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In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical-computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.

Here, we present the theoretical-computational modeling of the oxidation properties of four DNA nucleosides and nucleotides and a set of dinucleotides in solutions. Our estimates of the vertical ionization energies and reduction potentials, close to the corresponding experimental data, show that an accurate calculation of the molecular electronic properties in solutions requires a proper treatment of the effect of the environment. In particular, we found that the effect of the environment is to stabilize the oxidized state of the nucleobases resulting in a remarkable reduction-up to 6.6 eV-of the energy with respect to the gas phase. Our estimates of the aqueous and gas-phase vertical ionization energies, in good agreement with photoelectron spectroscopy experiments, also show that the effect on the reduction potential of the phosphate group and of the additional nucleotide in dinucleotides is rather limited.

The high DNA specificity of homing endonucleases makes them a powerful protein scaffold to engineer enzymes for genome manipulation. Understanding their molecular recognition of DNA is an important prerequisite to generate engineered enzymes able to cleave DNA in specific desired genome sites. Protein-DNA recognition studies have been mostly focused on specific direct contacts between amino acid side chains and bases to redesign the binding interface. However, the important role of indirect readout in the central region of the target DNA of the homing endonuclease I-CreI suggested that indirect readout may play a key role in the redesign of protein-DNA interactions. The sequences of the I-CreI central substrate region, 2NN, along with the adjacent 5NNN, are key for substrate cleavage. Here, we analyse the mechanism of target discrimination at the 5NNN region by the I-CreI protein, revealing its critical role in the location and occupancy of the catalytic metal ions, which is crucial for cleavage. Our data highlight the importance of indirect readout for target DNA cleavage, thus aiding I-CreI engineering when targeting new DNA sequences.

The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity., (© 2016 Wiley Periodicals, Inc.)

A combined theoretical-experimental study of the hyperchromic effect as occurring in the denaturation of a double stranded polyA-polyT is presented. Our theoretical/computational procedure allows us to reproduce the essential features of the experimental spectra and to characterize those molecular interactions responsible for the changes in the UV absorbance. We found that although excitonic intrastrand interactions strongly affect the absorbance, they are almost fully maintained in the single-stranded DNA. Our data indicate that hyperchromic effect originates from the higher delocalization of the excitonic states in the denaturated DNA with respect to the double-stranded conformation.

Homing endonucleases represent protein scaffolds that provide powerful tools for genome manipulation, as these enzymes possess a very low frequency of DNA cleavage in eukaryotic genomes due to their high specificity. The basis of protein-DNA recognition must be understood to generate tailored enzymes that target the DNA at sites of interest. Protein-DNA interaction engineering of homing endonucleases has demonstrated the potential of these approaches to create new specific instruments to target genes for inactivation or repair. Protein-DNA interface studies have been focused mostly on specific contacts between amino acid side chains and bases to redesign the binding interface. However, it has been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a homing endonuclease (I-CreI), which do not show specific protein-DNA interactions, is not devoid of content information. Here, we analyze the mechanism of target discrimination in this substrate region by the I-CreI protein, determining how it can occur independently of the specific protein-DNA interactions. Our data suggest the important role of indirect readout in this substrate region, opening the possibility for a fully rational search of new target sequences, thus improving the development of redesigned enzymes for therapeutic and biotechnological applications.

Here, we present the theoretical–computational modelling of the free energy barrier of the phosphodiester bond cleavage as occurring in the mesophilic variant of endonuclease I-DmoI bound to DNA. Our data, obtained by means of hybrid quantum mechanics/molecular mechanics approach, indicate that the influence of the environment, exerted by the enzyme, the solvent and the DNA, shifts the mechanism towards a more dissociative reaction pathway, compared to the unperturbed reaction. The perturbation of the environment results in an earlier transition state of hydrolysis, i.e. more similar to reagents. By such an approach, we estimate that the enzyme lowers the phosphorus–oxygen bond break free energy barrier of about 7.9 kcal/mol compared to the gas phase, which turns out to be consistent with experimental data. Such an approach points out the importance of an extended and accurate treatment of the environmental effects in the modelling of chemical reactions and confirms the reliability of our procedure in the modelling of important biochemical processes at a limited computational cost. [ABSTRACT FROM AUTHOR]

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported. [ABSTRACT FROM AUTHOR]