Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study

Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study

The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.

Hydrogen bonding between hydrides of the upper-right part of the periodic table

One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. The strength of the bond depends on numerous factors, among them the electronegativity of participating atoms. In this work we calculated the strength of hydrogen bonds between hydrides of the upper-right part of the periodic table (C, N, O, F, P, S, Cl, As, Se, Br) using quantum-chemical methods. The aim was to determine what influences the strength of strong and weak hydrogen bonds in simple hydrides. Various relationships were checked. A relation between the strength of the bond and the electronegativity of the participating atoms was found. We also observed a correlation between the strength of hydrogen bonds and the inter-atomic distances, along with the dependence on the charge transfer on the atom of the donor. We also report characteristic geometries of different dimers.

Design of fMet-tRNA and calculation of its bonding properties by quantum mechanics

It is generally accepted that initiation of protein synthesis in Escherichia coli starts with formyl-methionine, directed by the codons of AUG or GUG. In one case, reinitiating on the mRNA of amber mutants of UUG is used as the initiation codon. Early studies indeed showed that the triplets AUG, GUG, and UUG are the most effective in stimulating fMet-tRNA binding to ribosomes in vitro. We study the bonding properties of fMet-tRNA. The structure was optimized at the Hartree-Fock (HF) level of theory. We performed nonempirical quantum mechanical calculations at the HF and BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and water solvent at temperature of 310 K. Finally, we employed the density functional theory (DFT) and HF to calculate nuclear magnetic resonance spectra and infrared spectra.

Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine

Substituted Watson-Crick guanine-cytosine (GC) base pairs were recently shown to yield robust three-state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson-Crick adenine-thymine (AT) base pairs? We have theoretically analyzed AT pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X=NH(-), NH(2), NH(3) (+) (N series), O(-), OH or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. Thus, we explore the trend in geometrical shape and hydrogen bond strengths in AT pairs along a series of stepwise protonations of the substituents. Introducing a charge on the substituents leads to substantial and characteristic changes in the individual hydrogen bond lengths when compared to the neutral AT pair. However, the trends along the series of negative, neutral, and positive substituents are less systematic and less pronounced than for GC. In certain instances, internal proton transfer from thymine to adenine occurs. Our results suggest that AT is a less suitable candidate than GC in the quest for chemically controlled nanoswitches.