Dependence of the hydration shell structure in the minor groove of the DNA double helix on the groove width as revealed by monte carlo simulation

Abstract

The hydration shell of several conformations of the polynucleotides poly(dA).poly(dT), poly(dA).poly(dU), and poly(dA-dI).poly(dT-dC) has been simulated using the Monte Carlo method (Metropolis sampling). Calculations have shown that the structure of the hydration shell of the minor groove greatly depends on its width. In conformations with a narrowed minor groove, the first layer of the hydration shell of this groove has only one molecule per nucleotide pair that forms H bonds with purine N3 of one pair and pyrimidine O2 of the next pair. The second layer of the hydration shell of such conformations contains molecules that form H bonds between two adjacent molecules of the first layer. The probability of formation of hydration spine is about 20% while the bridges of the first layer are formed with a probability of about 70%. In the first layer of the minor groove of the B-DNA conformation with wide minor groove there are approximately two water molecules per base pair that form H bonds with purine N3 or pyrimidine O2 and with the sugar ring oxygen of the adjacent nucleotide. The probability of simultaneous H bonding of a water molecule with N3 (or O2) and O of sugar ring is about 30%. The results of simulation suggest that hydration spine proposed for the narrowed minor groove of oligonucleotide crystals [H. R. Drew, and R. E. Dickerson (1981) Journal of Molecular Biology, Vol. 151, pp. 535-556] can be formed in fibers of poly(dA).poly(dT), poly(dA).poly(dU), and poly(dA-dI).poly(dT-dC) as well as in DNA fragments of these sequences in solution.(ABSTRACT TRUNCATED AT 250 WORDS)

Hydration of a B–DNA fragment in the method of atom–atom correlation functions with the reference interaction site model approximation

“…We realize that the current molecular model is limited in many respects since the DNA molecule was electro-neutral here due to a parametric account of the phosphate screening. Nevertheless, the existing experience of calculations of DNA hydration by various methods indicates that this approximation appears to be quite adequate in the region restricted by the first coordination sphere 5,6,29 . The method used by us can be extended to include free mobile ions in the model and thus to study macromolecules in ionic solutions.…”

“…There is a large number of reviews devoted to the problem of biopolymer hydration 3 . One of common approaches to these difficult problems is based on computer simulations using either Molecular Dynamics or Monte Carlo methods [4][5][6] . The main limitation of these direct simulation techniques is in the huge computational expense for reaching the equilibrium state even for comparatively small molecular weights.…”

Dimerization Energetics of DNA Minor Groove Binders

“…In this work, to determine the H-bonds of MGB ligands with the aqueous medium, we calculated the average number of water molecules that form hydrogen bonds with hydrophilic atoms (N, O, S) in the examined molecules (the hydration index solv ) within last 40 ps of MD. A hydrogen bond was assumed to emerge if the distance between the electronegative atoms of a ligand and the oxygen or hydrogen atoms of water molecules did not exceed 3.2 or 2.4Å, respectively [26]. The energy of H-bond with water was evaluated on the basis of the empirical expression…”

Computational investigation of the role of hydration in nucleic acid structure and function

“…Monte Carlo simulations were performed for the following systems: (1) 64 water molecules in a cube with the edge of 12.4 A and periodic boundary conditions [17,24]; (2) Watson-Crick A:U and G:C pairs [18,19] and mispairs [23] with 25 water molecules in cylinders 9 A in diameter and 4 8, high; (3) helical stacks of 6 base pairs arranged as in a certain conformation of double helix and 180 water molecules (pyrimidine N1 and purine N9 atoms were methylated) with helical periodic boundary conditions along the helical axis [19,20]; (4) B-DNA duplex fragments of 6 nucleotide pairs and 180 water molecules with helical periodic boundary conditions along the helical axis [21,22,25]. For three-and foursystems, dimensions of the volumes accessible to water molecules are determined by parameters of double helices.…”