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Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling by Alexa M. Salsbury; Tanner J. Dean; Justin A. Lemkul is a Physics and Astronomy article available to read on EtoBox.

What is Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling about?

G-quadruplexes (GQs) are highly ordered nucleic acid structures that play fundamental roles in regulating gene expression and maintaining genomic stability. GQs are topologically diverse and enriched in promoter sequences of growth regulatory genes and proto-oncogenes, suggesting they may serve as attractive targets for drug design at the level of transcription rather than inhibiting the activity of the protein products of these genes. The c-kit promoter contains three adjacent GQ-forming sequences that have proposed antagonistic effects on gene expression and thus are promising drug targets for diseases like gastrointestinal stromal tumors, mast cell disease, and leukemia. Since GQ stability is influenced by primary structure, secondary structure, and ion interactions, a greater understanding of GQ structure, dynamics, and ion binding properties is needed to develop novel, GQ-targeting therapeutics. Here, we performed molecular dynamics (MD) simulations to systematically study the c-kit2 and c-kit\* GQs, evaluating nonpolarizable and polarizable force fields (FFs) and examining the effects of base substitutions and cation type (K + , Na + , and Li + ) on the dynamics of their isol

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Author

Alexa M. Salsbury; Tanner J. Dean; Justin A. Lemkul

Publisher

American Chemical Society; American Chemical Society (ACS) (ISSN 1549-9618)

Published

2020

Language

EN

Field

Physics and Astronomy (Physical Sciences)