METHODS AND COMPOSITIONS USEFUL FOR NUCLEIC ACID SEQUENCING
Disclosed herein, inter alia, are modified nucleotides and methods of using the same in nucleic acid sequencing reactions.
1 - 39 . (canceled)
40 . A kit comprising a sequencing solution and a chase solution, wherein
(a) the sequencing solution comprises a plurality of sequencing nucleotides, wherein each sequencing nucleotide of the plurality of sequencing nucleotides comprises a detectable label moiety and a reversible terminator; and
(b) the chase solution comprises a plurality of chase nucleotides, wherein each chase nucleotide of the plurality of chase nucleotides comprises a retarding moiety and a reversible terminator.
41 . The kit of claim 40 , wherein the sequencing solution comprises:
(i) a plurality of adenine nucleotides, or analogs thereof;
(ii) a plurality of thymine nucleotides, or analogs thereof, or a plurality of uracil nucleotides, or analogs thereof;
(iii) a plurality of cytosine nucleotides, or analogs thereof; and
(iv) a plurality of guanine nucleotides, or analogs thereof.
42 . The kit of claim 41 , wherein
(i) each nucleotide of the plurality of adenine nucleotides, or analogs thereof comprises a first detectable label moiety;
(ii) each nucleotide of a plurality of thymine nucleotides, or analogs thereof, or a plurality of uracil nucleotides, or analogs thereof, comprises a second detectable label moiety;
(iii) each nucleotide of a plurality of cytosine nucleotides, or analogs thereof, of the plurality comprises a third detectable label moiety; and
(iv) each nucleotide of a plurality of guanine nucleotides, or analogs thereof, comprises a fourth detectable label moiety, and the detectable label moieties are different.
43 . The kit of claim 40 , wherein the chase solution comprises:
(i) a plurality of adenine nucleotides, or analogs thereof;
(ii) a plurality of thymine nucleotides, or analogs thereof, or a plurality of uracil nucleotides, or analogs thereof;
(iii) a plurality of cytosine nucleotides, or analogs thereof; and
(iv) a plurality of guanine nucleotides, or analogs thereof.
44 . The kit of claim 40 , wherein each of the chase nucleotides comprises the same retarding moiety.
45 . The kit of claim 40 , wherein one or more of the chase nucleotides and/or one or more of the sequencing nucleotides comprises a nucleotide with a free 3′-OH.
46 . The kit of claim 40 , further comprising one or more depletion polynucleotides and i) a depletion polymerase that is active to selectively incorporate the nucleotides comprising a free 3′-OH; or (ii) one or more nucleotide cyclases active to selectively cyclize the nucleotides comprising a free 3′-OH.
47 . The kit of claim 40 , wherein the retarding moiety slows the rate of incorporation of a next nucleotide by a factor of 2 to a factor of 20 as compared to a control nucleotide.
48 . The kit of claim 47 , wherein the retarding moiety decreases incorporation of a next nucleotide by a factor of 2, a factor of 3, a factor of 4, a factor of 5, a factor of 6, a factor of 7, a factor of 8, a factor of 9, a factor of 10, a factor of 11, a factor of 12, a factor of 13, a factor of 14, a factor of 15, a factor of 16, a factor of 17, a factor of 18, a factor of 19, or a factor of 20 as compared to a control nucleotide.
49 . The kit of claim 42 , wherein the retarding moiety is a fluorescent moiety capable of emitting light at an emission maximum, wherein the emission maximum is below 530 nm.
50 . The kit of claim 42 , wherein the retarding moiety is a fluorescent moiety capable of emitting light at an emission maximum, wherein the emission maximum is above 750 nm.
51 . The kit of claim 42 , wherein the retarding moiety is a quenching moiety.
52 . The kit of claim 51 , wherein the retarding moiety is capable of quenching light comprising a wavelength of 400-530 nm, 480-580 nm, 550-650 nm, 480-720 nm, or 550-720 nm.
53 . The kit of claim 41 , wherein the retarding moiety is selected from:
where m is 4, 12, or 24,
54 . The kit of claim 42 , comprising a flow cell.
55 . A sequencing device comprising the kit of claim 53 .