Regensburg 2016 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 16: Posters - Computational Biophysics

BP 16.7: Poster

Montag, 7. März 2016, 17:30–19:30, Poster C

New insights to the thermodynamic stability of DNA i-motif: A perspective from advanced computational sampling methods — •Raghvendra Pratap Singh, Vasileios Tatsis, and Andreas Heuer — Corrensstr. 30 , D-48149, Institute of Physical Chemistry, University of Münster, Germany

Under high temperature and low pH conditions, cytosine rich stretches of nucleic acids are able to fold in a novel localized tetrameric form via the protonation of N3 nitrogen of Cytosines. The protonation of N3 nitrogen facilitates the nucleic acids to form non Watson-Crick pairing (C+C). Recent studies suggest that this unique fold can be used as a template to create longer quadruplex nanowires for Bio-nanotechnology applications. The studies suggest that it could be a significant target for certain Cancer treatments. Here we present microsecond long MD simulation using advance-sampling technique of Metadynamics/Bias-exchange Metadynamics for protonated and deprotonated single stranded i-motif at ambient temperature (300K) and in high temperature (500K). Additionally, We studied unfolding simulations of experimentally solved crystal structures along with mutants of the base structure to study the impact of mutations on the thermodynamics of the DNA i-motif. A detailed comparative scenario on the stability and energetics of i-motif and induced mutants will be presented.

References [1] Guéron, M., Leroy, J.L, Current Opinion in Structural Biology 10(3),326-331(2000) [2] Ren, J., Qu, X., Trent, J.O., Chaires, J.B. Nucleic Acids Research 30, 2307*2315 (2002)