Unit:
Department of PhysicsLibrary of the School of Science
Dissertation committee:
1. Κωνσταντίνος Σιμσερίδης, Αναπληρωτής Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ (επιβλέπων)
2. Σπυρίδων Γαρδέλης, Αναπληρωτής Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ (μέλος Tριμελούς Συμβουλευτικής Επιτροπής)
3. Ιωάννης Λελίδης, Αναπληρωτής Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ (μέλος Tριμελούς Συμβουλευτικής Επιτροπής)
4. Βλάσιος Λυκοδήμος, Αναπληρωτής Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ
5. Νικόλαος Στεφάνου, Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ
6. Δημήτριος Φραντζεσκάκης, Καθηγητής, Τμήμα Φυσικής ΕΚΠΑ
7. Rosa Di Felice, Professor, Physics and Astronomy and Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
Original Title:
Electronic structure of aperiodic and natural nucleic acid segments and influence of mutations in charge transfer and transport properties
Translated title:
Electronic structure of aperiodic and natural nucleic acid segments and influence of mutations in charge transfer and transport properties
Summary:
Today, the investigation of biomolecules' structure and properties - especially these of the nucleic acids (DNA, RNA) - is emerged as a high significance issue. The electronic structure of DNA attracts considerable interest among a broad spectrum of interdisciplinary scientists and engineers. Its charge transfer and transport properties are being studied with respect not only to its biological functions and its significance, e.g., in carcinogenesis and mutagenesis, but also to its potential applications in molecular electronics.
This research aims to the study of the electronic structure of nucleic acid bases and similar almost planar organic molecules, as well as the investigation of charge transfer and charge transport properties along B-DNA sequences, by employing a simple and broadly used theoretical method, i.e., Tight-Binding (TB). It also discusses the possibility of using charge transport as a diagnostic tool in discrimination between pathogenic and nonpathogenic mutations.
The semi-empirical Linear Combination of Atomic Orbitals (LCAO) method is introduced to calculate the ionization and excitation energies of nucleic acid bases and similar biologically important molecules as well as assemblies of DNA bases, along with a novel parameterization employing all valence orbitals.
Then, we outline the TB method for charge transfer of an extra carrier along DNA, and we also introduce the physical quantities studied. More specifically, we employ a TB wire model, where the base pairs are the sites of the chain, to study the spectral and charge transfer properties of periodic sequences with increasing repetition unit, as well as deterministic aperiodic DNA segments.
In addition, we address the impact of structural flexibility on the electronic structure and charge transfer ability of B-DNA. To this end, we apply our LCAO method to 20 AA and GG dimers, extracted from representative structures in a classical Molecular Dynamics trajectory of a 20mer, and study some useful physical quantities.
Finally, we move on to investigate charge transport along DNA molecules, using the Schrödinger equation together with the transfer-matrix method in order to finally obtain current-voltage I-V curves. We examine ideal and natural geometries concerning two categories of mutations: (i) DNA sequences that contain point substitution mutations, and (ii) sequences extracted from segments of human chromosomes, modified by expansion of the CAG triplet to mimic diseases (STR expansion mutations).
Main subject category:
Science
Keywords:
Tight-Binding, charge transfer, charge transport, DNA, mutations
Number of references:
244
