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, Sebastian Doniach

Applied Physics Department, Stanford University, Stanford, California 94305, USA.

Physical review. E, Statistical, nonlinear, and soft matter physics 2012 Aug

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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.

Citation

Adelene Y L Sim, Jan Lipfert, Daniel Herschlag, Sebastian Doniach. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Physical review. E, Statistical, nonlinear, and soft matter physics. 2012 Aug;86(2 Pt 1):021901