Determining and predicting 3D structure and dynamics for RNA is challenging, but can reveal structure-function relationships and facilitate design of therapeutics. Computational models can predict the structure, energetics, and dynamics of RNA in an inexpensive and efficient way. In chapter 2, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations, AMBER force fields OL3 and ROC-RNA were used for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented; however, an improved RNA force field is needed to accurately model single strands, especially terminal nucleotides. In chapter 3, quantum mechanics models for nucleobases were studied. Optimized geometries were compared to the small molecule crystal structures in the Cambridge Structural Database. The results showed QM can provide reliable geometrical restraints for both isolated and paired bases.
|Advisor:||Turner, Douglas H.|
|Commitee:||Mathews, David H., Krugh, Thomas R.|
|School:||University of Rochester|
|Department:||School of Arts and Sciences|
|School Location:||United States -- New York|
|Source:||DAI-B 82/7(E), Dissertation Abstracts International|
|Subjects:||Computational chemistry, Chemistry|
|Keywords:||Force field, Molecular dynamics, NMR, Quantum mechanics, RNA|
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