Real-time sequence determination
First Claim
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1. A composition comprising a polymerizing agent including at least one molecular and/or atomic tag located at or near, associated with or covalently bonded to a site on the polymerizing agent, where a detectable property of the tag undergoes a change before, during and/or after monomer incorporation.
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Abstract
A sequencing methodology is disclosed that allows a single DNA or RNA molecule or portion thereof to be sequenced directly and in substantially real time. The methodology involves engineering a polymerase and/or dNTPs with atomic and/or molecular tags that have a detectable property that is monitored by a detection system.
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Citations
33 Claims
- 1. A composition comprising a polymerizing agent including at least one molecular and/or atomic tag located at or near, associated with or covalently bonded to a site on the polymerizing agent, where a detectable property of the tag undergoes a change before, during and/or after monomer incorporation.
- 7. A composition comprising a polymerase or reverse transcriptase including at least one molecular and/or atomic tag located at or near, associated with or covalently bonded to a site on the polymerase, where a detectable property has a first value when the polymerase is in a first state and a second value when the polymerase is in a second state during monomer incorporation, and where the polymerizing agent changes from the first state to the second state and back again during each monomer incorporation.
- 10. A composition comprising a polymerizing agent including a molecular and/or atomic tag associated with or covalently bonded to a site on the polymerase and a monomer including a molecular and/or atomic tag, where at least one of the tags has a detectable property that undergoes a change before, during and/or after monomer incorporation due to an interaction between the polymerizing agent tag and the monomer tag.
- 20. A composition comprising a polymerase or reverse transcriptase including a pair of tags located at or near, associated with or covalently bonded to a site of the polymerase, where a detectable property of at least one of the tags undergoes a change before, during and/or after monomer incorporation.
- 24. The composition of claim 22, wherein the polymerase comprises Taq DNA polymerase I having a tag attached at a site selected from the group consisting of 513-518, 643, 647, 649 and 653-661 and mixtures or combinations thereof of the Taq polymerase, where the tag comprises a fluorescent molecule.
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24-1. A single molecule sequencing apparatus comprising a substrate having a first chamber in which at least one tagged polymerase is confined therein and a second chamber including tagged dNTPs and a channel interconnecting the chambers, where a detectable property of at least one tag undergoes a detectable change during a monomer incorporation cycle.
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26. A mutant Taq polymerase comprising native Taq polymerase with a cysteine residue replacement at a site selected from the group consisting of513-518, 643, 647, 649 and 653-661 and mixtures or combinations thereof.
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27. The polymerase of claim 27, wherein the cysteine residue includes a tag covalently bonded thereto through the SH group.
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28. A system for retrieving stored information comprising:
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a unknown nucleotide sequence representing a data stream;
a single-molecule sequencer including a polymerase having a tag associated therewith and monomers for the polymerase, each monomer having a tag associated therewith;
an excitation source adapted to excite the at least one of the tags; and
a detector adapted to detect a response from at least one of the tag, where the response changes during polymerization of a complementary sequence and the changes in response represent a content of the data stream.
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29. A system for determining sequence information from a single molecule comprising:
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a unknown nucleotide sequence;
a single-molecule sequencer comprising a polymerase having a tag associated therewith and monomers for the polymerase, each monomer having a tag associated therewith;
a excitation source adapted to excite at least one of the tags; and
a detector adapted to detect a response from at least one of the tags, where the response changes during polymerization of a complementary sequence and the changes in the response represent the identity of each nucleotide in the unknown sequence.
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30. A method for sequencing a molecular sequence comprising:
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supplying an unknown sequence of nucleotides or nucleotide analogs to a single-molecule sequencer comprising a polymerase having a fluorescent donor covalently attached thereto and monomers for the polymerase, each monomer having a unique fluorescent acceptor covalently bonded thereto;
exciting the fluorescent donor with a light from an excitation light source;
detecting emitted fluorescent light from the acceptor during a monomer incorporation cycle via a fluorescent light detector, where an intensity and/or frequency of the emitted light for the acceptors changes during each monomer incorporation cycle; and
converting the changes into an identity of each nucleotide or nucleotide analog in the unknown sequence.
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31. A method of sequencing an individual nucleic acid molecule or numerous individual molecules in parallel including the steps of:
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immobilizing a member of the replication complex comprising a polymerase including a tag attached thereto, a primer or a template sufficiently spaced apart to allow resolution detection of each complex on a solid support;
incubating the replication complex with cooperatively-tagged nucleotides, each nucleotide including a unique tag at its gamma-phosphate, where each nucleotide can be individually detected;
detecting each nucleotide incorporated by the polymerase as the polymerase transitions between its open and closed form, which causes a change in a detectable property of at least one of the tags or as the pyrophosphate group is released by the polymerase; and
relating the changes in the detectable property to the sequence of nucleotides in an unknown nucleic acid sequence.
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32. A γ
- -phosphate modified nucleoside comprising γ
-phosphate modified dATP, dCTP, dGTP and dTTP.
- -phosphate modified nucleoside comprising γ
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33. A primer sequence or portion thereof selected from the group consisting of Sequence 1 through 29.
Specification