COMPOSITIONS AND METHODS FOR NUCLEIC ACID AMPLIFICATION
First Claim
Patent Images
1. A method for nucleic acid amplification comprising:
- a) providing a double stranded template nucleic acid comprising a first strand and a second strand;
b) mixing the double stranded template nucleic acid with a first primer and a second primer, wherein;
i) the first primer comprises a first plurality of nucleobases that are not canonical DNA nucleobases, wherein each nucleobase of the first plurality of nucleobases that are not canonical DNA nucleobases is distanced from another by about 3 to about 8 nucleobases, and wherein one nucleobase of the first plurality of nucleobases that are not canonical DNA nucleobases is a 3′
terminal nucleobase bound to a preceding nucleobase in the first primer by a phosphorothioate bond, andii) the second primer comprises a second plurality of nucleobases that are not canonical DNA nucleobases, wherein each nucleobase of the second plurality of nucleobases that are not canonical DNA nucleobases is distanced from another by about 3 to about 8 nucleobases, and wherein one nucleobase of the second plurality of nucleobases that are not canonical DNA nucleobases is a 3′
terminal nucleobase bound to a preceding nucleobase in the second primer by a phosphorothioate bond; and
c) amplifying the double stranded template nucleic acid by extending the first primer to form a first extension strand and extending the second primer to form a second extension strand; and
d) removing the first primer from the first extension strand and the second primer from the second extension strand.
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Abstract
The present disclosure provides compositions, methods and systems for the efficient removal of a non-target nucleic acid sequence from a double stranded nucleic acid amplification product. A non-target nucleic acid sequence may be a primer sequence incorporated into the double stranded nucleic acid molecule during a nucleic acid synthesis or amplification reaction. The non-target nucleic acid sequence may include a nucleobases that are not canonical DNA nucleobases, such as uracil, that can be selectively removed as part of the non-target sequence removal process.
46 Citations
56 Claims
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1. A method for nucleic acid amplification comprising:
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a) providing a double stranded template nucleic acid comprising a first strand and a second strand; b) mixing the double stranded template nucleic acid with a first primer and a second primer, wherein; i) the first primer comprises a first plurality of nucleobases that are not canonical DNA nucleobases, wherein each nucleobase of the first plurality of nucleobases that are not canonical DNA nucleobases is distanced from another by about 3 to about 8 nucleobases, and wherein one nucleobase of the first plurality of nucleobases that are not canonical DNA nucleobases is a 3′
terminal nucleobase bound to a preceding nucleobase in the first primer by a phosphorothioate bond, andii) the second primer comprises a second plurality of nucleobases that are not canonical DNA nucleobases, wherein each nucleobase of the second plurality of nucleobases that are not canonical DNA nucleobases is distanced from another by about 3 to about 8 nucleobases, and wherein one nucleobase of the second plurality of nucleobases that are not canonical DNA nucleobases is a 3′
terminal nucleobase bound to a preceding nucleobase in the second primer by a phosphorothioate bond; andc) amplifying the double stranded template nucleic acid by extending the first primer to form a first extension strand and extending the second primer to form a second extension strand; and d) removing the first primer from the first extension strand and the second primer from the second extension strand. - View Dependent Claims (2, 3, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
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4. (canceled)
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10. (canceled)
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14. (canceled)
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27. A method for amplifying a template nucleic acid, the method comprising:
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a) providing a template nucleic acid comprising (i) a first template strand comprising in 5′
to 3′
order;
a first primer binding site and a target nucleic acid, and (ii) a second template strand comprising in 5′
to 3′
order;
a second primer binding site and a nucleic acid sequence complementary to the target nucleic acid;b) annealing a first primer to the first primer binding site, and annealing a second primer to the second primer binding site, wherein; the first primer comprises 3 or 4 uracil nucleobases, each uracil nucleobase distanced from another uracil nucleobase in the first primer by about 3 to about 8 non-uracil nucleobases, the second primer comprises 3 or 4 uracil nucleobases, each uracil nucleobase distanced from another uracil nucleobase in the second primer by about 3 to about 8 non-uracil nucleobases, one uracil nucleobase of the 3 or 4 uracil nucleobases in the first primer is a 3′
terminal uracil nucleobase bound to a preceding nucleobase in the first primer by a first nuclease resistant bond, andone uracil nucleobase of the 3 or 4 uracil nucleobases in the second primer is a 3′
terminal uracil nucleobase bound to a preceding nucleobase in the second primer by a second nuclease resistant bond;c) forming an amplicon nucleic acid by;
extending the first primer and the second primer to generate a first extension strand comprising the first primer and the target nucleic acid, and extending the second primer to generate a second extension strand comprising the second primer and the nucleic acid sequence complementary to the target nucleic acid; andd) removing the first primer and the second primer from the amplicon nucleic acid.
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28-41. -41. (canceled)
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42. A nucleic acid library comprising a plurality of double-stranded nucleic acids, each of the plurality of the double-stranded nucleic acids comprising:
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a) a first strand comprising in 5′
to 3′
order;
a first primer and a target nucleic acid, wherein the first primer comprises a first plurality of uracil nucleobases, wherein each uracil nucleobase of the first plurality of uracil nucleobases is distanced from another uracil nucleobase in the first primer by about 3 to about 8 non-uracil nucleobases, and wherein one uracil nucleobase of the first plurality of uracil nucleobases is a 3′
terminal uracil nucleobase bound to a preceding nucleobase in the first primer by a first nuclease resistant bond; andb) a second strand comprising in 5′
to 3′
order;
a second primer and a nucleic acid sequence complementary to the target nucleic acid, wherein the second primer comprises a second plurality of uracil nucleobases, wherein each uracil nucleobase of the second plurality of uracil nucleobases is distanced from another uracil nucleobase in the second primer by about 3 to about 8 non-uracil nucleobases, and wherein one uracil nucleobase of the second plurality of uracil nucleobases is a 3′
terminal uracil nucleobase bound to a preceding nucleobase in the second primer by a second nuclease resistant bond.
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43-54. -54. (canceled)
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55. A universal primer comprising:
- a non-naturally occurring sequence of nucleic acids comprising 3 or more uracil nucleobases;
wherein one of the 3 or more uracil nucleobases is a 3′
terminal uracil nucleobase bound to a preceding nucleobase in the universal primer by a phosphorothioate bond; and
wherein each of the 3 or more uracil nucleobases is distanced from a subsequent or a preceding uracil nucleobase in the universal primer by about 3 to about 8 non-uracil nucleobases.
- a non-naturally occurring sequence of nucleic acids comprising 3 or more uracil nucleobases;
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56-63. -63. (canceled)
Specification