Method for detecting a nucleic acid involving the production of a triggering RNA and transcription amplification
First Claim
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1. A method for detecting the presence of an assayed nucleic acid sequence in a sample, comprising the steps of:
- (a) reacting the sample with a detection ensemble comprising;
a first DNA molecule having a promoter sequence at the 3'"'"' end and a 5'"'"' end sequence which is complementary to the 5'"'"' end portion of the assayed nucleic acid sequence;
a second DNA molecule comprising a single-stranded 3'"'"' end sequence being complementary to a 3'"'"' end portion of the assayed nucleic acid sequence, and further comprising a sequence, at the 5'"'"' end which can be transcribed into a triggering RNA sequence capable of initiating a reaction in an appropriate transcription system in which an RNA molecule having a signal RNA sequence is being produced;
wherein the 3'"'"' end sequence of the second DNA molecule and the 5'"'"' end sequence of the first DNA are complementary to at least part of said assayed nucleic acid sequence leaving an intermediary portion in the assayed nucleic acid having no complementary counterpart in either the first or the second DNA molecules, in which case the detection ensemble further comprisesa third DNA sequence being complementary to said intermediate portion;
(b) incubating under conditions to allow hybridization of said first DNA molecule and said second DNA molecule and were present also said third DNA molecule with said assayed nucleic acid sequence, and optionally adding a ligase to allow ligation of adjacent ends of said first, second and third DNA molecules;
(c) adding transcription reagents comprising a DNA dependent-RNA polymerase and RNA nucleotides and incubating under conditions to allow the formation of RNA transcripts having said triggering RNA sequence;
(d) contacting the RNA transcripts with an RNA amplification ensemble, a priori, lacking the triggering RNA, in which a triggering RNA sequence induces formation of RNA molecules containing the signal RNA sequence; and
(e) detecting the presence of said signal RNA sequence, positive results indicating the presence of said assayed nucleic acid sequence in said sample.
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Abstract
A method for detecting the presence of an assayed nucleic acid in a sample is an essentially two-stage procedure. In a first stage the sample is reacted in a manner which gives rise to the production of a triggering RNA where the sample contains the assays sequence. In the second stage, the reaction product is incubated under appropriate conditions with an amplification reagent ensemble whereby, in the presence of triggering RNA a large amount of a nucleic product is obtained. The detection of this product thus indicates the presence of the assayed sequence in the sample.
149 Citations
21 Claims
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1. A method for detecting the presence of an assayed nucleic acid sequence in a sample, comprising the steps of:
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(a) reacting the sample with a detection ensemble comprising; a first DNA molecule having a promoter sequence at the 3'"'"' end and a 5'"'"' end sequence which is complementary to the 5'"'"' end portion of the assayed nucleic acid sequence; a second DNA molecule comprising a single-stranded 3'"'"' end sequence being complementary to a 3'"'"' end portion of the assayed nucleic acid sequence, and further comprising a sequence, at the 5'"'"' end which can be transcribed into a triggering RNA sequence capable of initiating a reaction in an appropriate transcription system in which an RNA molecule having a signal RNA sequence is being produced;
wherein the 3'"'"' end sequence of the second DNA molecule and the 5'"'"' end sequence of the first DNA are complementary to at least part of said assayed nucleic acid sequence leaving an intermediary portion in the assayed nucleic acid having no complementary counterpart in either the first or the second DNA molecules, in which case the detection ensemble further comprisesa third DNA sequence being complementary to said intermediate portion; (b) incubating under conditions to allow hybridization of said first DNA molecule and said second DNA molecule and were present also said third DNA molecule with said assayed nucleic acid sequence, and optionally adding a ligase to allow ligation of adjacent ends of said first, second and third DNA molecules; (c) adding transcription reagents comprising a DNA dependent-RNA polymerase and RNA nucleotides and incubating under conditions to allow the formation of RNA transcripts having said triggering RNA sequence; (d) contacting the RNA transcripts with an RNA amplification ensemble, a priori, lacking the triggering RNA, in which a triggering RNA sequence induces formation of RNA molecules containing the signal RNA sequence; and (e) detecting the presence of said signal RNA sequence, positive results indicating the presence of said assayed nucleic acid sequence in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 11, 12, 13, 19)
