup.4 is an aptamer. In another additional embodiment, R.sup.1 is an antibody and R.sup.4 is a double stranded DNA.
[0037] In an additional embodiment for molecular biosensors having formula (I), exemplary linkers, R.sup.2 and R.sup.5, will functionally keep R.sup.3 and R.sup.6 in close proximity such that when R.sup.1 and R.sup.4 each bind to the target molecule, R.sup.8 and R.sup.9 associate in a manner such that a detectable signal is produced. R.sup.2 and R.sup.5 may each be a nucleotide sequence from about 10 to about 100 nucleotides in length. In one embodiment, R.sup.2 and R.sup.5 are from 10 to about 25 nucleotides in length. In another embodiment, R.sup.2 and R.sup.5 are from about 25 to about 50 nucleotides in length. In a further embodiment, R.sup.2 and R.sup.5 are from about 50 to about 75 nucleotides in length. In yet another embodiment, R.sup.2 and R.sup.5 are from about 75 to about 100 nucleotides in length. In each embodiment, the nucleotides comprising the linkers may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment R.sup.2 and R.sup.5 are comprised of DNA bases. In another embodiment, R.sup.2 and R.sup.5 are comprised of RNA bases. In yet another embodiment, R.sup.2 and R.sup.5 are comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2′ position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases may include 2′-fluoro nucleotides, 2′-amino nucleotides, 5′-aminoallyl-2′-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, R.sup.2 and R.sup.5 may be nucleotide mimics. Examples of nucleotide mimics may include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholine oligomers (PMO). Alternatively, R.sup.2 and R.sup.5 may be a bifunctional chemical linker, or a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers may include sulfoSMCC (sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate), and Ic-SPDP (N-succinimidyl-6-(3′-(2-pyridyldithio)-propionamido)-hexanoate). In another embodiment the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers may include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. Additional suitable linkers may include the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, R.sup.2 and R.sup.5 are from 0 to about 500 angstroms in length. In another embodiment, R.sup.2 and R.sup.5 are from about 20 to about 400 angstroms in length. In yet another embodiment, R.sup.2 and R.sup.5 are from about 50 to about 250 angstroms in length.
[0038] In a further embodiment for molecular biosensors having formula (I), R.sup.3 comprises R.sup.7 and R.sup.8, and R.sup.6 comprises R.sup.9. Generally speaking, except for R.sup.8 and R.sup.9, R.sup.3 and R.sup.6 are not complementary. Wand R.sup.9 are nucleotide sequences that are complementary to each other such that they preferably do not associate unless R.sup.1 and R.sup.4 bind to separate epitopes on a target molecule. When R.sup.1 and R.sup.4 bind to separate epitopes of a target molecule, R.sup.8 and R.sup.9 are brought into relative proximity resulting in an increase in their local concentration, which drives the association of R.sup.8 and R.sup.9.
[0039] To ensure that R.sup.8 and R.sup.9 only associate when R.sup.1 and R.sup.4 bind to separate epitopes of a target, R.sup.8 and R.sup.9 generally have a length such that the free energy of association is from about −5 to about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In other embodiments, the free energy of association between R.sup.8 and R.sup.9 is about −5 kcal/mole, about −6 kcal/mole, about −7 kcal/mole, about −8 kcal/mole, about −9 kcal/mole, about −10 kcal/mole, about −11 kcal/mole, or greater than about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In additional embodiments, R.sup.8 and R.sup.9 may range from about 4 to about 20 nucleotides in length. In other embodiments, R.sup.8 and R.sup.9 may be about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or greater than about 10 nucleotides in length.
[0040] In some embodiments, R.sup.3 comprises R.sup.7—R.sup.8, such that R.sup.7 is located 5′ to R.sup.8. In other embodiments, R.sup.3 comprises R.sup.8—R.sup.7, such that R.sup.8 is located 5′ to R.sup.7.
[0041] In an exemplary embodiment, R.sup.8 and R.sup.9 are at the 3′ ends of R.sup.3 and R.sup.6, such that association of R.sup.8 and R.sup.9 forms a complex where the 3′ ends can be extended using R.sup.3 and R.sup.6 as a template to form a double-stranded nucleotide sequence comprising R.sup.7. Polymerases suitable for extending R.sup.8 and R.sup.9 are known in the art. For example, non-limiting examples of nucleotide polymerases suitable for extending nucleic acid sequences of the invention may include Bsu DNA Polymerase, DNA Polymerase I (E. coli), DNA Polymerase I Large (Klenow) Fragment, Klenow Fragment (3″.fwdarw.5′ exo-), phi29 DNA Polymerase, T4 DNA Polymerase, T7 DNA Polymerase (unmodified), or any of the thermophilic polymerases, such as the full length or large fragment of Bst DNA Polymerase, Taq DNA Polymerase, 9° N.sub.m DNA Polymerase, Crimson Taq DNA Polymerase, Deep VentR™ (exo-) DNA Polymerase, Deep VentR™ DNA Polymerase, DyNAzyme™ EXT DNA Polymerase, DyNAzyme™ II Hot Start DNA Polymerase, Hemo KlenTaq™, Phusion® High-Fidelity DNA Polymerase, Sulfolobus DNA Polymerase IV, Therminator™ DNA Polymerase, VentR® DNA Polymerase.
[0042] Generally speaking, for molecular biosensors having formula (I) R.sup.3 comprises at least one restriction endonuclease recognition site. In some embodiments, however, R.sup.3 may comprise more than one restriction endonuclease recognition site. For instance, R.sup.3 may comprise at least two, three, four, or five endonuclease recognition sites. Similarly, R.sup.6 may comprise at least one, two, three, four or five endonuclease recognition sites.
[0043] Typically, a restriction enzyme recognizing a restriction enzyme recognition site cannot cleave or nick a single stranded nucleotide sequence. Association of the epitope binding agents with a target molecule and the subsequent extension of the 3′ ends of R.sup.8 and R.sup.9 in the presence of a polymerase forms a double-stranded endonuclease recognition site that may be cleaved or nicked by a restriction endonuclease. As is commonly known by persons skilled in the art, restriction endonucleases may hydrolyze both strands of the nucleic acid duplex to cleave the nucleic acid duplex, or hydrolyze one of the strands of the nucleic acid duplex, thus producing double-stranded nucleic acid molecules that are “nicked”, rather than cleaved. In preferred embodiments of molecular biosensors having formula (I), R.sup.7 comprises an endonuclease recognition sequence for a nicking restriction enzyme. A nicking restriction endonuclease may hydrolyze the bottom or the top strand of a nucleic acid duplex. By way of non-limiting example, recognition sites for nicking restriction enzymes may include Nt.BstNBI, Nb.BsrD, Nb.BtsI, Nt.AlwI, Nb.BbvCI, Nt.BbvC and Nb.BsmI.
