Nucleic acid hairpin probes and uses thereof
First Claim
1. A method for detecting a target nucleotide sequence in a sample, which method comprises the steps of:
- a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a stein region comprising a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region tat is complementary to a target nucleotide sequence to be detected;
b) contacting said probe provided in step a) with a sample containing or suspected of containing said target nucleotide sequence under conditions that favor intermolecular hybridization between said probe and said target nucleotide sequence over intramolecular hybridization of said probe itself, whereby said contacting breaks said intramolecular hybridization of said probe itself by dissociating said double stranded segment of said probe and forms a first intermolecular hybrid between said target and a region consisting of at least a portion of one stand of said stem and at least a portion of said loop within said probe that is complementary to said target nucleotide sequence; and
c) assessing said intermolecular hybrid formed in step b), wherein said assessing is effected by addition of a secondary probe tat specifically hybridizes with at least a portion of said intermolecular hybrid, thereby forming a secondary intermolecular hybrid formed between said secondary probe and said first intermolecular hybrid wherein said detection of said secondary intermolecular hybrid indicates the presence and/or amount of said target nucleotide sequence in said sample.
1 Assignment
0 Petitions
Accused Products
Abstract
This invention relates generally to nucleic acid hybridization analysis. More specifically, an oligonucleotide probe for hybridization analysis is provided, which probe comprises a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be hybridized with. Arrays comprising the hairpin probes immobilized on a solid support and methods for nucleic acid hybridization analysis using the probes or array of immobilized probes are also provided. Methods for transcribing and/or amplifying a probe DNA sequence using a hairpin probe are further provided.
97 Citations
28 Claims
-
1. A method for detecting a target nucleotide sequence in a sample, which method comprises the steps of:
-
a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a stein region comprising a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region tat is complementary to a target nucleotide sequence to be detected;
b) contacting said probe provided in step a) with a sample containing or suspected of containing said target nucleotide sequence under conditions that favor intermolecular hybridization between said probe and said target nucleotide sequence over intramolecular hybridization of said probe itself, whereby said contacting breaks said intramolecular hybridization of said probe itself by dissociating said double stranded segment of said probe and forms a first intermolecular hybrid between said target and a region consisting of at least a portion of one stand of said stem and at least a portion of said loop within said probe that is complementary to said target nucleotide sequence; and
c) assessing said intermolecular hybrid formed in step b), wherein said assessing is effected by addition of a secondary probe tat specifically hybridizes with at least a portion of said intermolecular hybrid, thereby forming a secondary intermolecular hybrid formed between said secondary probe and said first intermolecular hybrid wherein said detection of said secondary intermolecular hybrid indicates the presence and/or amount of said target nucleotide sequence in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
-
Specification