Nanopore-based single DNA molecule characterization, identification and isolation using speed bumps
First Claim
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1. A method for sequencing a nucleic acid molecule, the method comprising:
- (a) providing a chip comprising at least one nanopore in a membrane that is disposed adjacent or in proximity to an electrode, wherein said electrode is adapted to detect said nucleic acid molecule or a portion thereof;
(b) passing the nucleic acid molecule through said nanopore at a dwell time of at least about 10 microseconds; and
(c) detecting one or more nucleic acid bases of the nucleic acid molecule as it passes through the nanopore,wherein said detecting comprises identifying up to about 5 bases of said nucleic acid molecule.
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Abstract
The present invention relates to a method of using nanopores to obtain sequence information of sample DNAs in ss test DNAs. The method comprises using speed bumps to stall the ss test DNAs in the nanopores at random positions of the ss test DNAs to obtain sequence information of each and every nucleotides of the sample DNAs, and to construct the whole sequences of the sample DNAs. The present invention also relates to identification and/or isolation of test DNAs having desired sequence(s) using nanopore detectors facilitated by speed bump.
227 Citations
50 Claims
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1. A method for sequencing a nucleic acid molecule, the method comprising:
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(a) providing a chip comprising at least one nanopore in a membrane that is disposed adjacent or in proximity to an electrode, wherein said electrode is adapted to detect said nucleic acid molecule or a portion thereof; (b) passing the nucleic acid molecule through said nanopore at a dwell time of at least about 10 microseconds; and (c) detecting one or more nucleic acid bases of the nucleic acid molecule as it passes through the nanopore, wherein said detecting comprises identifying up to about 5 bases of said nucleic acid molecule. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method for sequencing a nucleic acid molecule, the method comprising:
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(a) providing a chip comprising at least one nanopore in a membrane that is disposed adjacent or in proximity to an electrode, wherein said electrode is adapted to detect said nucleic acid molecule or a portion thereof; (b) associating a plurality of speed bump molecules with the nucleic acid molecule along the length of the nucleic acid molecule; (c) passing the nucleic acid molecule through said nanopore at a dwell time of at least about 10 microseconds; and (d) detecting one or more nucleic acid bases of the nucleic acid molecule as it passes through the nanopore. - View Dependent Claims (12, 13, 14, 15, 16, 17)
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18. A method for sequencing a nucleic acid molecule, comprising:
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(a) providing a chip comprising at least one nanopore in a membrane that is disposed adjacent or in proximity to an electrode, wherein said electrode is adapted to detect said nucleic acid molecule or a portion thereof; (b) directing said nucleic acid molecule through said nanopore, wherein progression of said nucleic acid molecule through the nanopore is stopped or stalled with the aid of at least one speed bump molecule associated with said nucleic acid molecule; and (c) sequencing said nucleic acid molecule or a portion thereof as the nucleic acid molecule passes through the nanopore. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35)
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36. A method for obtaining sequence information of a nucleic acid molecule, the method comprising:
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a) forming a duplex segment containing at least one speed bump molecule associated with said nucleic acid molecule; b) flowing the nucleic acid molecule through a nanopore in a membrane, wherein said membrane is disposed adjacent to or in proximity to an electrode, and wherein upon flowing the nucleic molecule through the nanopore, said duplex segment is directed towards said nanopore; and c) obtaining electrical signals from said electrode upon the flow of said nucleic acid molecule through said nanopore, wherein said electrical signals are associated with the interaction of one or more bases of said nucleic acid molecule and said nanopore, and wherein said flow of said nucleic acid molecule is reduced with the aid of said duplex segment. - View Dependent Claims (37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50)
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Specification