[0044] In each of the foregoing embodiments for molecular biosensors having formula (I), the first nucleic acid construct, R.sup.1—R.sup.2—R.sup.3 and the second nucleic acid construct, R.sup.4—R.sup.5—R.sup.6, may optionally be attached to each other by a linker R.sup.LA to create tight binding bivalent ligands. Typically, the attachment is by covalent bond formation. Alternatively, the attachment may be by non covalent bond formation. In one embodiment, R.sup.LA attaches R.sup.1 of the first nucleic acid construct to R.sup.4 of the second nucleic acid construct to form a molecule comprising:
##STR00001##
[0045] In a further embodiment, R.sup.LA attaches R.sup.2 of the first nucleic acid construct to R5 of the second nucleic acid construct to form a molecule comprising:
##STR00002##
[0046] In yet another embodiment, R.sup.LA attaches R.sup.3 of the first nucleic acid construct to R.sup.7 of the second nucleic acid construct to form a molecule comprising:
##STR00003##
[0047] Generally speaking, R.sup.LA may be a nucleotide sequence from about 10 to about 100 nucleotides in length. The nucleotides comprising R.sup.LA may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment, R.sup.LA is comprised of DNA bases. In another embodiment, R.sup.LA is comprised of RNA bases. In yet another embodiment, R.sup.LA is comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2′ position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases may include 2′-fluoro nucleotides, 2′-amino nucleotides, 5′-aminoallyl-2′-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, R.sup.LA is comprised of nucleotide mimics. Examples of nucleotide mimics may include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholine oligomers (PMO). Alternatively, R.sup.LA may be a bifunctional chemical linker or a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers may include sulfoSMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate), and Ic-SPDP (N-Succinimidyl-6-(3′-(2-PyridylDithio)-Propionamido)-hexanoate). In another embodiment, the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers may include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. An exemplary R.sup.LA is the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, R.sup.LA is from about 1 to about 500 angstroms in length. In another embodiment, R.sup.LA is from about 20 to about 400 angstroms in length. In yet another embodiment, R.sup.LA is from about 50 to about 250 angstroms in length.
(b) Means of Detection
[0048] As discussed above, when R.sup.8 and R.sup.9 are extended in the presence of a polymerase, the newly synthesized double-stranded endonuclease recognition sequence may be nicked by a nicking restriction endonuclease that recognizes the double-stranded restriction enzyme recognition site. A DNA polymerase may then extend a second nucleic acid from the nick, thereby displacing the first nicked strand to form a displaced strand. The second extended strand may then be nicked, repeating the extension and displacement steps such that multiple copies of the displaced strand are produced, thereby amplifying the signal from the biosensor. The displaced strand may then be detected via several different methods. Three such methods are detailed below.
i. Double-Stranded Nucleic Acid Stains
[0049] In some embodiments, a displaced strand may be detected and/or quantitated by contacting a displaced strand with a complementary nucleic acid sequence. The resulting double-stranded nucleotide sequence may be detected using nucleic acid staining methods specific for double-stranded sequences. Non-limiting examples of nucleic acid stains that may be used for detecting double-stranded nucleotide sequences may include ethidium bromide, thiazole orange, propidium iodide, DAPI, Hoechst dyes, acridine orange, 7-AAD, LDS 751, hydroxystilbamidine, and cyanine dyes such as TOTO-1, POPO-1, BOBO-1, YOYO-1, JOJO-1, LOLO-1, POPO-3, YOYO-3, TOTO-3, BOBO-3, PicoGreen, SYBR Gold, SYBR Green I and SYBR Green II.
ii. Type IIS Endonuclease Construct
[0050] In another embodiment, a displaced strand may be detected and/or quantitated by associating with a Type IIS endonuclease nucleic acid construct. The nucleic acid construct may generally comprise two strands, where the first strand comprises R.sup.10—R.sup.12—R.sup.14 and the second strand comprises R.sup.11—R.sup.13. R.sup.14 is complementary to the displaced strand, and when associated with a displaced strand, comprises a Type IIS endonuclease recognition site. R.sup.12 is complementary to R.sup.13, and together, R.sup.12 and R.sup.13 comprise a cleavage site for a Type IIS endonuclease. R.sup.12 and R.sup.13 are of such a length that the two strands (i.e. R.sup.10—R.sup.12—R.sup.14 and R.sup.11—R.sup.13) stay hybridized in the absence of the displaced strand. R.sup.10 and R.sup.11 comprise a detection means, such that when R.sup.12 and R.sup.13 are cleaved by a Type IIS endonuclease, R.sup.10 and R.sup.11 are released from the Type IIS endonuclease construct and produce a detectable signal. Suitable detection means for R.sup.10 and R.sup.11 may comprise fluorescent resonance energy transfer (FRET), lanthamide resonance energy transfer (LRET), fluorescence cross-correlation spectroscopy, fluorescence quenching, fluorescence polarization, flow cytometry, scintillation proximity, luminescence resonance energy transfer, direct quenching, ground-state complex formation, chemiluminescence energy transfer, bioluminescence resonance energy transfer, excimer formation, colorimetric substrates detection, phosphorescence, electrochemical changes, and redox potential changes. (See
iii. Linker Construct
[0051] In some embodiments, a displaced strand may be detected by a linker construct. Usually, a linker construct comprises R.sup.15—R.sup.16—R.sup.17—R.sup.18—R.sup.19—R.sup.20—R.sup.21. R.sup.18 is a nucleotide sequence that is complementary to the displaced strand, and together with the displaced strand, comprises an endonuclease recognition site. R.sup.17 and R.sup.19 are linkers, and may be defined as R.sup.2 and R.sup.5 above. R.sup.16 and R.sup.20 are complementary nucleic acid sequences, and may be defined as R.sup.8 and R.sup.9 above. R.sup.15 and R.sup.21 comprise a detection means, and may be defined as R.sup.10 and R.sup.11 above. (See
[0052] When R.sup.18 binds to a displaced strand, a double-stranded restriction endonuclease recognition site is formed. In the presence of a restriction endonuclease, R.sup.18 and the displaced strand are cleaved at the endonuclease recognition site. This destabilizes the association of R.sup.16 and R.sup.20, resulting in the separation of R.sup.15 and R.sup.21. This separation results in a detectable and quantifiable change in signal intensity.
