Nucleic acid melting under small tension

Melting of double-stranded nucleic acid such as DNA is a fundamental part of several biological processes. Double-stranded nucleic acid in vivo is subject to small tensile forces induced by thermal fluctuations and active processes. Although these forces in general accelerate bond dissociation, recent experimental and theoretical studies suggest a counterintuitive, stabilizing effect of force on the DNA duplex (roll-over effect). To investigate the effect of ~pN axial force on nucleic acid duplex stability, we developed a novel single-molecule force assay, which utilizes the intrinsic bending rigidity of DNA to exert weak pulling forces down to the entropic force limit. Combining this assay with single-molecule FRET, we measured the melting rates of short (~10 nt) nucleic acid duplexes (DNA-DNA or DNA-RNA) in the presence of weak tension. Interestingly, some duplexes melted more slowly with ~pN tension than without it, indicative of the roll-over effect, while other duplexes showed monotonically faster melting with increasing tension. Our findings indicate that the transition state of duplex melting is structurally diverse, depending on the nucleotide composition and sequence, and suggest that genome stability could be locally modulated in a nontrivial manner due to tension.