Targeted rolling circle amplification
First Claim
Patent Images
1. A method of amplifying a nucleic acid target region, the method comprising:
- a) providing a nucleic acid template, which template is a circular nucleic acid having a double-stranded central region and two single-stranded hairpin end regions;
wherein the double-stranded central region comprises a first polynucleotide sequence and a second polynucleotide sequence complementary to the first polynucleotide sequence, which first and second polynucleotide sequences collectively comprise the target region, a recognition site for a first restriction endonuclease, and a recognition site for a second restriction endonuclease, which recognition sites flank the target region; and
wherein the circular nucleic acid comprises a first primer binding sequence;
b) binding a first primer to the first primer binding sequence;
c) performing polymerase-mediated template-directed primer extension of the first primer with a polymerase comprising strand displacement activity, thereby producing a first nucleic acid product comprising at least two copies of the first polynucleotide sequence and the second polynucleotide sequence, at least one copy of each of which is not base paired to the template;
d) digesting the first product with the first and second restriction endonucleases and releasing at least one first product fragment having a double-stranded region that comprises the target region, ande) ligating a first hairpin adapter to one end of the first product fragment and ligating a second hairpin adapter to the other end of the first product fragment, thereby producing at least one first circular progeny nucleic acid.
2 Assignments
0 Petitions
Accused Products
Abstract
Methods for amplifying a desired target region of a nucleic acid through rolling circle amplification with a strand-displacing polymerase are provided. Concatameric hairpin products are resolved with endonuclease digestion, and the resulting amplified product hairpins or fragments can be circularized and employed as templates in a subsequent round of amplification. The methods are effective for targeted amplification of even highly repetitive sequences. Compositions, kits, and systems related to or useful in the methods are also described.
-
Citations
21 Claims
-
1. A method of amplifying a nucleic acid target region, the method comprising:
-
a) providing a nucleic acid template, which template is a circular nucleic acid having a double-stranded central region and two single-stranded hairpin end regions;
wherein the double-stranded central region comprises a first polynucleotide sequence and a second polynucleotide sequence complementary to the first polynucleotide sequence, which first and second polynucleotide sequences collectively comprise the target region, a recognition site for a first restriction endonuclease, and a recognition site for a second restriction endonuclease, which recognition sites flank the target region; and
wherein the circular nucleic acid comprises a first primer binding sequence;b) binding a first primer to the first primer binding sequence; c) performing polymerase-mediated template-directed primer extension of the first primer with a polymerase comprising strand displacement activity, thereby producing a first nucleic acid product comprising at least two copies of the first polynucleotide sequence and the second polynucleotide sequence, at least one copy of each of which is not base paired to the template; d) digesting the first product with the first and second restriction endonucleases and releasing at least one first product fragment having a double-stranded region that comprises the target region, and e) ligating a first hairpin adapter to one end of the first product fragment and ligating a second hairpin adapter to the other end of the first product fragment, thereby producing at least one first circular progeny nucleic acid. - View Dependent Claims (2, 3, 4, 5, 16, 17, 18, 19, 20, 21)
-
-
6. A method of amplifying a nucleic acid target region, the method comprising:
-
a) providing a nucleic acid template, which template is a circular nucleic acid having a double-stranded central region and two single-stranded hairpin end regions;
wherein the double-stranded central region comprises a first polynucleotide sequence and a second polynucleotide sequence complementary to the first polynucleotide sequence, which first and second polynucleotide sequences collectively comprise the target region and a recognition site for a first site-specific endonuclease; and
wherein the circular nucleic acid comprises a first primer binding sequence;b) binding a first primer to the first primer binding sequence; c) performing polymerase-mediated template-directed primer extension of the first primer with a polymerase comprising strand displacement activity, thereby producing a first nucleic acid product comprising at least two copies of the first polynucleotide sequence and the second polynucleotide sequence, at least one copy of each of which is not base paired to the template; d) cutting the first product with the first endonuclease and releasing at least one first product hairpin having at least one single-stranded hairpin end region, a double-stranded region that comprises the target region, a free 5′
terminus, and a free 3′
terminus; ande) circularizing the at least one first product hairpin, thereby producing at least one first circular progeny nucleic acid. - View Dependent Claims (7, 8, 9, 10, 11, 12, 13, 14, 15)
-
Specification