Influence of Base Composition, Base Sequence, and Duplex Structure on DNA Hydration: Apparent Molar Volumes and Apparent Molar Adiabatic Compressibilities of Synthetic and Natural DNA Duplexes at 25.degree.C

Abstract

Using high-precision densitometric and ultrasonic measurements, we have determined, at 25 degrees C, the apparent molar volumes, phi V, and the apparent molar compressibilities, phi KS, of five natural and three synthetic B-form DNA duplexes with varying base compositions and base sequences. We find that phi V ranges from 152.0 to 186.6 cm3 mol-1, while phi KS ranges from -73.0 x 10(-4) to -32.6 x 10(-4) cm3 mol-1 bar-1. We interpret these data in terms of DNA hydration which, by the definition employed in this work, refers to those water molecules whose density and compressibility differ from those of bulk water due to interactions with the DNA solute. This definition implies that hydration depends not just on the quantity but also on the quality of the solvent molecules perturbed by the solute. In fact, we find that the number of water molecules perturbed by the DNA duplexes (the quantity of water in their hydration shells) is approximately the same for all of the B-form double helixes studied, while the quality of this water differs as measured by its density and compressibility, thereby yielding differences in the overall hydration properties. Specifically, we find a linear relationship between the density and the coefficient of adiabatic compressibility, beta Sh, of water in the hydration shell of the DNA duplexes, with the range of values for beta Sh being only 65-80% of the value of bulk water.(ABSTRACT TRUNCATED AT 250 WORDS)

Thermodynamic relations for DNA phase transitions

“…Different studies looked at the effect of hydrostatic pressure, e.g., the stability of hairpins, B-DNA, the stalling of transcription elongation complexes [56][57][58][59][60][61]. The melting temperature T c seems to depend on the hydrostatic pressure, P , only at a very high P .…”

“…Besides the conjugate pairs (T, S), and (g, x), there could be other types of external forces, e.g., isotropic hydrostatic or osmotic pressure affecting the volume of the polymer, and a stretching force (f ) that distorts and elongates the chain. Although there are evidences of hydrostatic or osmotic pressure affecting protein-DNA interaction [56][57][58][59][60][61], there is only a very weak effect on the melting of DNA. In contrast, a stretching force may lead to an "overstretching" transition where the length of the DNA increases by a factor of 1.7 [8,17,25,26].…”

A molecular simulation picture of DNA hydration around A- and B-DNA

“…24 From such studies the following picture emerges: In general, water in the hydration layer around DNA is less mobile 61,62 with residence times of up to several hundred ps (at 298 K) 63,64 at some hydration sites. At the same time the density of water around DNA is increased over bulk water 65 since the tetrahedral water coordination in bulk is replaced by more compact geometries as a consequence of hydrogen bonding to the DNA molecule instead. 66 -68 A common measure for the hydration shell around DNA is the number of water molecules that display different properties from bulk water.…”

A simple low-cost simulation protocol for approximate localization of structural water molecules in DNA oligonucleotides

“…Using high-precision densiometric and ultrasonic measurements, Chalikian and co-workers 4 determined the apparent molar volumes and compressibilities of DNA oligomers with varying base compositions and base sequences, and reached some general conclusions about the hydration of B-DNA duplexes: the CG base-pairs are more hydrated than the AT base-pairs and mixed base sequences are less hydrated than either CG or AT B-DNA homopolymers. In agreement with this experimental study, we observed in most studies, independently of base sequence or duplex conformation, the superior hydration of the CG base-pairs in relation to the AT base-pairs; our simulations also showed a higher hydration of the CG and AT pairs of nucleotides in homopolymeric B-DNAs in comparison to B-DNAs with mixed sequences, suggesting that our protocol is able to discriminate B-DNA homoligomers from B-DNA heteroligomers (see Table 5).…”

“…Many ligands, such as amino acids, drugs or even other nucleotides, interact with nucleic acids either through a water bridge or by replacing structural water molecules bound to specific sites or, most commonly, by both types of contacts. 1 Although the preferential hydration sites of nucleic bases are quite conservative according to comparative crystallographic data, 2 different nucleotide sequences, 3 base compositions, 4 and conformations 5 affect hydration in a very complex manner. In order to understand the function of this type of biomolecule in the cell environment or even inside cell organelles, it is important to investigate nucleic acid hydration sites more extensively, including the dynamics of the first hydration shells, the energetics of water binding, and the role of hydration and ions in nucleic acid conformations and ligand recognition-binding processes as well.…”