Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering

Adelene Y. L. Sim, Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
Phys. Rev. E 86, 021901 – Published 1 August 2012
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Abstract

Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8–100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.

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  • Received 9 May 2012

DOI:https://doi.org/10.1103/PhysRevE.86.021901

©2012 American Physical Society

Authors & Affiliations

Adelene Y. L. Sim1, Jan Lipfert2, Daniel Herschlag3, and Sebastian Doniach1,4,5

  • 1Applied Physics Department, Stanford University, Stanford, California 94305, USA
  • 2Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
  • 3Biochemistry Department, Stanford University, Stanford, California 94305, USA
  • 4Physics Department, Stanford University, Stanford, California 94305, USA
  • 5Biophyics Program, Stanford University, Stanford, California 94305, USA

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Vol. 86, Iss. 2 — August 2012

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