Reversible di-nucleotide terminator sequencing
First Claim
Patent Images
1. A method for determining a sequence of a template polynucleotide, the method comprising:
- a) hybridizing a first primer to the template polynucleotide;
b) contacting at least one labeled reversible di-nucleotide terminator and a DNA polymerase with the first primer to extend the first primer along the template by polymerase-mediated polymerization of the labeled reversible di-nucleotide terminator to form a first extension product, wherein the labeled reversible di-nucleotide terminator includes a first nucleotide connected to a second nucleotide and includes a detectable moiety linked to the first nucleotide and includes a blocking moiety linked to the second nucleotide;
c) detecting the detectable moiety of the polymerized labeled reversible di-nucleotide terminator of step (b);
d) identifying a probe family to which the polymerized labeled reversible di-nucleotide terminator in step (b) belongs, the probe family having a plurality of labeled reversible di-nucleotide terminators of varying sequence each having the same type of a detectable moiety;
e) removing the blocking group on the polymerized labeled reversible di-nucleotide terminator of step (b) to generate a free 3′
OH group;
f) repeating steps (b), (c), (d), and optionally (e), to generate a first accumulated extension product;
g) generating a set of candidate ordered series of the probe families which correlate with an ordered series of the polymerized labeled reversible di-nucleotide terminators in steps (b), (c) and (d); and
h) determining the sequence of the template polynucleotide based at least in part on the first set of candidate ordered series of the probe families.
1 Assignment
0 Petitions
Accused Products
Abstract
The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, reversible di-nucleotide compounds are employed along with cleaving reactions that remove a label and a blocking moiety. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of reversible di-nucleotide compounds. In some embodiments, the di-nucleotides do not contain conventional nucleotide triphosphates, but rather employ amino acid phosphoramidate nucleotides (AAPNs).
49 Citations
16 Claims
-
1. A method for determining a sequence of a template polynucleotide, the method comprising:
-
a) hybridizing a first primer to the template polynucleotide; b) contacting at least one labeled reversible di-nucleotide terminator and a DNA polymerase with the first primer to extend the first primer along the template by polymerase-mediated polymerization of the labeled reversible di-nucleotide terminator to form a first extension product, wherein the labeled reversible di-nucleotide terminator includes a first nucleotide connected to a second nucleotide and includes a detectable moiety linked to the first nucleotide and includes a blocking moiety linked to the second nucleotide; c) detecting the detectable moiety of the polymerized labeled reversible di-nucleotide terminator of step (b); d) identifying a probe family to which the polymerized labeled reversible di-nucleotide terminator in step (b) belongs, the probe family having a plurality of labeled reversible di-nucleotide terminators of varying sequence each having the same type of a detectable moiety; e) removing the blocking group on the polymerized labeled reversible di-nucleotide terminator of step (b) to generate a free 3′
OH group;f) repeating steps (b), (c), (d), and optionally (e), to generate a first accumulated extension product; g) generating a set of candidate ordered series of the probe families which correlate with an ordered series of the polymerized labeled reversible di-nucleotide terminators in steps (b), (c) and (d); and h) determining the sequence of the template polynucleotide based at least in part on the first set of candidate ordered series of the probe families. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
-
-
11. A method for determining a sequence of a template polynucleotide, the method comprising:
-
a) hybridizing a first primer to the template polynucleotide; b) contacting at least one labeled reversible di-nucleotide terminator and a DNA polymerase with the first primer to extend the first primer along the template by polymerase-mediated polymerization of the labeled reversible di-nucleotide terminator to form a first extension product, wherein the labeled reversible di-nucleotide terminator includes a first nucleotide connected to a second nucleotide and includes a detectable moiety linked to the first nucleotide and includes a blocking moiety linked to the second nucleotide, and wherein the labeled reversible di-nucleotide terminator is a member of a probe family having a plurality of labeled reversible di-nucleotide terminators each having the same type of a first nucleotide linked to the same type of a detectable moiety and having a different type of a second nucleotide; c) detecting the detectable moiety of the polymerized labeled reversible di-nucleotide terminator of step (b); d) identifying the probe family to which the polymerized labeled reversible di-nucleotide terminator in step (b) belongs; e) removing the blocking group on the polymerized labeled reversible di-nucleotide terminator of step (b) to generate a free 3′
OH group;f) repeating steps (b), (c), (d), and optionally (e), to generate a first accumulated extension product; g) generating a first set of candidate ordered series of the probe families which correlate with an ordered series of the polymerized labeled reversible di-nucleotide terminators in steps (b), (c) and (d); and h) determining the sequence of the template polynucleotide based at least in part on the first set of candidate ordered series of the probe families. - View Dependent Claims (12, 13)
-
-
14. A method for determining a sequence of a template polynucleotide, the method comprising:
-
a) hybridizing a first primer to the template polynucleotide; b) contacting at least one labeled reversible di-nucleotide terminator and a DNA polymerase with the first primer to extend the first primer along the template by polymerase-mediated polymerization of the labeled reversible di-nucleotide terminator to form a first extension product, wherein the labeled reversible di-nucleotide terminator includes a first nucleotide connected to a second nucleotide and includes a detectable moiety linked to the first nucleotide and includes a blocking moiety linked to the second nucleotide; c) detecting the detectable moiety of the polymerized labeled reversible di-nucleotide terminator of step (b); d) identifying a probe family to which the polymerized labeled reversible di-nucleotide terminator in step (b) belongs, the probe family having a plurality of labeled reversible di-nucleotide terminators of varying sequence each having the same type of a detectable moiety; e) removing the blocking group on the polymerized labeled reversible di-nucleotide terminator of step (b) to generate a free 3′
OH group;f) repeating steps (b), (c), (d), and optionally (e), to generate a first accumulated extension product; g) generating a set of candidate ordered series of the probe families which correlate with an ordered series of the polymerized labeled reversible di-nucleotide terminators in steps (b), (c) and (d); and h) decoding the first set of candidate ordered series of the probe families to identify the most likely member of the first set of candidate ordered series. - View Dependent Claims (15, 16)
-
Specification