Methods and compositions for universal detection of nucleic acids
First Claim
1. An analyte nucleic acid detection reaction mixture, used to detect a target nucleic acid subsequence of interest, the mixture comprising:
- an analyte nucleic acid comprising the target nucleic acid subsequence of interest, the analyte nucleic acid further comprising first, second and third tag sequences, the second tag sequence being located between the first and third tag sequences; and
both the first and the second tag sequences are universal tag sequences;
a first universal primer comprising a first tag complement subsequence that is complementary to the first tag sequence, a subsequence that comprises the second tag sequence, and a detectable label; and
,a second universal primer comprising a sequence that comprises the third tag sequence.
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Abstract
Provided are methods and compositions for detecting the presence or amount of one or more target nucleic acids in a sample. Methods of the present invention include linking universal nucleic acid segments into a single molecule in a linking reaction dependent on a target nucleic acid of interest. A variety of universal segment linking strategies are provided, including preamplification by polymerase chain reaction, ligation-based strategies, reverse transcription and linear polymerase extension. Linking the universal segments into a single molecule generates a tagged target nucleic acid which is detected in a manner dependent on an intramolecular interaction between one universal segment and a second portion of the tagged target nucleic acid. In certain embodiments, the intramolecular interaction includes the formation of a hairpin having a stem between a universal segment at one end of the tagged target nucleic acid and a second universal segment at the opposite end of the tagged target nucleic acid. A variety of detection formats are provided, including solution-phase and surface-based formats. The methods and compositions are well-suited for highly multiplexed nucleic acid detection, and are applicable for the detection of any target nucleic acid of interest in both research and clinical settings.
10 Citations
29 Claims
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1. An analyte nucleic acid detection reaction mixture, used to detect a target nucleic acid subsequence of interest, the mixture comprising:
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an analyte nucleic acid comprising the target nucleic acid subsequence of interest, the analyte nucleic acid further comprising first, second and third tag sequences, the second tag sequence being located between the first and third tag sequences; and
both the first and the second tag sequences are universal tag sequences;a first universal primer comprising a first tag complement subsequence that is complementary to the first tag sequence, a subsequence that comprises the second tag sequence, and a detectable label; and
,a second universal primer comprising a sequence that comprises the third tag sequence. - 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, 29)
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Specification