Inversion probes
First Claim
1. A hybridization probe for detecting a target polynucleotide, comprising:
- (a) a loop comprising a target-complementary sequence of bases joined to a loop backbone, said target-complementary sequence of bases extending from a first boundary to a second boundary;
(b) a first arm joined to said target-complementary sequence of bases at said first boundary through a first arm linkage, said first arm comprising a first arm sequence of bases joined to a first arm backbone;
(c) a second arm joined to said target-complementary sequence of bases at said second boundary through a second arm linkage, said second arm comprising a second arm sequence of bases joined to a second arm backbone;
wherein both of said first arm linkage and said second arm linkage are inversion linkages different from each other, said hybridization probe being a dual inversion probe, each of said inversion linkages optionally including a non-nucleotide linker, and(d) at least one detectable label joined to said loop, said first arm, said second arm or, said non-nucleotide linker,wherein said first arm and said second arm interact with each other in the absence of said target polynucleotide to form a stem duplex.
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Accused Products
Abstract
Unitary hybridization probes having stem-and-loop structures, wherein the stem portion of the structure comprises a pair of interactive arms that are substantially prevented from interacting with target polynucleotides. One arm of the invented parallel-stem hybridization probe has a backbone polarity opposite that of the target-complementary loop sequence of the probe. Rather than interacting in an antiparallel fashion, the arms of parallel-stem hybridization probes interact in a parallel fashion. The arms of the invented dual inversion probes interact in a conventional antiparallel fashion, but have backbone polarities opposite that of the target-complementary loop portion of the probe. Arm portions of the inversion probes do not substantially contribute to sequence-dependent stabilization of probe:target hybrids. Incorporating inversion linkages into the structures of these probes dramatically simplifies the process of designing stem-and-loop hybridization probes.
43 Citations
19 Claims
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1. A hybridization probe for detecting a target polynucleotide, comprising:
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(a) a loop comprising a target-complementary sequence of bases joined to a loop backbone, said target-complementary sequence of bases extending from a first boundary to a second boundary; (b) a first arm joined to said target-complementary sequence of bases at said first boundary through a first arm linkage, said first arm comprising a first arm sequence of bases joined to a first arm backbone; (c) a second arm joined to said target-complementary sequence of bases at said second boundary through a second arm linkage, said second arm comprising a second arm sequence of bases joined to a second arm backbone; wherein both of said first arm linkage and said second arm linkage are inversion linkages different from each other, said hybridization probe being a dual inversion probe, each of said inversion linkages optionally including a non-nucleotide linker, and (d) at least one detectable label joined to said loop, said first arm, said second arm or, said non-nucleotide linker, wherein said first arm and said second arm interact with each other in the absence of said target polynucleotide to form a stem duplex. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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Specification