Final Report Summary - QUANTUMBIOLOGY (DNA replication and biomolecular recognition)
The 'DNA replication and biomolecular recognition' (QUANTUMBIOLOGY) project - financed through a Marie Curie European Reintegration Grant (Call: FP7-PEOPLE-2007-2-2-ERG) - has been executed from 1 May 2009 till 29 February 2012 by Dr Jordi Poater at the Universitat de Girona (Girona, Spain). The project was proposed on the fact that deoxyribonucleic acid (DNA) replication is at the core of life, and even though an important number of studies aims to unravel the mechanism of this complex biochemical reaction, it is still incompletely understood. The main objectives proposed in the application were to understand the electronic nature of molecular recognition in DNA base pairs, and more importantly, to understand the mechanism of the highly accurate, enzyme-assisted DNA replication, in particular the role of hydrogen bonding and steric factors.
With respect to this latter, the most relevant results were published last year ('Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, pi-stacking and solvent effects', Chemical Communications 2011, 47, 7326-7328). In that work, using state-of-the-art dispersion-corrected density functional theory (vide infra), we computationally explored the magnitude of, and interplay between some of the various factors that, in concert, yield the observed fidelity of DNA replication. This was the first high-level quantum chemical study on DNA replication covering not only the formation of DNA base pairs but also pi-pi stacking interactions in a model system consisting of four DNA bases. Our theoretical analyses focused on the factors relevant to chemical primer extension, i.e. in the absence of DNA polymerase. Investigations on chemical primer extension, both computational and experimental, are relevant not only for understanding the factors that determine the intrinsic (polymerase-free) fidelity but in particular also for understanding the role of DNA polymerase because they reveal how replication fidelity is affected in the absence of the enzyme. Related to the most important results presented, we showed, among others, that the intrinsic affinity (i.e. in the absence of an enzyme) of the template-primer complex to select the correct natural DNA base derives from the cooperative action of hydrogen-bonding patterns and solvent effects. On the other hand, stacking interactions play a less pronounced role for the selectivity but they are important for the overall stability.
In addition, we have theoretically analysed a complete series of Watson-Crick and mismatched DNA base pairs, both in vacuo and in solution ('Hydrogen bonds and solvent effects on DNA base pairs and mismatches', Computational and Theoretical Chemistry 2012, accepted for publication). Solvation causes a weakening of the hydrogen bond lengths between the DNA bases due to their lengthening caused by the stabilisation of the lone pairs involved in these bonds. We have also proven that chlorouracil can mimic the behaviour of thymine, and thus perfectly incorporate into a DNA strain, as recently found experimentally with Escherichia coli. Moreover, through quantitative bond analyses in the framework of Kohn-Sham density functional theory (DFT) we have confirmed how the contribution of occupied-virtual orbital interactions to the hydrogen bonds is of the same order of magnitude as electrostatic interactions.
The research above has benefitted from the experience of Dr Poater in the analysis of electronic structure of both organic and inorganic systems, with especial emphasis in the corresponding aromaticity of the compounds, or in chemical reactivity. This knowledge has been transferred to the present project. Thus, the present project also includes the analysis of adenine and guanine quartets, the aromaticity analysis of hydroxypyrones or other heteroaomatic rings linke in DNA basis, the reactivity of silyl substituted compounds or the study of relevant chelating ligands for Alzheimer's disease.
The research subjects treated in the present project have been proven to be extremely relevant at medical research level, and invariably raises new issues of concern of society. It is important to mention the interdisciplinary scope of this research, which has integrated from computational physical chemistry to computational biochemistry and computational life sciences as well. To achieve interdisciplinary needs, the project has benefitted from both the experience of Dr Poater as a postdoc in the Vrije Universiteit Amsterdam (Marie Curie Fellow 2006-07), as well as the research carried out in the host organisation.