II. Three-Component Molecular Biosensors
[0053] Another aspect of the invention encompasses a three-component biosensor capable of signal amplification. In a three-component embodiment, analogous to a two-component sensor, detection of a target molecule typically involves target-molecule induced co-association of two epitope-binding agent constructs that each recognize distinct epitopes on the target molecule. Unlike the two-component embodiment, however, the epitope-binding agent constructs each comprise single stranded nucleic acid sequences that are complementary to two distinct regions of the oligonucleotide construct, as opposed to being complementary to each other (as in the two-component sensor). Co-association of the two epitope-binding agent constructs with a target molecule results in hybridization of each single stranded nucleic acid sequence to the oligonucleotide construct. This tripartite construct comprised of the two single stranded nucleic acid sequences and the oligonucleotide construct reconstitutes a restriction endonuclease recognition site. The endonuclease recognition site may be cleaved in the presence of a restriction endonuclease. Such cleavage destabilizes the association of the single stranded nucleic acid sequences and the (now cleaved) oligonucleotide construct, releasing the single stranded nucleic acid sequences. The single stranded nucleic acid sequences may then bind to another oligonucleotide construct, repeating the cleavage cycle and therefore amplifying the biosensor signal. Importantly, the oligonucleotide construct is capable of producing a detectable signal when cleaved.
[0054] In certain embodiments, the three-component molecular biosensor will comprise a solid support. In alternative embodiments, the three-component molecular biosensor will not comprise a solid support. Both of these embodiments are discussed in more detail below. In some embodiments, a three-component molecular biosensor may comprise a plurality of oligonucleotide constructs (e.g. R.sup.7—R.sup.8 or R.sup.7—R.sup.8—R.sup.9).
(a) Three Component Molecular Biosensors Comprising a Solid Support
[0055] In one embodiment, a three-component molecular biosensor will comprise an oligonucleotide construct attached to a solid support. Generally speaking, co-association of the two epitope-binding agent constructs with a target molecule results in hybridization of each single stranded nucleic acid sequence to the oligonucleotide construct, producing a tripartite double-stranded nucleic acid molecule that contains a restriction endonuclease recognition site. In the presence of a restriction endonuclease, the oligonucleotide construct may be cleaved to release a signaling molecule from the solid support. (See, for instance,
[0056] For example, in some embodiments the three-component molecular biosensor comprises at least three constructs, which together have formula (II):
R.sup.1—R.sup.2—R.sup.3;
R.sup.4—R.sup.5—R.sup.6; and
at least one R.sup.7—R.sup.8—R.sup.9; (II)
wherein: [0057] R.sup.1 is an epitope-binding agent that binds to a first epitope on a target molecule; [0058] R.sup.2 is a flexible linker attaching R.sup.1 to R.sup.3; [0059] R.sup.3 and R.sup.6 are a first pair of nucleotide sequences that are complementary to two distinct regions on R.sup.8; [0060] R.sup.5 is a flexible linker attaching R.sup.4 to R.sup.6; [0061] R.sup.4 is an epitope-binding agent that binds to a second epitope on a target molecule; [0062] R.sup.8 is a nucleotide construct comprising a first region that is complementary to R.sup.3 and a second region that is complementary to R.sup.6, such that when R.sup.3 and R.sup.6 associated with R.sup.8, an endonuclease restriction site is reconstituted; [0063] R.sup.7 is a signaling molecule; and [0064] R.sup.9 is a solid support.
[0065] The choice of epitope binding agents, R.sup.1 and R.sup.4, in molecular biosensors having formula (II) can and will vary depending upon the particular target molecule. By way of example, when the target molecule is a protein, R.sup.1 and R.sup.4 may be an aptamer, or antibody. By way of further example, when R.sup.1 and R.sup.4 are double stranded nucleic acid the target molecule is typically a macromolecule that binds to DNA or a DNA binding protein. In general, suitable choices for R.sup.1 and R.sup.4 will include two agents that each recognize distinct epitopes on the same target molecule. In certain embodiments, however, it is also envisioned that R.sup.1 and R.sup.4 may recognize distinct epitopes on different target molecules. Non-limiting examples of suitable epitope binding agents, depending upon the target molecule, may include agents selected from the group consisting of an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, modified nucleic acids, nucleic acid mimics, a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, and an ion. In an exemplary embodiment, R.sup.1 and R.sup.4 are each aptamers having a sequence ranging in length from about 20 to about 110 bases. In another embodiment, R.sup.1 and R.sup.4 are each antibodies selected from the group consisting of polyclonal antibodies, ascites, Fab fragments, Fab′ fragments, monoclonal antibodies, humanized antibodies, chimeric antibodies, and single-chain antibodies. In an alternative embodiment, R.sup.1 and R.sup.4 are peptides. In a preferred embodiment, R.sup.1 and R.sup.4 are each monoclonal antibodies. In an additional embodiment, R.sup.1 and R.sup.4 are each double stranded DNA. In a further embodiment, R.sup.1 is a double stranded nucleic acid and R.sup.4 is all aptamer. In an additional embodiment, R.sup.1 is an antibody and R.sup.4 is an aptamer. In another additional embodiment, R.sup.1 is an antibody and R.sup.4 is a double stranded DNA.
[0066] In an additional embodiment for molecular biosensors having formula (II), exemplary linkers, R.sup.2 and R.sup.5, will functionally keep R.sup.3 and R.sup.6 in appropriate proximity such that when R.sup.1 and R.sup.4 each bind to the target molecule, R.sup.3 and R.sup.6 associate with R.sup.8 producing a detectable signal. R.sup.2 and R.sup.5 may each be a nucleotide sequence from about 10 to about 100 nucleotides in length. In one embodiment, R.sup.2 and R.sup.5 are from about 10 to about 25 nucleotides in length. In another embodiment, R.sup.2 and R.sup.5 are from about 25 to about 50 nucleotides in length. In a further embodiment, R.sup.2 and R.sup.5 are from about 50 to about 75 nucleotides in length. In yet another embodiment, R.sup.2 and R.sup.5 are from about 75 to about 100 nucleotides in length. In each embodiment, the nucleotides comprising the linkers may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment R.sup.2 and R.sup.5 are comprised of DNA bases. In another embodiment, R.sup.2 and R.sup.5 are comprised of RNA bases. In yet another embodiment, R.sup.2 and R.sup.5 are comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2′ position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases may include 2′-fluoro nucleotides, 2′-amino nucleotides, 5′-aminoallyl-2′-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, R.sup.2 and R.sup.5 may be nucleotide mimics. Examples of nucleotide mimics may include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholine oligomers (PMO).
