Method for analyzing target nucleic acid, kit, and analyzer

A method for analyzing a target nucleic acid in a sample, the method comprising the step of:

• analyzing the target nucleic acid in the sample by bringing the sample into contact with a label and with a primer that can hybridize to the target nucleic acid,
• wherein the primer is immobilized on a solid phase, and the primer is a nucleic acid molecule comprising at least one of structures represented by the following formulae (16), (16b), (17), (17b), (18), and (18b),
• the label is covalently bound to the primer so as to be part of the primer,
• the label is a fluorescent dye moiety that exhibits an exciton effect, and the label does not emit light when the primer does not hybridize to the target nucleic acid, whereas the label emits light when the primer has hybridized to the target nucleic acid,
• the analysis is carried out by detecting light emission from the label caused by hybridization of the primer with the target nucleic acid,
• the target nucleic acid that has hybridized with the primer is removed by washing, the primer is hybridized again with another target nucleic acid, and the analysis is carried out again by detecting light emission from the label,
• the primer is hybridized to the target nucleic acid by bringing the primer into contact with the sample, thereby causing an amplification reaction of the target nucleic acid, and
• the analysis of the target nucleic acid is carried out by further measuring the degree of amplification of the target nucleic acid in the amplification reaction over time:
• where in the formulae (16), (16b), (17), (17b), (18), and (18b),
• B is an atomic group having a natural nucleobase (adenine, guanine, cytosine, thymine, or uracil) skeleton or an artificial nucleobase skeleton,
• E is:
• (i) an atomic group having a deoxyribose skeleton, a ribose skeleton, or a structure derived from either one of them;
• or
• (ii) an atomic group having a peptide structure or a peptoid structure,
• Z11 and Z12 are each the fluorescent dye moiety that exhibits an exciton effect, and may be identical to or different from each other,
• L1, L2, and L3 are each a linker (a linking atom or a linking atomic group), the main chain length (the number of main chain atoms) thereof is arbitrary, L1, L2, and L3 each may or may not contain each of C, N, O, S, P, and Si in the main chain, L1, L2, and L3 each may or may not contain each of a single bond, a double bond, a triple bond, an amide bond, an ester bond, a disulfide bond, an imino group, an ether bond, a thioether bond, and a thioester bond in the main chain, and L1, L2, and L3 may be identical to or different from each other,
• D is CR, N, P, P═O, B, or SiR, and R is a hydrogen atom, an alkyl group, or an arbitrary substituent, and
• b is a single bond, a double bond, or a triple bond,
• or alternatively,
• in the formulae (16) and (16b), L1 and L2 are each the linker, L3, D, and b may not be present, and L1 and L2 may be bonded directly to B, provided that:
• in the formulae (16), (17), and (18), E is an atomic group described in the item (i), and at least one O atom in a phosphoric acid linkage may be substituted with an S atom;
• in the formulae (16b), (17b), and (18b), E is an atomic group described in the item (ii);
• and
• in the formulae (17) and (17b), the respective Bs may be identical to or different from each other, and the respective Es may be identical to or different from each other.