Weakly Bound Water Molecules Shorten Single-Stranded DNA

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.

Deforming DNA: From Physics to Biology

“…[31] A more recent study, which compared stretching in aqueous and nonpolar solvents, has also found evidence for extra stabilization associated with water bridges. [33] It is interesting to add that when polymers, including single-stranded DNA, are strongly stretched (with forces in the nanonewton range), bond angles can strongly deform. This implies using quantum chemical treatments to describe their behavior and also opens up the fascinating prospect of mechanically modulating chemical reactions.…”

Supramolecular Chemistry and Mechanochemistry of Macromolecules: Recent Advances by Single-Molecule Force Spectroscopy

“…8a). It was found that there was a clear difference in the middle force regime, but no deviation in the low and high force regimes [31].…”

“…The biological function of DNA is closely related to the stability and the integrality of the double strands [63], and the mechanical stability of double-stranded DNA (dsDNA) strongly depends on the ambient conditions. Recently, Cui et al investigated the important role of water in determining or stabilizing the supramolecular structure of DNA by SMFS [31,32].…”

“…7a, b). Because the length of a repeating unit of ssDNA is 0.59 nm, QM-FJC is a structure relevant model [31,32]. The inability to fit the experimental data to the QM-WLC model (Fig.…”

“…It is known that both ssDNA and dsDNA chains are hydrated in the aqueous solution. Because the bases are hidden in the duplex, one dsDNA chain has less binding sites with water than that of the sum of [31] the two corresponding ssDNA chains [68]. Therefore, before the self-organization from ssDNA to dsDNA, a partial dehydration process of ssDNA should occur.…”