Method of analyzing a target nucleic acid sequence

A method of determining the sequence of a target nucleic acid comprising

• providing a microarray comprising a substrate on which a plurality of probe nucleic acids are immobilized, wherein the sequence of the plurality of probe nucleic acids are known;
• providing a labeled target nucleic acid containing a sequence capable of forming a stem and loop structure at an end of the target nucleic acid;
• hybridizing the labeled target nucleic acid and the probe nucleic acids, thereby forming hybridized products;
• incubating the hybridized products in an elongation solution, thereby elongating nucleotide sequence from a 3′-OH present in the hybridized region of the hybridized products;
• incubating the resultant products in a ligation solution to ligate the incubated probe nucleic acid to the incubated labeled target nucleic acid;
• and
• measuring signals generated by the ligated products;
• comparing a signal intensity from a hybridization product between a first probe nucleic acid and the labeled target nucleic acid with the intensity from a hybridization product between a second probe nucleic acid and a target nucleic acid;
• wherein if the signal generated from a hybridization product between a first probe nucleic acid and the labeled target nucleic acid is stronger than a signal generated by a hybridization product between a second probe nucleic acid and a target nucleic acid, it is determined that the labeled target nucleic acid contains a sequence that is perfectly complementary to the first probe nucleic acid.