Target activated nucleic acid biosensor and methods of using same
First Claim
1. A nucleic acid sensor molecule, the nucleic acid sensor molecule comprising a target molecule activation site, the target molecule activation site comprising a structure that recognizes a target molecule and an optical signaling unit, wherein said optical signaling unit includes at least one nucleotide coupled to a signaling moiety;
- and wherein said signaling moiety changes its optical properties upon allosteric modulation of said nucleic acid sensor molecule following recognition of said target molecule.
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Abstract
Methods for engineering a target activated biosensor are provided. Biosensors comprise a plurality of nucleic acid sensor molecules labeled with a first signaling moiety and a second signaling moiety. The nucleic acid sensor molecules recognizes target molecules which do not naturally bind to DNA. Binding of a target molecule to the sensor molecules triggers a change in the proximity of the signaling moieties which leads to a change in the optical properties of the nucleic acid sensor molecules on the biosensor. Reagents and systems for performing the method are also provided. The method is useful in diagnostic applications and drug optimization.
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Citations
80 Claims
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1. A nucleic acid sensor molecule, the nucleic acid sensor molecule comprising
a target molecule activation site, the target molecule activation site comprising a structure that recognizes a target molecule and an optical signaling unit, wherein said optical signaling unit includes at least one nucleotide coupled to a signaling moiety; - and wherein said signaling moiety changes its optical properties upon allosteric modulation of said nucleic acid sensor molecule following recognition of said target molecule.
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method of detecting a target molecule, the method comprising
providing a nucleic acid sensor molecule, the molecule comprising a target molecule activation site, the target molecule activation site comprising a structure that recognizes a target molecule and an optical signaling unit, wherein said optical signaling unit includes at least one nucleotide coupled to a signaling moiety; - and wherein said signaling moiety changing its optical properties upon allosteric modulation of said nucleic acid sensor molecule;
contacting said nucleic acid sensor molecule with a sample known to contain or suspected of containing a target molecule; and
detecting said light signal, wherein said light signal indicates the presence of said target molecule in said population. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19, 20, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 64)
- and wherein said signaling moiety changing its optical properties upon allosteric modulation of said nucleic acid sensor molecule;
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21. A method identifying a nucleic acid sensor molecule, the method comprising
providing a population of oligonucleotides, wherein said population comprises oligonucleotides comprising a first region comprising a random nucleotide sequence; -
contacting said population with a target molecule; and
identifying an oligonucleotide in said population that changes conformation upon recognizing said target molecule. - View Dependent Claims (22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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47. The polypeptide comprises the amino acid sequence of a phosphodiesterase (PDE) polypeptide.
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57. A plurality of nucleic acid sensor molecules, the plurality comprising two or more nucleic acid sensor molecules, said two or more nucleic acid sensor molecules comprising
a target molecule activation site, the target molecule activation site comprising a structure that recognizes a target molecule and an optical signaling unit, wherein said optical signaling unit includes at least one nucleotide coupled to a signaling moiety; - and wherein said signaling moiety changes its optical properties upon an allosteric modulation of said nucleic acid sensor molecule following recognition of said target molecule.
- View Dependent Claims (58, 59, 60, 61, 62, 63, 65, 66, 67)
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68. A diagnostic system for detecting a target molecule, the diagnostic system comprising
at least one nucleic acid biosensor, the nucleic acid sensor molecule comprising a target molecule activation site, the target molecule activation site comprising a structure that recognizes to a target molecule; - and
an optical signaling unit, wherein said optical signaling unit includes at least one nucleotide coupled to a signaling moiety; and
wherein said signaling moiety changes its optical properties upon allosteric modulation of said nucleic acid sensor molecule following recognition of said target molecule; and
a detector in optical communication with said nucleic acid biosensor, wherein said detector detects changes in the optical properties of said nucleic acid biosensor. - View Dependent Claims (69, 70, 71)
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72. A kit for detecting a target molecule, the kit comprising
at least one nucleic acid biosensor, the nucleic acid sensor molecule comprising a target molecule activation site, the target molecule activation site comprising a structure that specifically recognizes a target molecule, and wherein said optical signaling unit comprises a first nucleotide coupled to a first signaling moiety and a second nucleotide coupled a second signaling moiety, and wherein said first and second signaling moieties change proximity to each other upon allosteric modulation by said target molecule to** said target activation site; -
a reagent for attaching said first signaling moiety;
a reagent for attaching said second signaling moiety; and
, optionally,control target molecules; and
, optionallyone or more buffers for analyte detection.
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73. A method for identifying a drug compound, the method comprising
identifying a nucleic acid biosensor-based molecule profile of target molecules associated with a disease trait in a patient; -
administering a candidate compound to said patient; and
monitoring changes in said profile. - View Dependent Claims (74, 75, 76)
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77. A method for identifying a drug compound, the method comprising
identifying a plurality of pathway target molecules; -
administering a candidate compound to a patient having a disease trait; and
monitoring changes in the structure, level or activity of two or more said plurality of pathway target molecules using a nucleic acid biosensor biomolecule. - View Dependent Claims (78, 79, 80)
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Specification