According to one embodiment, there is provided a nucleic acid primer set that amplifies a ZEBOV gene. An F1 sequence includes at least 13 consecutive bases included in SEQ ID NO: 31 or 64. An F2 sequence includes at least 13 bases included in SEQ ID NO: 62 or 63. An F3 sequence includes at least 13 bases included in SEQ ID NO: 29, 36, 38, 55, 56, 57, 58, 59, 60, 61 or 61. A B1c sequence includes at least 13 bases included in SEQ ID NO: 68, 69, 70, 71, 72, 73, 74 or 75. A B2c sequence includes at least 13 bases included in SEQ ID NO: 65 or 66. A B3c sequence includes at least 13 bases included in SEQ ID NO: 34, 67, 82 or 83.

According to one embodiment, there is provided a nucleic acid primer set that amplifies a ZEBOV gene. An F1 sequence includes at least 13 consecutive bases included in SEQ ID NO: 31 or 64. An F2 sequence includes at least 13 bases included in SEQ ID NO: 62 or 63. An F3 sequence includes at least 13 bases included in SEQ ID NO: 29, 36, 38, 55, 56, 57, 58, 59, 60, 61 or 61. A B1c sequence includes at least 13 bases included in SEQ ID NO: 68, 69, 70, 71, 72, 73, 74 or 75. A B2c sequence includes at least 13 bases included in SEQ ID NO: 65 or 66. A B3c sequence includes at least 13 bases included in SEQ ID NO: 34, 67, 82 or 83.

[Problem] To provide a method for detecting a nucleic acid (such as DNA and RNA) under isothermal conditions, in particular a method by which a short-chain nucleic acid can be directly detected. [Solution] A method for detecting a target nucleic acid in a sample of the present invention comprises: (a) a step of preparing a first oligonucleotide which comprises, in the direction from 5′ to 3′, a first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence complementary to the target nucleic acid; (b) a step of carrying out a nucleic acid amplification reaction using the target nucleic acid contained in the sample as a primer in the presence of an endonuclease which recognizes the endonuclease recognition site that is used in a nicking reaction; and (c) a step of detecting an oligonucleotide which is obtained by the nucleic acid amplification reaction and comprises a sequence complementary to the first arbitrary sequence.

[Problem] To provide a method for detecting a nucleic acid (such as DNA and RNA) under isothermal conditions, in particular a method by which a short-chain nucleic acid can be directly detected. [Solution] A method for detecting a target nucleic acid in a sample of the present invention comprises: (a) a step of preparing a first oligonucleotide which comprises, in the direction from 5′ to 3′, a first arbitrary sequence, an endonuclease recognition site that is used in a nicking reaction, and a sequence complementary to the target nucleic acid; (b) a step of carrying out a nucleic acid amplification reaction using the target nucleic acid contained in the sample as a primer in the presence of an endonuclease which recognizes the endonuclease recognition site that is used in a nicking reaction; and (c) a step of detecting an oligonucleotide which is obtained by the nucleic acid amplification reaction and comprises a sequence complementary to the first arbitrary sequence.

There is disclosed a kit for detecting a single strand target nucleotide sequence comprising: at least one first nucleic acid probe from 10 to 14 bases, to the 5′ end of which at least one fluorophore is bound; at least one second nucleic acid probe from 35 to 50 bases, comprising, from the 5′ to the 3′ end: a first segment having a nucleotide sequence complementary to the first nucleic acid probe, at least one quencher, and a second segment having a nucleotide sequence complementary to at least part of the target nucleotide sequence, wherein the following relation is met:
|ΔG hybr.target3−probe2|>|ΔG hybr.probe1−probe2|.

There is disclosed a kit for detecting a single strand target nucleotide sequence comprising: at least one first nucleic acid probe from 10 to 14 bases, to the 5′ end of which at least one fluorophore is bound; at least one second nucleic acid probe from 35 to 50 bases, comprising, from the 5′ to the 3′ end: a first segment having a nucleotide sequence complementary to the first nucleic acid probe, at least one quencher, and a second segment having a nucleotide sequence complementary to at least part of the target nucleotide sequence, wherein the following relation is met:
|ΔG hybr.target3−probe2|>|ΔG hybr.probe1−probe2|.

The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.

The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.

A method for identifying a nucleotide in a template nucleic acid by (a) providing a plurality of primer-template nucleic acid hybrids, wherein the primers have an extendable 3′ end; (b) contacting the plurality with: (i) blocked nucleotides to produce a first subset of the primer-template nucleic acid hybrids that include a blocked nucleotide at the 3′ end, and (ii) a ternary complex inhibitor to produce a second subset of the primer-template nucleic acid hybrids that include a ternary complex inhibitor; (c) forming ternary complexes that each include a polymerase, a primer-template nucleic acid hybrid of the first subset, and a cognate nucleotide; and (d) detecting the ternary complexes, thereby identifying a nucleotide in the template nucleic acid.

A method for investigating intra- and/or intermolecular interactions involving RNA is provided. The method includes a) synthesizing a RNA/DNA heteroduplex (RDH) comprising a RNA strand of interest paired to a DNA strand; b) binding a first end of the DNA strand and a corresponding first end of the RNA strand to a first element of a nanoscale manipulating device, and a second end of the DNA strand to a second element of the nanoscale manipulating device, leaving a second end of the RNA strand free; c) moving the first and second elements of the manipulating device apart from each other, stretching the DNA strand and causing the RNA strand to peel off the heteroduplex; and d) moving the first and second elements of the nanoscale manipulating device towards each other, allowing the DNA strand to relax and causing the RNA strand to bind again to it. Measurement of a force-displacement relationship during steps c) and d) provides information on intra- and/or intermolecular interactions involving the RNA strand. Also provided is an apparatus for carrying out the method.