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Nucleic Acids Res. 2017 Apr 20;45(7):3932-3943. doi: 10.1093/nar/gkx140.

The impact of base stacking on the conformations and electrostatics of single-stranded DNA.

Author information

1
School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
2
Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
3
Department of Physics, Gettysburg College, Gettysburg, PA 17325, USA.

Abstract

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems.

PMID:
28334825
PMCID:
PMC5397193
DOI:
10.1093/nar/gkx140
[Indexed for MEDLINE]
Free PMC Article

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