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J Am Chem Soc. 2006 May 24;128(20):6636-9.

Weakly bound water molecules shorten single-stranded DNA.

Author information

  • 1Lehrstuhl für Angewandte Physik and Centre for Nanoscience, Ludwig-Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany. cuisx@scu.edu.cn

Abstract

In this paper, we measure the single chain elasticity of an oligomer single-stranded DNA (ssDNA) in both aqueous and nonaqueous, apolar liquid environments by AFM-based single molecule force spectroscopy. We find a marked deviation between the force-extension relations recorded for the two conditions. This difference is attributed to the additional energy required to break the H-bond-directed water bridges around the ssDNA chain in aqueous solutions, which are nonexistent in organic solvents. The results obtained in 8 M guanidine-HCl solution provide more evidence that water bridges around ssDNA originate the observed deviation. On the basis of the results obtained by an ab initio quantum mechanics calculation, a parameter-free freely rotating chain model is proposed. We find that this model is in perfect agreement with the experimental force-extension curve obtained in organic solvents, which further corroborates our assumption. On the basis of the experimental results, it is suggested that the weak H-bonding between ssDNA and water molecules may be a precondition for stable double-stranded DNA to exist in water.

PMID:
16704264
[PubMed - indexed for MEDLINE]
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