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Coarse-Grained Simu...
Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations
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- Rebič, Matúš (author)
- Stockholms universitet,Institutionen för material- och miljökemi (MMK),Science for Life Laboratory (SciLifeLab),P. J. Šafárik University, Slovakia
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- Mocci, Francesca (author)
- Stockholms universitet,Institutionen för material- och miljökemi (MMK),Science for Life Laboratory (SciLifeLab),University of Cagliari, Italy
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Uličný, Jozef (author)
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- Lyubartsev, Alexander P. (author)
- Stockholms universitet,Institutionen för material- och miljökemi (MMK),Science for Life Laboratory (SciLifeLab),University of Cagliari, Italy
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- Laaksonen, Aatto (author)
- Stockholms universitet,Institutionen för material- och miljökemi (MMK),Science for Life Laboratory (SciLifeLab),University of Cagliari, Italy; Stellenbosch University, South Africa
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(creator_code:org_t)
- 2017-02-03
- 2017
- English.
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In: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 2:2, s. 386-396
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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