Multiplexed analysis of nucleic acid hybridization thermodynamics using integrated arrays
First Claim
1. A method for assaying a presence of a target nucleic acid molecule in a sample, comprising:
- (a) providing (i) a surface comprising a probe coupled to an energy donor, wherein said probe is configured to selectively couple to said target nucleic acid molecule, and (ii) an optical detector below said surface, wherein said optical detector is configured to detect at least one optical signal generated upon energy transfer between an energy acceptor coupled to said target nucleic acid molecule and said energy donor and wherein said optical detector and said surface are integrated with a chip;
(b) bringing said sample containing or suspected of containing said target nucleic acid molecule in contact with said surface under conditions sufficient to permit said probe to selectively couple to said target nucleic acid molecule;
(c) using said optical detector to measure said at least one optical signal in real-time while subjecting said surface to a temperature change, wherein said at least one optical signal is indicative of an interaction between said energy acceptor and said energy donor pair, and wherein said energy acceptor quenches optical activity of said energy donor; and
(d) generating signal versus temperature data using measurements of said at least one optical signal with said temperature change, thereby assaying said presence of said target nucleic acid molecule in said sample.
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Abstract
The present disclosure provides methods and devices for simultaneous identification of a plurality of target nucleic acid sequences in a single sample chamber that includes an addressable array of nucleic acid probes attached to a solid surface. Addressable signals can be generated and measured, in real-time, upon hybridization of target sequences at the individual probe locations within the array while the temperature of the system is varied. Such generated signals, as a function temperature, can then be used to compute the properties of nucleic acid hybridization at each addressable location which is ultimately utilized to estimate the sequence of the target nucleic acids. In particular, an integrated semiconductor biosensor array device can be used to measure the addressable signals.
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Citations
16 Claims
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1. A method for assaying a presence of a target nucleic acid molecule in a sample, comprising:
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(a) providing (i) a surface comprising a probe coupled to an energy donor, wherein said probe is configured to selectively couple to said target nucleic acid molecule, and (ii) an optical detector below said surface, wherein said optical detector is configured to detect at least one optical signal generated upon energy transfer between an energy acceptor coupled to said target nucleic acid molecule and said energy donor and wherein said optical detector and said surface are integrated with a chip; (b) bringing said sample containing or suspected of containing said target nucleic acid molecule in contact with said surface under conditions sufficient to permit said probe to selectively couple to said target nucleic acid molecule; (c) using said optical detector to measure said at least one optical signal in real-time while subjecting said surface to a temperature change, wherein said at least one optical signal is indicative of an interaction between said energy acceptor and said energy donor pair, and wherein said energy acceptor quenches optical activity of said energy donor; and (d) generating signal versus temperature data using measurements of said at least one optical signal with said temperature change, thereby assaying said presence of said target nucleic acid molecule in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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Specification