The invention provides a
nucleic acid compound purification method, a
nucleic acid compound purification kit and application. The
nucleic acid compound comprises a
polynucleotide fragment and a
protein combined on the
polynucleotide fragment, or the nucleic acid compound is a
polynucleotide fragment of which at least part of
nucleotide is modified so as to lose the complementary
pairing capability of nucleic acid or nucleic acid analogues. Immobilizing a nucleic acid or a
nucleic acid analogue which contains a
protein binding sequence on the polynucleotide fragment or a
nucleotide which is complementary to the
nucleotide before the modified nucleotide is modified to obtain a
solid phase capture element; and S2, incubating the nucleic acid compound to be purified with the
solid phase capture element, and capturing and removing polynucleotide fragments which are not self-bonded with eggs or are not successfully modified by the
solid phase capture element through base
complementation to obtain the purified nucleic acid compound. The purity of the
linker compound purified through sequence
complementation is purer than that of the compound which is not purified through the purification method, and a
library constructed by taking the
linker compound as the
raw material can obtain a better sequencing effect.