[0067] Alternatively, R.sup.2 and R.sup.5 may be a bifunctional chemical linker or a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers may include sulfoSMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate), and Ic-SPDP (N-Succinimidyl-6-(3′-(2-PyridylDithio)-Propionamido)-hexanoate). In another embodiment the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers may include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. Additional suitable linkers may include the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, R.sup.2 and R.sup.5 are from 0 to about 500 angstroms in length. In another embodiment, R.sup.2 and R.sup.5 are from about 20 to about 400 angstroms in length. In yet another embodiment, R.sup.2 and R.sup.5 are from about 50 to about 250 angstroms in length.
[0068] R.sup.7 of formula (II) is a signaling molecule. Suitable signaling molecules are known in the art. Non-limiting examples may include luminescent molecules, chemiluminescent molecules, fluorochromes, fluorescent quenching agents, colored molecules, radioisotopes, scintillants, massive labels (for detection via mass changes), biotin, avidin, streptavidin, protein A, protein G, antibodies or fragments thereof, Grb2, polyhistidine, Ni.sup.2+, Flag tags, myc tags, heavy metals, enzymes, alkaline phosphatase, peroxidase, luciferase, electron donors/acceptors, acridinium esters, and colorimetric substrates. The skilled artisan would readily recognize other useful labels that are not mentioned above, which may be employed in the operation of the present invention.
[0069] For molecular biosensors having formula (II), R.sup.8 comprises a first region that is complementary to R.sup.6, and a second region that is complementary to R.sup.3. R.sup.8 may be from about 8 to about 100 nucleotides in length. In other embodiments, R.sup.8 is from about 10 to about 15 nucleotides in length, or from about 15 to about 20 nucleotides in length, or from about 20 to about 25 nucleotides in length, or from about 25 to about 30 nucleotides in length, or from about 30 to about 35 nucleotides in length, or from about 35 to about 40 nucleotides in length, or from about 40 to about 45 nucleotides in length, or from about 45 to about 50 nucleotides in length, or from about 50 to about 55 nucleotides in length, or from about 55 to about 60 nucleotides in length, or from about 60 to about 65 nucleotides in length, or from about 65 to about 70 nucleotides in length, or from about 70 to about 75 nucleotides in length, or from about 75 to about 80 nucleotides in length, or from about 80 to about 85 nucleotides in length, or from about 85 to about 90 nucleotides in length, or from about 90 to about 95 nucleotides in length, or greater than about 95 nucleotides in length.
[0070] When R.sup.3 and R.sup.6 associate with R.sup.8, a tripartite double-stranded DNA molecule is formed that contains a restriction endonuclease recognition sequence. In the presence of a restriction endonuclease, R.sup.8 is cleaved, releasing R.sup.7 from the solid support R.sup.9. In an exemplary embodiment, R.sup.3 and R.sup.6 do not form a stable complex with R.sup.8 after R.sup.8 is cleaved, freeing R.sup.3 and R.sup.6 to bind to another R.sup.8 and repeat the cleavage cycle. This amplifies the biosensor signal.
[0071] In an exemplary embodiment, R.sup.8 will comprise formula (III):
R.sup.10—R.sup.11—R.sup.12—R.sup.13 (III)
wherein: [0072] R.sup.10 and R.sup.13 are single-stranded nucleotide sequences not complementary to any of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, or R.sup.6; [0073] R.sup.11 is a nucleotide sequence complementary to R.sup.3; and [0074] R.sup.12 is a nucleotide sequence that is complementary to R.sup.6.
[0075] In some embodiments, R.sup.10 and R.sup.13 may independently be from about 0 to about 20 nucleotides in length. In other embodiments, R.sup.10 and R.sup.13 may independently be from about 2 to about 4 nucleotides in length, or from about 4 to about 6 nucleotides in length, or from about 6 to about 8 nucleotides in length, or from about 8 to about 10 nucleotides in length, or from about 10 to about 12 nucleotides in length, or from about 12 to about 14 nucleotides in length, or from about 14 to about 16 nucleotides in length, or from about 16 to about 18 nucleotides in length, or from about 18 to about 20 nucleotides in length, or greater than about 20 nucleotides in length.
[0076] Generally speaking, R.sup.11 and R.sup.12 have a length such that the free energy of association between R.sup.11 and R.sup.3 and R.sup.12 and R.sup.6 is from about −5 to about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In other embodiments, the free energy of association between R.sup.11 and R.sup.3 and R.sup.12 and R.sup.6 is about −5 kcal/mole, about −6 kcal/mole, about −7 kcal/mole, about −8 kcal/mole, about −9 kcal/mole, about −10 kcal/mole, about −11 kcal/mole, or greater than about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In additional embodiments, R.sup.11 and R.sup.12 may range from about 4 to about 20 nucleotides in length. In other embodiments, R.sup.11 and R.sup.12 may be about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or greater than about 10 nucleotides in length.
[0077] In one embodiment, when R.sup.8 comprises formula (III), the cleavage site of the restriction endonuclease recognition sequence produced by the association of R.sup.3 and R.sup.6 with R.sup.8 is located between R.sup.11 and R.sup.12. In this manner, in the presence of a suitable restriction endonuclease, R.sup.8 will be cleaved between R.sup.11 and R.sup.12, but R.sup.3 and R.sup.6 remain intact. Suitable restriction endonuclease recognition sequences are recognized by restriction enzymes that cleave double stranded nucleic acid, but not single stranded nucleic acid. Such enzymes and the corresponding recognition sites are known in the art. By way of non-limiting example, these enzymes may include AccI, AgeI, BamHI, BglI, BgIII, BsiWI, BstBI, ClaI, CviQI, DdeI, DpnI, DraI, EagI, EcoRI, EcoRV, FseI, FspI, HaelI, HaeII, HhaI, HincII, HinDIII, HpaI, HpaII, KpnI, KspI, MboI, MfeI, NaeI, NarI, NcoI, NdeI, NheI, NotI, PhoI, PstI, PvuI, PvulI, SacI, SacI, SalI, SbfI, SmaI, SpeI, SphI, StuI, TaqI, TliI, TfiI, XbaI, XhoI, XmaI, XmnI, and ZraI.
