Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG) d(GCGCTTAAGCGC): Monte Carlo computer simulation
P. S. SUBRAMANIAN, G. RAVISHANKER, AND D. L. BEVERIDGE
Chemistry Department, Hall-Atwater Laboratories, Wesleyan University, Middletown, CT 06457 Communicated by Max Tishler, October 8, 1987
A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo computer simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG)- d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indicative of discrete salvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 43594363] for both A-T and C-G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.
Proc. Nati. Acad. Sci. USA Vol. 85, pp. 1836-1840, March 1988
The DNA molecule is now well known to exist in a variety of conformational families, both right-handed (A, B, C, D, etc.) and left-handed (Z,, Z,,) helical duplexes (1). The relative stability of the various conformational forms of DNA is observed to be highly sensitive to environmental effectsi. e., hydration and ionic strength. Hydration, dehydration, and reorganization of the ion atmosphere are also important in the thermodynamics of protein binding to DNA and in drug-DNA interactions (2). Whereas a considerable literature on the environmental effects on DNA exists (1), our knowledge of detail at the molecular level is fairly sparse. Our principal source of information to date comes from the positions of ordered water molecules observed in x-ray crystallography of DNA oligonucleotides (3). Particularly, the dodecamer duplex d(CGCGAATFCGCG)-d(GCGCTTAAGCGC) has been found by Dickerson and coworkers (4-6) to crystallize as a hydrate in the B-form of DNA, which corresponds closely to the Watson-Crick double helix and features a distinct parallel groove motif, alternating wide (major) with narrow (minor). Although the amount of water that turned out to be crystallographically ordered is small (-25%), interesting and provocative features of the hydration emerged, as discussed in detail by Drew and Dickerson (ref. 7, but see also ref. 8). In particular, an ordered water structure was discovered in the minor groove of the AATT region. It has been indicated that this so-called "spine of hydration" was specific to A-T-rich tracts, where the N-3 atom of adenine and the O2 atom of thymine are readily available as hydrogen bond acceptors in interactions with water molecules. The N2 donor group on guanine has been thought to disrupt the spine, but hydration of the COG region of the dodecamer was blocked in the crystal by a spermine ion and by helix-helix packing and thus was not observed. The spine of hydration has been subsequently considered (9) to be a central stabilizing feature of the B-DNA structure, and that disruption of the spine as by dehydration would effect a conformational change to the A- or Z-form, depending on sequence and other environmental conditions. Sequences rich in A-T base pairs are known to preferentially stabilize B-form DNA (10), and the spine of hydration has provided a possible explanation (9). Further evidence for the stabilizing nature of the spine comes from an experiment based on CD spectra, whereby an A-form calf thymus DNA in complex with the minor groove binding molecule netropsin is pulled into a B-like form (11). Thermodynamic binding studies by Breslauer and coworkers (12, 13) on netropsin binding to the poly[d(A-T)]-poly[d(A-T)] duplex revealed a positive binding entropy that has been associated (14) with the Dickerson water spine. However, Marky and Breslauer (15) have found a similar binding entropy for formation between netropsin and the poly[d(G-C)].poly[d(G-C)] duplex and suggest alternative interpretations of the entropy data involving non-spine-hydration shells less sensitive to sequence or binding-induced release of counterions.