Overall, the research carried out by Dr Poater along these three years under the European Reintegration Grant has conducted to 19 peer-reviewed publications in important journals, the delivery of 6 conferences and the presentation of 3 posters in different international meetings. In addition, Dr Poater has supervised two Doctor of Philosophy (PhD) theses. This is translated in a researcher with 76 publications that have received almost 1 800 citations, with an H-index of 23, and who appears as 'Scientist' at the Essentials Science Indicators of the ISI Web of Knowledge as being top 1 % cited researcher.
With respect to this latter, the most relevant results were published last year ('Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, pi-stacking and solvent effects', Chemical Communications 2011, 47, 7326-7328). In that work, using state-of-the-art dispersion-corrected density functional theory (vide infra), we computationally explored the magnitude of, and interplay between some of the various factors that, in concert, yield the observed fidelity of DNA replication. This was the first high-level quantum chemical study on DNA replication covering not only the formation of DNA base pairs but also pi-pi stacking interactions in a model system consisting of four DNA bases. Our theoretical analyses focused on the factors relevant to chemical primer extension, i.e. in the absence of DNA polymerase. Investigations on chemical primer extension, both computational and experimental, are relevant not only for understanding the factors that determine the intrinsic (polymerase-free) fidelity but in particular also for understanding the role of DNA polymerase because they reveal how replication fidelity is affected in the absence of the enzyme. Related to the most important results presented, we showed, among others, that the intrinsic affinity (i.e. in the absence of an enzyme) of the template-primer complex to select the correct natural DNA base derives from the cooperative action of hydrogen-bonding patterns and solvent effects. On the other hand, stacking interactions play a less pronounced role for the selectivity but they are important for the overall stability.
In addition, we have theoretically analysed a complete series of Watson-Crick and mismatched DNA base pairs, both in vacuo and in solution ('Hydrogen bonds and solvent effects on DNA base pairs and mismatches', Computational and Theoretical Chemistry 2012, accepted for publication). Solvation causes a weakening of the hydrogen bond lengths between the DNA bases due to their lengthening caused by the stabilisation of the lone pairs involved in these bonds. We have also proven that chlorouracil can mimic the behaviour of thymine, and thus perfectly incorporate into a DNA strain, as recently found experimentally with Escherichia coli. Moreover, through quantitative bond analyses in the framework of Kohn-Sham density functional theory (DFT) we have confirmed how the contribution of occupied-virtual orbital interactions to the hydrogen bonds is of the same order of magnitude as electrostatic interactions.
The research above has benefitted from the experience of Dr Poater in the analysis of electronic structure of both organic and inorganic systems, with especial emphasis in the corresponding aromaticity of the compounds, or in chemical reactivity. This knowledge has been transferred to the present project. Thus, the present project also includes the analysis of adenine and guanine quartets, the aromaticity analysis of hydroxypyrones or other heteroaomatic rings linke in DNA basis, the reactivity of silyl substituted compounds or the study of relevant chelating ligands for Alzheimer's disease.
The research subjects treated in the present project have been proven to be extremely relevant at medical research level, and invariably raises new issues of concern of society. It is important to mention the interdisciplinary scope of this research, which has integrated from computational physical chemistry to computational biochemistry and computational life sciences as well. To achieve interdisciplinary needs, the project has benefitted from both the experience of Dr Poater as a postdoc in the Vrije Universiteit Amsterdam (Marie Curie Fellow 2006-07), as well as the research carried out in the host organisation.
Overall, the research carried out by Dr Poater along these three years under the European Reintegration Grant has conducted to 19 peer-reviewed publications in important journals, the delivery of 6 conferences and the presentation of 3 posters in different international meetings. In addition, Dr Poater has supervised two Doctor of Philosophy (PhD) theses. This is translated in a researcher with 76 publications that have received almost 1 800 citations, with an H-index of 23, and who appears as 'Scientist' at the Essentials Science Indicators of the ISI Web of Knowledge as being top 1 % cited researcher.