Weakly bound water molecules shorten single-stranded DNA.
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.
Cui
Shuxun
S
Lehrstuhl für Angewandte Physik and Centre for Nanoscience, Ludwig-Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany. cuisx@scu.edu.cn
Albrecht
Christian
C
Kühner
Ferdinand
F
Gaub
Hermann E
HE
D000433:1-Propanol; D001555:Benzene Derivatives / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004548:Elasticity; D019791:Guanidine; D006860:Hydrogen Bonding; D018625:Microscopy, Atomic Force; D011789:Quantum Theory; D012997:Solvents; D014867:Water / Q000737:chemistry*
D001555:Benzene Derivatives; D004277:DNA, Single-Stranded; D012997:Solvents; D014867:Water; D000433:1-Propanol; D019791:Guanidine