[0078] In another exemplary embodiment, R.sup.8 will comprise formula (IV):
R.sup.10—R.sup.11—R.sup.12—R.sup.13—R.sup.14—R.sup.15 (IV)
wherein: [0079] R.sup.11, R.sup.12, R.sup.13, and R.sup.14 are single stranded oligonucleotide sequences not complementary to each other or any of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, or R.sup.6; [0080] R.sup.10 and R.sup.15 are double-stranded nucleic acid sequences; [0081] R.sup.12 is a nucleotide sequence complementary to R.sup.3; and [0082] R.sup.13 is a nucleotide sequence that is complementary to R.sup.6.
[0083] R.sup.11 and R.sup.14 may independently be from about 0 to about 20 nucleotides in length. In other embodiments, R.sup.11 and R.sup.14 may independently be from about 2 to about 4 nucleotides in length, or from about 4 to about 6 nucleotides in length, or from about 6 to about 8 nucleotides in length, or from about 8 to about 10 nucleotides in length, or from about 10 to about 12 nucleotides in length, or from about 12 to about 14 nucleotides in length, or from about 14 to about 16 nucleotides in length, or from about 16 to about 18 nucleotides in length, or from about 18 to about 20 nucleotides in length, or greater than about 20 nucleotides in length;
[0084] R.sup.10 and R.sup.15 may independently be from about 0 to about 20 base pairs in length. In other embodiments, R.sup.10 and R.sup.15 may independently be from about 2 to about 4 base pairs in length, or from about 4 to about 6 base pairs in length, or from about 6 to about 8 base pairs in length, or from about 8 to about 10 base pairs in length, or from about 10 to about 12 base pairs in length, or from about 12 to about 14 base pairs in length, or from about 14 to about 16 base pairs in length, or from about 16 to about 18 base pairs in length, or from about 18 to about 20 base pairs in length, or greater than about 20 base pairs in length;
[0085] R.sup.12 and R.sup.13 generally have a length such that the free energy of association between R.sup.12 and R.sup.3 and R.sup.13 and R.sup.6 is from about −5 to about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In other embodiments, the free energy of association between R.sup.12 and R.sup.3 and R.sup.13 and R.sup.6 is about −5 kcal/mole, about −6 kcal/mole, about −7 kcal/mole, about −8 kcal/mole, about −9 kcal/mole, about −10 kcal/mole, about −11 kcal/mole, or greater than about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In additional embodiments, R.sup.12 and R.sup.13 may range from about 4 to about 20 nucleotides in length. In other embodiments, R.sup.12 and R.sup.13 may be about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or greater than about 20 nucleotides in length.
[0086] In yet another exemplary embodiment, R.sup.8 may comprise formula (V):
R.sup.10—R.sup.11—R.sup.12—R.sup.13—R.sup.14—R.sup.15—R.sup.16 (V)
wherein:
[0087] R.sup.11, R.sup.12, R.sup.14, R.sup.15 and R.sup.16 are single stranded oligonucleotide sequences independently not complementary to each other or any of R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, or R.sup.6; [0088] R.sup.10 and R.sup.13 are double-stranded nucleic acid sequences; [0089] R.sup.11 is a nucleotide sequence complementary to R.sup.3; and [0090] R.sup.15 is a nucleotide sequence that is complementary to R.sup.6.
[0091] R.sup.12, R.sup.14, and R.sup.16 may independently be from about 0 to about 20 nucleotides in length. In other embodiments, R.sup.12, R.sup.14, and R.sup.16 may independently be from about 2 to about 4 nucleotides in length, or from about 4 to about 6 nucleotides in length, or from about 6 to about 8 nucleotides in length, or from about 8 to about 10 nucleotides in length, or from about 10 to about 12 nucleotides in length, or from about 12 to about 14 nucleotides in length, or from about 14 to about 16 nucleotides in length, or from about 16 to about 18 nucleotides in length, or from about 18 to about 20 nucleotides in length, or greater than about 20 nucleotides in length.
[0092] R.sup.10 and R.sup.13 may independently be from about 0 to about 20 base pairs in length. In other embodiments, R.sup.10 and R.sup.13 may independently be from about 2 to about 4 base pairs in length, or from about 4 to about 6 base pairs in length, or from about 6 to about 8 base pairs in length, or from about 8 to about 10 base pairs in length, or from about 10 to about 12 base pairs in length, or from about 12 to about 14 base pairs in length, or from about 14 to about 16 base pairs in length, or from about 16 to about 18 base pairs in length, or from about 18 to about 20 base pairs in length, or greater than about 20 base pairs in length.
[0093] R.sup.11 and R.sup.15 generally have a length such that the free energy of association between R.sup.11 and R.sup.3 and R.sup.15 and R.sup.6 is from about −5 to about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In other embodiments, the free energy of association between R.sup.11 and R.sup.3 and R.sup.15 and R.sup.6 is about −5 kcal/mole, about −6 kcal/mole, about −7 kcal/mole, about −8 kcal/mole, about −9 kcal/mole, about −10 kcal/mole, about −11 kcal/mole, or greater than about −12 kcal/mole at a temperature from about 21° C. to about 40° C. and at a salt concentration from about 1 mM to about 100 mM. In additional embodiments, R.sup.11 and R.sup.15 may range from about 4 to about 20 nucleotides in length. In other embodiments, R.sup.11 and R.sup.15 may be about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, or greater than about 10 nucleotides in length.
[0094] When R.sup.8 comprises formula (IV) or formula (V), a cleavage site of a restriction endonuclease recognition sequence produced by the association of R.sup.3 and R.sup.6 with R.sup.8 may be located within R.sup.10 for either formula (IV) or formula (V), R.sup.15 for formula (IV), R.sup.13 for formula (V), or a combination thereof. Suitable restriction endonuclease recognition sequences for these embodiments are recognized by restriction enzymes that cleave double stranded nucleic acid outside the recognition sequence of the restriction enzyme. Such enzymes and the corresponding recognition and cleavage sites are known in the art. By way of non-limiting example, these sites may include AcuI, AlwI, BaeI, BbsI, BbvI, BccI, BceAI, BcgI, BciVI, BfuAI, BmrI, BpmI, BpuEI, BsaI, BsaXI, BseRI, BsgI, BsmAI, BsmBI, BsmFI, BspCNI, BspMI, BspQI, BtgZI, CspCI, EarI, EciI, EcoP15I, FokI, HgaI, HphI, HpyAV, MboII, MlyI, MmeI, MmeAIII, PleI, SapI, SfaNI.
