Dissertation/Thesis Abstract

The structural heterogeneity and dynamics of base stacking and unstacking in nucleic acids
by Sedova, Ada, Ph.D., State University of New York at Albany, 2015, 241; 3704807
Abstract (Summary)

Base stacking provides stability to nucleic acid duplexes, and base unstacking is involved in numerous biological functions related to nucleic acids, including replication, repair, transcription, and translation. The patterns of base stacking and unstacking in available nucleic acid crystal structures were classified after separation into their individual single strand dinucleotide components and clustering using a k-means-based ensemble clustering method. The A- and B-form proximity of these dinucleotide structures were assessed to discover that RNA dinucleotides can approach B-form-like structures. Umbrella sampling molecular dynamics simulations were used to obtain the potential of mean force profiles for base unstacking at 5'-termini for all 16 dinucleotides. A rate calculation method was investigated and implemented using small test compounds and applied to a base unstacking transition to predict a rate for 5'-terminal base fraying. The findings can be applied for localized nucleic acid structure prediction, and for comparison of molecular dynamics simulation-based investigations of nucleic acid distortions to experimental structural data.

Indexing (document details)
Advisor: Banavali, Nilesh K.
Commitee: Garcia, Angel, Jaeger, Joachim, Morse, Randall, Pata, Janice
School: State University of New York at Albany
Department: Biomedical Sciences
School Location: United States -- New York
Source: DAI-B 76/10(E), Dissertation Abstracts International
Subjects: Biochemistry, Bioinformatics, Biophysics
Keywords: Base stacking, Clustering, Molecular dynamics, Nucleic acids, Rate calulations, Structural analysis
Publication Number: 3704807
ISBN: 9781321774146
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