Theoretical investigation of the hydrogen atom transfer in the hydrated A–T base pair

Modeling the action of environment on proton tunneling in the adenine-thymine base pair

Effect of environment coupling on the quantum-biological phenomenon of proton tunneling in the hydrogen bonds of the adenine-thymine base pair in DNA was modeled within the framework of quantum statistics and perturbation theory. A number of important thermodynamic indicators including partition function, free energy, and entropy were then calculated and examined. The proton was then assumed to be subject to an attraction represented by a double-well potential energy surface with a small asymmetry, which was considered as the perturbation introduced to the system. The action of environment manifested itself in the form of a global minimum in the free energy curve, as an implicit implication of the tendency of the system toward randomness and disorder, at which no spontaneous change such as quantum tunneling will accordingly occur. Furthermore, assuming the free energy to be in a close neighborhood of its minimum truly explained the smallness of the contribution of environment coupling to the tunneling probability reported in the literature based on the fact that the closer the free energy to its minimum, the less the transition probability to this point.

Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.

Quantum mechanical investigation of G-quartet systems of DNA

Minima of the electric field and positions of K⁺ and Na⁺ (zero of the x-coordinate is the center of the cavity).

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled.

Possible use of BN-modified fullerene as a nano-biosensor to detect adenine–thymine Watson–Crick base pair in mutagenic tautomeric form: Theoretical approach

The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu 2+ cation and their interactions with BN doped fullerene ( C 58 BN ). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu 2+ complexes.

Modelling proton tunnelling in the adenine–thymine base pair

Environment-assisted quantum tunnelling is unlikely to play a significant role in adenine–thymine tautomerisation.

Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study

Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.

Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion

The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.