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Kanna, Charan Raju, 2015. Computational studies on DNA: insights into structure and dynamics. Second cycle, A2E. Uppsala: SLU, Department of Plant Biology (from 140101)

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Abstract

The best-characterized epigenetic modification is DNA methylation, which was found to shape
significantly gene expression in mammalian cells, though bacteria and plants display less sequence
specificity. The cytosine methylation of DNA sequence here was studied by the molecular dynamic
(MD) method. We found that the optimized structures are not significantly altered between
unmethylated, methylated sequences. However, sampling of the molecule dynamical landscape via
long MD simulations showed that the altered sequences could adopt different conformations
(revealed in the twist and roll angles) from the unmodified DNA, which are dependent on the
§sequence environment. We propose that this conformational diversity may play a role on protein
recognition.
The G-rich sequences are studied with MD simulations to check the propensity of the sequence to
adopt to A-form or B-form of DNA. The results showed that the DNA sequence adopts most of the
time in A-form and also spend sometime in between A-form and B-form. The groove widths
showed the conformation in B-form. By analyzing the DNA in different contexts using
computational methods we were able to test limits that force field methods offer for these systems.
We propose that this conformational diversity may play a role in protein recognition.
Finally, we have studied the conformational changes of DNA sequence with uracil as a base.
Sometimes in the replication process uracil can be formed and the mismatch base pair in the DNA
sequence is removed by the enzyme UDG (Uracil-DNA sequence). In the present work MD
simulations were used to study the structure, dynamics and base pair kinetics of DNA sequence.
The opening and closing kinetics of the T-A base pair were studied. A fast base pair opening was
observed and also additionally base flipping was spotted. A very fast opening of the bases may be
responsible for the fast closing of the bases. In order to characterize the complete study of base pair
kinetics in relation to T-A versus U-A base pairs is currently under way.

Main title:Computational studies on DNA: insights into structure and dynamics
Authors:Kanna, Charan Raju
Supervisor:Hennig, Lars
Examiner:Carlborg, Örjan
Series:UNSPECIFIED
Volume/Sequential designation:UNSPECIFIED
Year of Publication:2015
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:NM003 Biotechnology - Master's Programme 120 HEC
Department:(NL, NJ) > Department of Plant Biology (from 140101)
Keywords:epigenetic modifications, DNA methylation, G-rich sequence, uracil, molecular dynamics, demethylation
URN:NBN:urn:nbn:se:slu:epsilon-s-5066
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-5066
Subjects:Plant genetics and breeding
Language:English
Deposited On:18 Jan 2016 15:07
Metadata Last Modified:18 Jan 2016 15:07

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