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9. A method for detecting the presence of an assayed nucleic acid sequence in a sample, comprising the steps of:
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(a) reacting the sample with a detection ensemble comprising; a single-stranded DNA molecule having from its 3'"'"' to its 5'"'"' end three sequence portions linked to one another comprising a first arbitrary portion, a second arbitrary portion of 1-5 bases long, and a 5'"'"' end sequence which is complementary to the 5'"'"' end portion of the assayed nucleic acid sequence; a second DNA molecule comprising a single-stranded 3'"'"' end sequence being complementary to a 3'"'"' end portion of the assayed nucleic acid sequence, and further comprising a third arbitrary portion which third arbitrary portion is double-stranded; (b) incubating under conditions to allow hybridization of the assayed nucleic acid sequence to said single-stranded DNA molecule and to said second DNA molecule to produce DNA hybrids; (c) raising the temperature to a point in which only essentially perfectly matched hybrids formed in step (b) remain hybridized while all other hybrids in which the individual strands do not perfectly match to one another are melted; (d) adding a blocker DNA molecule, being a single-stranded DNA molecule comprising at its 5'"'"' end a sequence complementary to said second arbitrary portion and a sequence, at its 3'"'"' end complementary to the 5'"'"' end portion to the assayed DNA, providing conditions allowing hybridization of said blocker molecule with fee said single-stranded DNA molecule; (e) adding a promoter DNA molecule, comprising a double-stranded functional promoter and a sequence complementary to the first and second arbitrary portions attached to the non-template strand of the promoter, and providing conditions for hybridization, whereby a hybrid comprising the assayed DNA sequence, said promoter DNA molecule, said single-stranded DNA and said second DNA molecule is obtained from which an RNA transcript can be transcribed; (f) adding transcription reagents comprising a DNA-dependent RNA polymerase and RNA nucleotides and incubating under conditions to allow the formation of RNA transcripts having a triggering RNA sequence capable of initiating a reaction in an appropriate transcription system in which an RNA molecule having a signal RNA sequence is being produced; (g) contacting the RNA transcripts with an RNA amplification ensemble in which the triggering RNA sequence induces formation of RNA molecules containing the signal RNA sequence; and (h) detecting the presence of said signal RNA sequence, positive results indicating the presence of said assayed nucleic acid sequence in said sample. - View Dependent Claims (10)
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14. A kit for use in detecting a nucleic acid sequence in a sample comprising:
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a first DNA molecule comprising a double stranded promotor at its 3'"'"' end and a single stranded sequence complementary to a 5'"'"' end portion of the assayed nucleic acid sequence; a second DNA molecule comprising a single-stranded sequence complementary to a 3'"'"' end portion of the assayed nucleic acid sequence, and further comprising a sequence which can be transcribed into a detectable RNA molecule; and an RNA polymerase for transcribing said first and second oligonucleiotides; wherein said detectable RNA molecule comprises (a) a self-replicating signal molecule, (b) the transcripts of said first and second DNA molecules, and (c) a stop sequence to prevent replication of the transcripts of said first and second DNA molecules. - View Dependent Claims (15, 16, 20)
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17. Assay components for selectively amplifying an RNA molecule in a sample, said components comprising:
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a first promoter having a single stranded sequence at the 3'"'"' end of its non-coding strand adapted to hybridize to the 3'"'"' end of said RNA molecule; a second promoter having a single stranded sequence at the 3'"'"' end of its non-coding strand adapted to hybridize to the 3'"'"' end of the transcript of said RNA molecule; ribozymes adapted to cleave any portion of a first or second promoter which is transcribed; and
,RNA polymerase adapted to recognize said first and second promoters and transcribe the sequences downstream thereof. - View Dependent Claims (18, 21)
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Specification