Thesis
Molecular dynamics simulation of DNA lesions
Washington State University
Master of Science (MS), Washington State University
2005
Handle:
https://hdl.handle.net/2376/432
Abstract
Damage to DNA by physiological process byproducts or by introduced factors such as ionizing radiation leads to aging and carcinogenesis in multicellular organisms. Such damage manifests itself most fundamentally at the molecular level as a chemical alteration or lesion in a portion of the DNA. Although damage to isolated molecules is difficult to examine experimentally due to the very fine time and length scales involved, computer simulations can bridge the gap between theory and simulation to examine single DNA oligonucleotides under approximately physiological conditions. Molecular dynamics simulations, which approximate changes in molecular conformation over time using classical mechanics, have been used to examine a variety of lesions with particular attention to changes in hydration and free energy brought about by lesion introduction. Changes in hydration are often dramatic with the lesion's introduction, as are changes in free energy. Simulations in the context of thermodynamic cycles indicates reasonable preliminary agreement between simulated and experimental lesion duplex destabilization. It appears, however, that multiple lesions in close proximity are not more energetically significant than the sum of their parts.
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Details
- Title
- Molecular dynamics simulation of DNA lesions
- Creators
- Matthew Brian Ernst
- Contributors
- John H. Miller (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Electrical Engineering and Computer Science, School of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; [Pullman, Washington] :
- Identifiers
- 99900525048101842
- Language
- English
- Resource Type
- Thesis