Rolling circle amplification assay for nucleic acid analysis
First Claim
1. A plurality of padlock probes, each probe comprising:
- a nucleic acid sequence, the sequence including two target hybridization end regions on opposing ends of each padlock probe, the target hybridization end regions complementary to a target hybridization region on a single strand target nucleic acid sequence, wherein the target hybridization end regions may hybridize to the single strand target nucleic acid sequence to form a probe/target duplex, wherein each pair of target hybridization end regions are proximate to each other when hybridized to the target nucleic acid strand; and
a stuffer region located between said target hybridization end regions, said stuffer region having a primer complementary sequence and a restriction site complementary sequence, wherein each of said padlock probes has the same primer complementary sequence and restriction site complementary sequence;
wherein each probe may act as a template for production of tandem sequence DNA by ligation and amplification of the probe if a specific target nucleic sequence is present;
wherein tandem sequence DNA produced from each template padlock probe may be segmented into a set of non-tandem detection fragments of a discrete length, wherein the discrete length of detection fragments produced from each padlock probe differs in length from any detection fragment produced from any other padlock probe in the plurality of padlock probes.
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Abstract
Method and reagents for analysis of nucleic acid sequences is disclosed. In this method a plurality of padlock probes is provided. Each padlock probe may hybridize to a locus on a target nucleic acid under hybridization conditions. If a targeted variant is present at the locus, the padlock probe may be ligated to form an amplification target circle. The amplification target circle acts as a template for production of tandem-sequence DNA. The tandem-sequence DNA may then be digested into non-tandem detection fragments which are subsequently separated and detected. The plurality of padlock probes are designed such that ligation of the probes, amplification of the target circle, and digestion of the tandem-sequence DNA subsequently produced, and detection may all be effected with the same set of reagents. Each probe targets a unique locus variant on the target nucleic acid sequence and produces a detection fragment that may be distinguished from detection fragments produced from other padlock probe in the plurality of padlock probes by using a fragment analysis detector.
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Citations
28 Claims
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1. A plurality of padlock probes, each probe comprising:
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a nucleic acid sequence, the sequence including two target hybridization end regions on opposing ends of each padlock probe, the target hybridization end regions complementary to a target hybridization region on a single strand target nucleic acid sequence, wherein the target hybridization end regions may hybridize to the single strand target nucleic acid sequence to form a probe/target duplex, wherein each pair of target hybridization end regions are proximate to each other when hybridized to the target nucleic acid strand; and
a stuffer region located between said target hybridization end regions, said stuffer region having a primer complementary sequence and a restriction site complementary sequence, wherein each of said padlock probes has the same primer complementary sequence and restriction site complementary sequence;
wherein each probe may act as a template for production of tandem sequence DNA by ligation and amplification of the probe if a specific target nucleic sequence is present;
wherein tandem sequence DNA produced from each template padlock probe may be segmented into a set of non-tandem detection fragments of a discrete length, wherein the discrete length of detection fragments produced from each padlock probe differs in length from any detection fragment produced from any other padlock probe in the plurality of padlock probes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method for high throughput analysis of genetic loci, the method comprising the steps:
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a) providing a target nucleic acid sample;
b) combining the target nucleic acid sample with a plurality of padlock probes to form padlock probe/target hybrids, wherein each probe is a nucleic acid sequence including, two target hybridization end regions on opposing ends of the padlock probe, the target hybridization end regions complementary to a target hybridization region on a single strand target nucleic acid sequence, wherein the target hybridization end regions hybridize to the single strand target nucleic acid sequence to form a probe/target duplex, wherein each pair of target hybridization end regions are proximate to each other when hybridized to the target nucleic acid strand, and a stuffer region located between said target hybridization end regions, said stuffer region having a primer complementary sequence and restriction site complementary sequence, wherein each of said plurality of said padlock probes has the same primer complementary sequence and restriction site complementary sequence;
c) mixing ligase with the padlock probe/target nucleic acid duplex to form a ligation mixture, and incubating the ligation mixture under conditions that promote ligation of the padlock probes to form amplification target circles;
d) mixing a primer which is complementary to said primer complementary sequence with the amplification target circles, and incubating the primer/amplification target circles mixture under conditions that promote hybridization between the amplification target circles and the primers;
e) mixing a DNA polymerase with the primer/amplification target circles mixture, to produce a rolling circle replication mixture, and incubating the rolling circle amplification mixture under conditions that promote rolling circle replication of the amplification target circles, wherein replication of the amplification target circles results in the formation of tandem sequence DNA;
f) cutting each tandem sequence DNA at the generated restriction enzyme site into sets of non-tandem DNA fragments of a discrete length, wherein each amplification target circle produces tandem sequence DNA that is cut into sets of non-tandem DNA fragments of a unique discrete size;
g) separating by length said sets of non-tandem DNA fragments; and
h) detecting said sets of separated non-tandem DNA fragments. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification