Mostly natural DNA sequencing by synthesis
First Claim
1. A method of determining a target DNA sequence, said method comprising:
- a) hybridizing a plurality of polynucleotides that comprise the target DNA sequence with a primer to form a plurality of hybridized templates;
b) contacting the plurality of hybridized templates with i) a DNA polymerase and ii) a first single nucleotide solution, wherein the single nucleotide solution comprises non-terminating, labeled and non-labeled nucleotides, and wherein said percentage of labeled nucleotides incorporated by the DNA polymerase is 20% or less of the total number of nucleotides incorporated, under conditions to allow target DNA-dependent extension from the primer if the appropriate single nucleotide is present;
c) washing to remove unincorporated nucleotides; and
d) detecting the presence or absence of an incorporated, labeled nucleotide among the plurality of hybridized templates, wherein, when the presence of an incorporated, labeled nucleotide is detected, the presence and size, or absence of a stretch of more than one base of the same type in tandem is also detected,thereby determining the target DNA sequence.
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Abstract
The invention provides a new method for DNA sequencing called “natural sequencing by synthesis” (nSBS). According to the method, DNA that includes a desired sequence is synthesized using a dNTP mix with a small percentage of fluorescently-labeled nucleotides. The fluorescent label is cleavable. In contrast to previous methods that utilize 100% labeled nucleic acids, use of a small percentage of labeled nucleic acids minimizes the distortion of the natural structure of the extending DNA strand and the DNA polymerase. Using the disclosed methods with less than 10,000 copies of template DNA and 10% of the nucleotides labeled, long homopolymer stretches up to 20 bases can be sequenced with high accuracy and Q20 (with 99% accuracy) read lengths of up to 1,000 bases can be achieved. A Q20 read length of greater than 100 bases can potentially be achieved, even if the sequencing is performed with 1,000 copies of a template and 10% of the nucleotides labeled.
16 Citations
16 Claims
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1. A method of determining a target DNA sequence, said method comprising:
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a) hybridizing a plurality of polynucleotides that comprise the target DNA sequence with a primer to form a plurality of hybridized templates; b) contacting the plurality of hybridized templates with i) a DNA polymerase and ii) a first single nucleotide solution, wherein the single nucleotide solution comprises non-terminating, labeled and non-labeled nucleotides, and wherein said percentage of labeled nucleotides incorporated by the DNA polymerase is 20% or less of the total number of nucleotides incorporated, under conditions to allow target DNA-dependent extension from the primer if the appropriate single nucleotide is present; c) washing to remove unincorporated nucleotides; and d) detecting the presence or absence of an incorporated, labeled nucleotide among the plurality of hybridized templates, wherein, when the presence of an incorporated, labeled nucleotide is detected, the presence and size, or absence of a stretch of more than one base of the same type in tandem is also detected, thereby determining the target DNA sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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Specification