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DOI	10.1073/pnas.1911632116
	Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
	Nguyen H.T.; Hori N.; Thirumalai D.
发表日期	2019
ISSN	0027-8424
起始页码	21022
结束页码	21030
卷号	116 期号:42
英文摘要	RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM theory for ion–phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to predict accurately the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties. © 2019 National Academy of Sciences. All rights reserved.
英文关键词	Free energy; Ion preferential interaction coefficients; Reference interaction site model (RISM); RNA folding; Three-interaction site (TIS) model
语种	英语
scopus关键词	calcium; divalent cation; magnesium; monovalent cation; phosphate; ribosome RNA; divalent cation; ion; monovalent cation; RNA; Article; conformation; controlled study; DNA sequence; hydrogen bond; mathematical model; measurement accuracy; polymerization; priority journal; quantitative analysis; RNA binding; RNA folding; RNA structure; simulation; static electricity; structure analysis; theory; thermodynamics; metabolism; physiology; RNA folding; Cations, Divalent; Cations, Monovalent; Ions; RNA; RNA Folding; Thermodynamics
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/160341
作者单位	Nguyen, H.T., Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States; Hori, N., Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States; Thirumalai, D., Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States
推荐引用方式 GB/T 7714	Nguyen H.T.,Hori N.,Thirumalai D.. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations[J],2019,116(42).
APA	Nguyen H.T.,Hori N.,&Thirumalai D..(2019).Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.Proceedings of the National Academy of Sciences of the United States of America,116(42).
MLA	Nguyen H.T.,et al."Theory and simulations for RNA folding in mixtures of monovalent and divalent cations".Proceedings of the National Academy of Sciences of the United States of America 116.42(2019).