[0095] In some embodiments for molecular biosensors having Formula (IV) or Formula (V), R.sup.7 may comprise two signaling molecules, each attached to one strand of a double-stranded nucleotide sequence comprising R.sup.8. Cleavage of the restriction enzyme recognition site results in the release and separation of the two signaling molecules, resulting in a detectable and quantifiable change in signal intensity. Exemplary detections means suitable for use in the molecular biosensors include fluorescent resonance energy transfer (FRET), lanthamide resonance energy transfer (LRET), fluorescence cross-correlation spectroscopy, fluorescence quenching, fluorescence polarization, flow cytometry, scintillation proximity, luminescence resonance energy transfer, direct quenching, ground-state complex formation, chemiluminescence energy transfer, bioluminescence resonance energy transfer, excimer formation, colorimetric substrates detection, phosphorescence, electrochemical changes, and redox potential changes.
[0096] In some embodiments, R.sup.9 is a solid support having R.sup.8 attached thereto. Non-limiting examples of suitable solid supports may include microtitre plates, test tubes, beads, resins and other polymers, as well as other surfaces either known in the art or described herein. The solid support may be a material that may be modified to contain discrete individual sites appropriate for the attachment or association of the construct and is amenable to at least one detection method. Non-limiting examples of solid support materials include glass, modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), nylon or nitrocellulose, polysaccharides, nylon, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses and plastics. The size and shape of the solid support may also vary without departing from the scope of the invention. A solid support may be planar, a solid support may be a well, i.e. a 384 well plate, or alternatively, a solid support may be a bead or a slide.
[0097] R.sup.8 may be attached to the R.sup.9 in a wide variety of ways, as will be appreciated by those in the art. R.sup.8, for example, may either be synthesized first, with subsequent attachment to the solid support, or may be directly synthesized on the solid support. R.sup.9 and R.sup.8 may be derivatized with chemical functional groups for subsequent attachment of the two. For example, the solid support may be derivatized with a chemical functional group including, but not limited to, amino groups, carboxyl groups, oxo groups or thiol groups. Using these functional groups, the R.sup.8 may be attached using functional groups either directly or indirectly using linkers. Alternatively, R.sup.8 may also be attached to the surface non-covalently. For example, a biotinylated R.sup.8 can be prepared, which may bind to surfaces covalently coated with streptavidin, resulting in attachment. Alternatively, R.sup.8 may be synthesized on the surface using techniques such as photopolymerization and photolithography. Additional methods of attaching R.sup.8 to a surface and methods of synthesizing nucleic acids on surfaces are well known in the art, i.e. VLSIPS technology from Affymetrix (e.g., see U.S. Pat. No. 6,566,495, and Rockett and Dix, “DNA arrays: technology, options and toxicological applications,” Xenobiotica 30(2):155-177, all of which are hereby incorporated by reference in their entirety).
[0098] In each of the foregoing embodiments for molecular biosensors having formula (III), the first nucleic acid construct, R.sup.1—R.sup.2—R.sup.3 and the second nucleic acid construct, R.sup.4—R.sup.5—R.sup.6, may optionally be attached to each other by a linker R.sup.LA to create tight binding bivalent ligands. Typically, the attachment is by covalent bond formation. Alternatively, the attachment may be by non covalent bond formation. In one embodiment, R.sup.LA attaches R.sup.1 of the first nucleic acid construct to R.sup.4 of the second nucleic acid construct to form a molecule comprising:
##STR00004##
[0099] In a further embodiment, R.sup.LA attaches R.sup.2 of the first nucleic acid construct to R.sup.5 of the second nucleic acid construct to form a molecule comprising:
##STR00005##
[0100] In yet another embodiment, R.sup.LA attaches R3 of the first nucleic acid construct to R7 of the second nucleic acid construct to form a molecule comprising:
##STR00006##
[0101] Generally speaking, R.sup.LA may be a nucleotide sequence from about 10 to about 100 nucleotides in length. The nucleotides comprising R.sup.LA may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment, R.sup.LA is comprised of DNA bases. In another embodiment, R.sup.LA is comprised of RNA bases. In yet another embodiment, R.sup.LA is comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2′ position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases include 2′-fluoro nucleotides, 2′-amino nucleotides, 5′-aminoallyl-2′-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, R.sup.LA is comprised of nucleotide mimics. Examples of nucleotide mimics include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholine oligomers (PMO). Alternatively, R.sup.LA may be a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers include sulfoSMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate), and Ic-SPDP (N-Succinimidyl-6-(3′-(2-PyridylDithio)-Propionamido)-hexanoate). In another embodiment, the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. An exemplary R.sup.LA is the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, R.sup.LA is from about 1 to about 500 angstroms in length. In another embodiment, R.sup.LA is from about 20 to about 400 angstroms in length. In yet another embodiment, R.sup.LA is from about 50 to about 250 angstroms in length.
(b) Three Component Molecular Biosensors without a Solid Support
[0102] In an alternative embodiment of the three-component biosensor, the biosensor does not comprise a solid support. For instance, in some embodiments, the three-component molecular biosensor comprises three constructs, which together have formula (VI):
R.sup.1—R.sup.2—R.sup.3;
R.sup.4—R.sup.5—R.sup.6; and
at least one R.sup.7—R.sup.8; (VI)
wherein: [0103] R.sup.1 is an epitope-binding agent that binds to a first epitope on a target molecule; [0104] R.sup.2 is a flexible linker attaching R.sup.1 to R.sup.3; [0105] R.sup.3 and R.sup.6 are a first pair of nucleotide sequences that are complementary to two distinct regions on R.sup.8; [0106] R.sup.5 is a flexible linker attaching R.sup.4 to R.sup.6; [0107] R.sup.6 is an epitope-binding agent that binds to a second epitope on a target molecule; [0108] R.sup.8 is a nucleotide construct comprising a first region that is complementary to R.sup.3 and a second region that is complementary to R.sup.6, such that when R.sup.3 and R.sup.6 associated with R.sup.8, an endonuclease restriction site is reconstituted; [0109] R.sup.7 is a signaling molecule.
[0110] R.sup.1, R.sup.2, R.sup.3, R.sup.4, R.sup.5, R.sup.6, and R.sup.7 may be as defined above for three-component molecular biosensors having formula (II). R.sup.8 may be as described in Section (II)(a) above.
[0111] In some embodiments for molecular biosensors having Formula (VI), R.sup.7 may comprise two signaling molecules, each attached to one strand of a double-stranded nucleotide sequence comprising R.sup.8. Cleavage of the restriction enzyme recognition site results in the release and separation of the two signaling molecules, resulting in a detectable and quantifiable change in signal intensity. Exemplary detections means suitable for use in the molecular biosensors include fluorescent resonance energy transfer (FRET), lanthamide resonance energy transfer (LRET), fluorescence cross-correlation spectroscopy, fluorescence quenching, fluorescence polarization, flow cytometry, scintillation proximity, luminescence resonance energy transfer, direct quenching, ground-state complex formation, chemiluminescence energy transfer, bioluminescence resonance energy transfer, excimer formation, colorimetric substrates detection, phosphorescence, electrochemical changes, and redox potential changes.
