Enhanced fluorescent detection of nucleic acid based on hairpin DNA-assisted toehold-mediated strand displacement reaction

Abstract

A new hairpin DNA regulated strand displacement strategy for detection of nucleic acid is proposed via the conformational transformation of hairpin DNA. In this entropy-driven signal amplification strategy, we introduce a hairpin structure (single strand B) into a duplex strand which makes the entire strand displacement process easier and faster when the target DNA exists. The strand migration process of displacing the single strand B with the target is a process of constantly displacing bases. As the number of displaced bases increases, the stem ends of the B strand tend to be in a flexible state. When the number of bases is large enough, the two parts of the stem in B strand will undergo complementary base pairing. Therefore, in the subsequent displacement process, target DNA will displace strand B avoiding completely displacing all the bases at the end of the B strand. Regardless of thermodynamics or kinetics, the formation of this hairpin structure has a certain impetus for the displacement reaction. Since the entire reaction process is truly enzyme-free, simple to operate and low in cost, and thus is expected to provide a novel strategy for clinical analysis.