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Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). P. J. Šafárik University, Slovakia.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Cagliari, Italy.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Cagliari, Italy.
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Number of Authors: 5
2017 (English)In: ACS Omega, ISSN 2470-1343, Vol. 2, no 2, 386-396 p.Article in journal (Refereed) Published
Abstract [en]

We present a coarse-grained (CG) model of a rodlike higher-order quadruplex with explicit monovalent salts, which was developed from radial distribution functions of an underlying reference atomistic molecular dynamics simulation using inverse Monte Carlo technique. This work improves our previous CG model and extends its applicability beyond the minimal salt conditions, allowing its use at variable ionic strengths. The strategies necessary for the model development are clearly explained and discussed. The effects of the number of stacked quadruplexes and varied salt concentration on the elasticity of the rodlike higher-order quadruplex structures are analyzed. The CG model reproduces the deformations of the terminal parts in agreement with experimental observations without introducing any special parameters for terminal beads and reveals slight differences in the rise and twist of the G-quartet arrangement along the studied biopolymer. The conclusions of our study can be generalized for other G-quartet-based structures.

Place, publisher, year, edition, pages
2017. Vol. 2, no 2, 386-396 p.
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:su:diva-142558DOI: 10.1021/acsomega.6b00419ISI: 000395863300004OAI: oai:DiVA.org:su-142558DiVA: diva2:1092630
Available from: 2017-05-03 Created: 2017-05-03 Last updated: 2017-05-03Bibliographically approved

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Rebič, MatúšLyubartsev, Alexander P.Laaksonen, Aatto
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