III. Methods for Utilizing a Molecular Biosensor
[0112] A further aspect of the invention encompasses the use of the molecular biosensors of the invention in several applications. In certain embodiments, the molecular biosensors are utilized in methods for detecting one or more target molecules. In other embodiments, the molecular biosensors may be utilized in kits and for therapeutic and diagnostic applications.
[0113] In one embodiment, the molecular biosensors may be utilized for detection of a target molecule. The method generally involves contacting a molecular biosensor of the invention with the target molecule. To detect a target molecule utilizing two-component biosensors, the method typically involves target-molecule induced co-association of two epitope-binding agents (present in the molecular biosensor of the invention) that each recognize distinct epitopes on the target molecule. The epitope-binding agents each comprise complementary oligonucleotides. Co-association of the two epitope-binding agents with the target molecule results in annealing of the two complementary oligonucleotides such that a detectable signal is produced. Typically, the detectable signal is produced by any of the detection means known in the art or as described herein. Alternatively, for three-component biosensors, co-association of the two epitope-binding agent constructs with the target molecule results in hybridization of each signaling oligos to the oligonucleotide construct. Binding of the two signaling oligo to the oligonucleotide construct brings them into proximity such that a detectable signal is produced.
[0114] In one particular embodiment, a method for the detection of a target molecule that is a protein or polypeptide is provided. The method generally involves detecting a polypeptide in a sample comprising the steps of contacting a sample with a molecular biosensor of the invention. By way of non-limiting example, the molecular biosensor may comprise two aptamers recognizing two distinct epitopes of a protein, a double stranded polynucleotide containing binding site for DNA binding protein and an aptamer recognizing a distinct epitope of the protein, an antibody and an aptamer recognizing distinct epitopes of the protein, a double stranded polynucleotide containing a binding site for a DNA binding protein and an antibody recognizing a distinct epitope of the protein, two antibodies recognizing two distinct epitopes of the protein, two double stranded polynucleotide fragments recognizing two distinct sites of the protein, two single stranded polynucleotide elements recognizing two distinct sequence elements of another single stranded polynucleotide.
[0115] The molecular biosensor may also detect formation of a protein-polynucleotide complex using a double stranded polynucleotide fragment (containing the binding site of the protein) labeled with a first signaling oligonucleotide and the protein labeled with a second signaling oligonucleotide (
[0116] In another embodiment, the molecular biosensors may be used to detect a target molecule that is a macromolecular complex in a sample. In this embodiment, the first epitope is preferably on one polypeptide and the second epitope is on another polypeptide, such that when a macromolecular complex is formed, the one and another polypeptides are bought into proximity, resulting in the stable interaction of the first aptamer construct and the second aptamer construct to produce a detectable signal, as described above.
Definitions
[0117] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them unless specified otherwise.
[0118] The term “antibody” generally means a polypeptide or protein that recognizes and can bind to an epitope of an antigen. An antibody, as used herein, may be a complete antibody as understood in the art, i.e., consisting of two heavy chains and two light chains, or be selected from a group comprising polyclonal antibodies, ascites, Fab fragments, Fab′ fragments, monoclonal antibodies, chimeric antibodies humanized antibodies, and a peptide comprising a hypervariable region of an antibody.
[0119] The term “aptamer” refers to a polynucleotide, generally a RNA or a DNA that has a useful biological activity in terms of biochemical activity, molecular recognition or binding attributes. Usually, an aptamer has a molecular activity such as binding to a target molecule at a specific epitope (region). It is generally accepted that an aptamer, which is specific in its binding to any polypeptide, may be synthesized and/or identified by in vitro evolution methods
[0120] As used herein, “detection method” means any of several methods known in the art to detect a molecular interaction event. The phrase “detectable signal”, as used herein, is essentially equivalent to “detection method.”
[0121] The term “epitope” refers generally to a particular region of a target molecule. Examples include an antigen, a hapten, a molecule, a polymer, a prion, a microbe, a cell, a peptide, polypeptide, protein, a nucleic acid, or macromolecular complex. An epitope may consist of a small peptide derived from a larger polypeptide. An epitope may be a two or three-dimensional surface or surface feature of a polypeptide, protein or macromolecular complex that comprises several non-contiguous peptide stretches or amino acid groups.
[0122] The term “epitope binding agent” refers to a substance that is capable of binding to a specific epitope of an antigen, a polypeptide, a nucleic acid, a protein or a macromolecular complex. Non-limiting examples of epitope binding agents include aptamers, thioaptamers, double-stranded DNA sequence, peptides and polypeptides, ligands and fragments of ligands, receptors and fragments of receptors, antibodies and fragments of antibodies, polynucleotides, coenzymes, coregulators, allosteric molecules, peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO) and ions. Peptide epitope binding agents include ligand regulated peptide epitope binding agents.
[0123] The term “epitope binding agent construct” refers to a construct that contains an epitope-binding agent and can serve in a “molecular biosensor” with another molecular biosensor. Preferably, an epitope binding agent construct also contains a “linker,” and an “oligo”. An epitope binding agent construct can also be referred to as a molecular recognition construct.
[0124] The term “target molecule,” as used herein, refers to a molecule that may be detected with a biosensor of the invention. By way of non-limiting example, a target may be a biomolecule such as an antigen, a polypeptide, a protein, a nucleic acid, a carbohydrate, or a macromolecular complex thereof. Alternatively, a target may be a hapten, a molecule, a polymer, a prion, a microbe, a cell, or a macromolecular complex thereof.
[0125] The term “signaling molecule,” as used herein, refers to any substance attachable to a polynucleotide, polypeptide, aptamer, nucleic acid component, or other substrate material, in which the substance is detectable by a detection method. Non-limiting examples of labels applicable to this invention include but are not limited to luminescent molecules, chemiluminescent molecules, fluorochromes, fluorescent quenching agents, colored molecules, radioisotopes, scintillants, massive labels (for detection via mass changes), biotin, avidin, streptavidin, protein A, protein G, antibodies or fragments thereof, Grb2, polyhistidine, Ni.sup.2+, Flag tags, myc tags, heavy metals, enzymes, alkaline phosphatase, peroxidase, luciferase, electron donors/acceptors, acridinium esters, and colorimetric substrates. The skilled artisan would readily recognize other useful labels that are not mentioned above, which may be employed in the operation of the present invention.
