DNA sequencing by mass spectrometry via exonuclease degradation
First Claim
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1. A multiplex mass spectrometric method for simultaneously determining the sequence of at least two different nucleic acids concurrently, comprising the steps of:
- (i) obtaining multiple copies of the at least two different nucleic acids, wherein at least one of the at least two different nucleic acids comprises mass modified nucleotides;
(ii) concurrently cleaving the at least two different nucleic acids unilaterally from a first end to a second end with an exonuclease to generate sequentially released individual nucleotides and optionally, at least two different sets of nucleic acid fragments;
(iii) identifying each of the sequentially released nucleotides by mass spectrometry or determining the molecular weight values of each of the sets of nucleic acid fragments by mass spectrometry; and
(iv) determining the sequence of the at least two different nucleic acids based on the molecular weight values of the sequentially released individual nucleotides or the sets of nucleic acid fragments.
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Abstract
Methods for determining the sequence of nucleic acids by cleaving the nucleic acid unilaterally from a first end with an exonuclease activity to sequentially release individual nucleotides, identifying each of the sequentially release nucleotides by mass spectrometry, and determining the sequence of the nucleic acid from the identified nucleotides are disclosed. The method is amenable to multiplexing for simulataneously determining more than one nuleic acid sequence.
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Citations
28 Claims
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1. A multiplex mass spectrometric method for simultaneously determining the sequence of at least two different nucleic acids concurrently, comprising the steps of:
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(i) obtaining multiple copies of the at least two different nucleic acids, wherein at least one of the at least two different nucleic acids comprises mass modified nucleotides; (ii) concurrently cleaving the at least two different nucleic acids unilaterally from a first end to a second end with an exonuclease to generate sequentially released individual nucleotides and optionally, at least two different sets of nucleic acid fragments; (iii) identifying each of the sequentially released nucleotides by mass spectrometry or determining the molecular weight values of each of the sets of nucleic acid fragments by mass spectrometry; and (iv) determining the sequence of the at least two different nucleic acids based on the molecular weight values of the sequentially released individual nucleotides or the sets of nucleic acid fragments. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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15. A kit for exonuclease sequencing at least two different species of nucleic acids by mass spectrometry, comprising
(i) an exonuclease for cleaving the nucleic acids unilaterally from a first end to sequentially release individual nucleotides; -
(ii) a set of nucleotides for synthesizing the different species of nucleic acids, at least a portion of the nucleotides being mass-modified such that sequentially released nucleotides of each of the different species of nucleic acids are distinguishable, (iii) a polymerase for synthesizing the nucleic acids from complementary templates and the set of nucleotides, and (iv) a solid support for immobilizing one of the nucleic acids or the exonuclease. - View Dependent Claims (16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28)
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23. The kit according to claim 23, wherein the mass-modifying functionality (M) is attached to a nucleotide moiety at a position selected from a group consisting of a 5'"'"' phosphate, a C-2'"'"' position of a sugar moiety, and a heterocyclic base.
Specification