Fluorescent labeled single-stranded nucleic acid and use thereof

A labeled single-stranded nucleic acid comprising at least two fluorescent atomic group pairs that exhibit an exciton effect within each fluorescent atomic group pair, wherein

• an emission peak wavelength of a fluorescent atomic group pair J is shorter than an excitation peak wavelength of a fluorescent atomic group pair K,
• the fluorescent atomic group pair J and the fluorescent atomic group pair K are both cations,
• the fluorescent atomic group pairs J and K have a Förster resonance energy transfer (FRET) effect between each other,
• each of a base having the fluorescent atomic group pair J or K that exhibits an exciton effect has a structure represented by the following formula (16), (16b), (17), or (17b):
• where in the formulae (16), (16b), (17), and (17b),
• Z11 and Z12 are each a fluorescent atomic group that exhibits an exciton effect, and may be identical to or different from each other,
• Z11 and Z12 constitute a fluorescent atomic group pair,
• B is an atomic group having a natural nucleobase skeleton or an artificial nucleobase skeleton, wherein the natural nucleobase is adenine, guanine, cytosine, thymine or uracil,
• 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,
• L1, L2, and L3 are each a linking atom or a linking atomic group, having any number of main chain atoms, each may or may not contain each of C, N, O, S, P, and Si in the main chain, 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 may be identical to or different from each other,
• D is CR, N, P, P═O, B, or SiR where R is a hydrogen atom, an alkyl group, or any 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 a linker, L3, D, and b may not be present, and L1 and L2 may be bound directly to B, provided that:
• in the formulae (16) and (17), 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) and (17b), E is an atomic group described in the item (ii);
• 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;
• and
• the base having the fluorescent atomic group pair J and the base having the fluorescent atomic group pair K are contained in the labeled single-stranded nucleic acid at a distance at which there are from 1 to 5 bases between the base having the fluorescent atomic group pair J and the base having the fluorescent atomic group pair K.