Computational Studies of UV Light Damages in Large Biomolecule - DNA
Date Issued
2007
Date
2007
Author(s)
Li, Jian-Hao
DOI
en-US
Abstract
The important damage type of DNA in cell, the thymine photodimerization, was studied. This UV caused CPD (cyclobutane pyrimidine dimer) structure can be deadly if the repairing is unsuccessful. We used Gaussian 03 Package to perform a theoretical computation analysis on this reaction. TDDFT, an efficient and accurate excitation calculation method that is just well developed in recent years, was used to study this electronic excited state reaction. In considering the environmental effects to this reaction, we have used the ONIOM method, a layer division scheme in Gaussian 03, to reduce the possible high cost of full ab initio calculation in large molecules.
There were four parts in our tasks. We used the most common form of DNA, B-DNA, as our objective.
The first part and second part were the direct excitation calculations on various sizes of molecules cut from the two strands near the reactive di-thymine site in ideal and X-ray determined B-DNA. After the TDDFT calculation the KS orbital transition analysis was performed. Some characteristics and electron redistribution patterns of the excitations on the di-thymine site in B-DNA, can be derived from this analysis.
In the third part the B-DNA self-complementary dodecamer CGCGAATTCGCG, which is often taken as the objective in experiments, was used in the ONIOM structure determination of B-DNA. The resulting structure can be used to perform similar TDDFT calculations of 1st and 2nd part for comparison. The effects of water molecules to excited states can also be studied.
In the fourth part, direct cis-syn thymine dimer ground state scans on the C5-C5 and C6-C6 bond were performed (excluding environmental effects). From the results the reaction path of thymine dimer formation in the excited states might be predicted.
Subjects
去氧核醣核酸
胸腺嘧啶二聚體
環丁烷嘧啶二聚體
紫外線
光損傷
皮膚癌
激發態
密度泛函理論
時間相關密度泛函理論
量子化學
第一原理
全始算
DNA
B-DNA
thymine dimer
Cyclobutane Pyrimidine Dimer
UV
skin cancer
photodamage
photodimerization
excimer
excitation
Density Functional Theory (DFT)
Time-Dependent Density Functional Theory (TDDFT)
Gaussian Package
OMIOM
QM/MM
Quantum Chemistry
First Principle
Ab Initio Calculation
SDGs
Type
thesis
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