Hydration changes upon DNA folding studied by osmotic stress experiments

Abstract

The thermal stability of nucleic acid structures is perturbed under the conditions that mimic the intracellular environment, typically rich in inert components and under osmotic stress. We now describe the thermodynamic stability of DNA oligonucleotide structures in the presence of high background concentrations of neutral cosolutes. Small cosolutes destabilize the basepair structures, and the DNA structures consisting of the same nearest-neighbor composition show similar thermodynamic parameters in the presence of various types of cosolutes. The osmotic stress experiments reveal that water binding to flexible loops, unstable mismatches, and an abasic site upon DNA folding are almost negligible, whereas the binding to stable mismatch pairs is significant. The studies using the basepair-mimic nucleosides and the peptide nucleic acid suggest that the sugar-phosphate backbone and the integrity of the basepair conformation make important contributions to the binding of water molecules to the DNA bases and helical grooves. The study of the DNA hydration provides the basis for understanding and predicting nucleic acid structures in nonaqueous solvent systems.

Figure 1

(A) DNA hairpin sets of 1a and 1b, and 2a and 2b, consisting of the same nearest-neighbor composition and the loop sequence. (B) Comparison of the values of ΔG° of the DNA hairpins 1a and 1b (upper) and 2a and 2b (lower) having the same nearest-neighbor composition in the absence and presence of cosolutes at 20 wt%. The ΔG° was calculated at 37°C, and the error value was determined from the data obtained using different DNA concentrations. (C) Plots of the hairpin stability ΔG° of 1a (circles) and 2a (triangles) versus the logarithm of the solution water activity changed by adding PEG200. (D) DNA sequences and the abbreviations used in Table 1 that are not given in the panel A. The sequence of 5a forms the hairpin structure with a hexa(ethylene glycol) loop represented by hEG.

Figure 2

(A) Comparison of the Δn_w numbers for the DNA structure formations consisting of the same basepairs. The data for the double-stranded duplex obtained in i), 1 M NaCl, ii), 10 mM MgCl₂, and iii), 1 mM [Co(NH₃)₆]Cl₃ are also compared. For the experiments using MgCl₂ and [Co(NH₃)₆]Cl₃, the buffer solutions containing 25 mM HEPES (pH 7.0) and 0.1 mM Na₂EDTA were used. (B) The Δn_w numbers for the 11-mer duplexes having different basepairs in the middle and the 9-mer duplex without trinucleotide interactions in the middle of the 11-mer sequence. F and X indicate the tetrahydrofuran abasic site and C^naph, respectively. (C) Two types of conformations of the tandem G/A mismatch formed in a DNA sequence 5′-pyrimidine-GA-purine-3′ (type I) and 5′-purine-GA-pyrimidine-3′ (type II). The Δn_w numbers of the DNA duplexes forming the type I and type II conformations and those forming corresponding fully matched duplexes or the single G/A mismatch sites are compared.

Figure 3

(A) Structure of the PNA monomer unit with the N-(2-aminoethyl)glycine backbone. (B) Four types of duplexes formed by the nonself-complementary PNA and DNA strands. (C) Changes in ΔG° (ΔΔG°) of the four types of duplexes by adding PEG; PNA duplex (squares), PNA/DNA duplex (diamonds), DNA/PNA duplex (triangles), and DNA duplex (circles).