EXAMPLES
[0126] The following examples illustrate various iterations of the invention.
Example 1. Two-Component Molecular Biosensors Comprising a Single Nicking Restriction Endonuclease Recognition Site
[0127] This example describes a method for the rapid and sensitive detection of a target molecule using a two-component molecular biosensor. This method is based on the target-driven association of two constructs containing epitope-binding agents that recognize two distinct epitopes of a target (
Double-Stranded Nucleic Acid Stains
[0128] The displaced DNA strand may be detected by annealing with a complementary nucleic acid sequence, to form double stranded DNA which may be detected using stains that specifically bind double stranded DNA (
Detection Using a Type IIS Endonuclease Construct
[0129] The displaced DNA strand may be detected by annealing to a type IIS endonuclease construct (
Detection Using a Linker Construct
[0130] The displaced strand may be detected by annealing to a linker construct (
Example 2. Two Component Molecular Biosensors Comprising Two Nicking Restriction Endonuclease Recognition Sites
[0131] In an alternative embodiment of the target detection method described in Example 1 above, the single-stranded nucleotide sequences of the epitope-binding agent constructs comprise two restriction enzyme recognition sites (
[0132] In other embodiments the restriction endonuclease sites may be proximal to each other. In these embodiments, the displaced strands are not complementary to each other, but may be detected by annealing to type IIS endonuclease constructs (
Example 3. Validation of Three Component Molecular Biosensor
[0133] This example describes a method for the rapid and sensitive detection of a target molecule using a three-component molecular biosensor (
[0134] To validate the assay described, epitope binding agent constructs were incubated with 0, 10, 20 and 30 nM concentrations of target molecule in the presence of an oligonucleotide construct in a master mix containing the restriction enzyme HincII. The reaction was then loaded onto an agarose gel, and the products of the restriction digestion reaction resolved. The results show that in the absence of target molecule, only 20% of the oligonucleotide construct was digested by the HincII enzyme. Adding increasing concentrations of the target molecule resulted in increasing digestion of the oligonucleotide construct (
Example 4. Three Component Molecular Biosensor Immobilized on Magnetic Beads
[0135] In this example, the oligonucleotide construct described in Example 3 was labeled with FAM, then conjugated with biotin and immobilized on streptavidin magnetic beads (SMB). The oligonucleotide construct was incubated with pre-equilibrated SMB in 50 mM Tris, 150 mM NaCL, 0.02% tween-20, pH 8.0 at room temperature for 50 minutes. The beads were then washed three times. Master mix (2 μl) was added into each tube, and other components were added as detailed in Table 1 below. The final volume of the reaction was 20 μl/tube in 1× reaction buffer (20 mM Tris, 100 mM NaCl, 2 mM MgCl.sub.2, 0.2 mM DTT, 0.2 mg/ml BSA) and HincII. The reaction was incubated at room temperature for 35 minutes, and 10 μl of the reaction was then transferred into a 384-well plate and read at ex. 485 nm, em. 535 nm (
[0136] A similar experiment was performed using an oligonucleotide construct labeled with horse radish peroxidase (HRP). Master mix (2 μl) was added into each tube, and other components were added as detailed in Table 1 below. The final volume of the reaction was 35 μl/tube in 1× reaction buffer (20 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.2 mg/ml BSA) and HincII. The reaction was incubated at room temperature for 40 minutes, and 30 μl of the reaction was then transferred into a 96-well plate and mixed with 40 μl chemiluminescent ELISA substrate, and luminescence read (
Example 5. Three Component Molecular Biosensor Immobilized on Magnetic Beads and Sequential Addition of Target and Restriction Enzyme
[0137] In a variation of the above conditions, the FAM-labeled oligonucleotide construct immobilized on beads was mixed with the epitope binding constructs and the target molecule, and the mixture incubated at RT in binding buffer (50 mM Tris, pH 8.0, 150 mM NaCl.sub.2, 0.02% Tween-20, 0.2 mg/ml BSA) for 20 min, then washed 1× with 50 μl binding buffer. This was followed by the addition of 1×HincII buffer (20 mM Tris, pH 8.0, 100 mM NaCl, 2 mM MgCl.sub.2, 0.2 mM DTT, 0.2 mg/ml BSA) with HincII, for a final volume of 25 μl. The mixture was incubated at room temperature for 50 min. HincII-mediated release of FAM signal was measured using 22 μl of the reaction in a 384 well plate (
Example 6. Three Component Molecular Biosensor Immobilized on Plate Surface
[0138] In this Example, a FAM or HRP-labeled oligonucleotide construct described in Example 3 was immobilized on a plate (
Example 7. Three Component Molecular Biosensor Comprising Signaling Oligonucleotide Construct with Double-Stranded Nucleotide Regions
[0139] This Example describes a method for the rapid and sensitive detection of a target molecule using a three-component molecular biosensor (
[0140] The oligonucleotide construct, the epitope-binding constructs, and the restriction enzyme BcgI were incubated in the presence or absence of molecular target in buffer (100 mM NaCl, 50 mM Tris, pH 7.9, 2 mM MgCl.sub.2, 0.2 mM DTT, 0.2 mg/ml BSA, 20 μM SAM) in a final reaction volume of 20 μl. The reaction mixture was incubated at room temperature. Samples were taken at time 0 and every 10 minutes for measurement of FAM fluorescence (Table 1 and
TABLE-US-00001 TABLE 1 Signaling oligonucleotide construct 60 nM Epiptope oiligonucleotide constrct 1 20 nM Epiptope oiligonucleotide constrct 1 20 nM Molecular target 0 20 nM Bcgl 2 units 2 units 0 min 0 0 10 min 125 393 20 min 345 888 30 min 643 1417 40 min 689 1833 50 min 925 2308 60 min 1086 2594 70 min 1208 2839 80 min 1210 3017 90 min 1508 3321 100 min 1524 3295
Example 8. Three Component Molecular Biosensor Comprising Signaling Oligonucleotide Construct with Double-Stranded Nucleotide Regions, with Amplified Signal
[0141] This Example describes a three-component molecular biosensor wherein the three component biosensor comprises two epitope-binding agent constructs and an oligonucleotide construct comprising regions that are double-stranded and regions that are single-stranded. The oligonucleotide construct also comprises two signaling molecules, each attached to one strand of the double-stranded region of the oligonucleotide construct. The single-stranded regions of the oligonucleotide construct of this example are not contiguous, such that the signaling oligonucleotide construct comprises alternating double-stranded and single stranded regions (