Dna fragment joining detecting method and kit thereof

A method for distinguishing an alternative splicing event, comprising:

• (a) probing a target nucleic acid with a split probe, comprising:
• (i) a first split probe being complementary to the 3′ end of a partner DNA fragment, a second split probe being complementary to the 5′ end of a target DNA fragment, and/or a third split probe being complementary to a third DNA fragment, wherein a gap of the first and second split probes targeting sites on the target nucleic acid is within 0-80 bp;
• or
• (ii) a first split probe being complementary to the 5′ end of a partner DNA fragment, a second split probe being complementary to the 3′ end of a target DNA fragment, and/or a third split probe being complementary to a third DNA fragment, wherein a gap of the first and second split probes targeting sites on the target nucleic acid is within 0-80 bp;
• (b) detecting a signal that reflects a binding between the split probe and the target nucleic acid;
• (c) determining
• (i) the partner DNA fragment as an upstream DNA fragment and/or the target DNA fragment as a downstream DNA fragment through confirming the signal based on the first split probe binding to the 3′ end of the partner DNA fragment and/or the second split probe binding to the 5′ end of the target DNA fragment;
• (ii) the partner DNA fragment as a downstream DNA fragment and/or the target DNA fragment as an upstream DNA fragment through confirming the signal based on the first split probe binding to the 5′ end of the partner DNA fragment and/or the second split probe binding to the 3′ end of the target DNA fragment, or
• (iii) the third DNA fragment that is joined with the partner DNA fragment and the target DNA fragment through confirming the signal based on the third split probe binding to the third DNA fragment;
• and
• (d) comparing whether a length of the target nucleic acid is identical to a reference sequence.

A kit for detecting a sample with a DNA fragment joining event and/or an alternative splicing event, comprising:

• (a) a set of oligonucleotides;
• (b) a split probe, comprising:
• (i) a first split probe being complementary to the 3′ end of a partner DNA fragment, a second split probe being complementary to the 5′ end of a target DNA fragment, and/or a third split probe being complementary to a third DNA fragment, wherein a gap of the first and second split probes targeting sites on a target nucleic acid is within 0-80 bp;
• or
• (ii) a first split probe being complementary to the 5′ end of a partner DNA fragment, a second split probe being complementary to the 3′ end of a target DNA fragment, and/or a third split probe being complementary to a third DNA fragment, wherein a gap of the first and second split probes targeting sites on a target nucleic acid is within 0-80 bp;
• and
• (c) a probe hybridization assay for detecting a split probe hybridization signal, for which comprises dyes, chemiluminescent dyes, fluorescent molecule, radioisotopes, spin labels, enzymes, haptens, quantum dots, beads, aminohexyls, and pyrenes.