Origin of overstretching transitions in single-stranded nucleic acids.

Journal Article (Journal Article)

We combined single-molecule force spectroscopy with nuclear magnetic resonance measurements and molecular mechanics simulations to examine overstretching transitions in single-stranded nucleic acids. In single-stranded DNA and single-stranded RNA there is a low-force transition that involves unwinding of the helical structure, along with base unstacking. We determined that the high-force transition that occurs in polydeoxyadenylic acid single-stranded DNA is caused by the cooperative forced flipping of the dihedral angle formed between four atoms, O5'-C5'-C4'-C3' (γ torsion), in the nucleic acid backbone within the canonical B-type helix. The γ torsion also flips under force in A-type helices, where the helix is shorter and wider as compared to the B-type helix, but this transition is less cooperative than in the B type and does not generate a high-force plateau in the force spectrums of A-type helices. We find that a similar high-force transition can be induced in polyadenylic acid single-stranded RNA by urea, presumably due to disrupting the intramolecular hydrogen bonding in the backbone. We hypothesize that a pronounced high-force transition observed for B-type helices of double stranded DNA also involves a cooperative flip of the γ torsion. These observations suggest new fundamental relationships between the canonical structures of single-and double-stranded DNA and the mechanism of their molecular elasticity.

Full Text

Duke Authors

Cited Authors

  • Scholl, ZN; Rabbi, M; Lee, D; Manson, L; S-Gracz, H; Marszalek, PE

Published Date

  • November 2013

Published In

Volume / Issue

  • 111 / 18

Start / End Page

  • 188302 -

PubMed ID

  • 24237568

Electronic International Standard Serial Number (EISSN)

  • 1079-7114

International Standard Serial Number (ISSN)

  • 0031-9007

Digital Object Identifier (DOI)

  • 10.1103/physrevlett.111.188302


  • eng