Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation.

Luo R; Head MS; Given JA; Gilson MK

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Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation.

机译：氯仿中的核酸碱基配对和N-甲基乙酰胺自缔合：亲和力和构象。

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A recently developed computational method, 'mining minima', is used to examine the hydrogen-bonding interactions of nucleic acid base-pairs and of the N-methylacetamide homodimer in chloroform. The mining minima algorithm aggressively samples molecular conformations, identifies the most important local minima, and computes their contributions to the overall free energy of the system. Here, the CHARMM 98 parameter set is used for the potential energy and the generalized Born/surface area solvent model is used to account for the influence of the solvent. Good agreement with experiment is obtained for the non-covalent binding affinities of a series of complexes. The computational approach used here is applicable to a range of molecular systems.

机译：最近开发的一种计算方法“最小挖掘”用于检查氯仿中核酸碱基对和N-甲基乙酰胺均二聚体的氢键相互作用。挖掘最小值算法积极地对分子构象进行采样，识别出最重要的局部最小值，并计算它们对系统总体自由能的贡献。此处，CHARMM 98参数集用于势能，而广义的Born /表面积溶剂模型用于说明溶剂的影响。对于一系列复合物的非共价结合亲和力，与实验取得了良好的一致性。此处使用的计算方法适用于一系列分子系统。

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《Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena》 |1999年第2期|共11页
作者
Luo R; Head MS; Given JA; Gilson MK;
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正文语种 eng
中图分类生物化学;生物物理学;
关键词
Acetamides; Base Pairing; Chloroform; Nucleic Acids; N methylacetamide; 乙酰胺类; 碱基对; 氯仿; 核酸类;

机译：Acetamides;Base Pairing;Chloroform;Nucleic Acids;N methylacetamide;乙酰胺类;碱基对;氯仿;核酸类;

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1. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation. [J] . Luo R, Head MS, Given JA, Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena . 1999,第1a2期

机译：氯仿中的核酸碱基配对和N-甲基乙酰胺自缔合：亲和力和构象。
2. Molecular Assemblies of Metal Complexes via Base-Pairing of Nucleic Acids in the Crystalline State [J] . Manabu Nakaya, Ryo Ohtani, Kunihisa Sugimoto, Chemistry: A European journal . 2017,第30期

机译：金属配合物的分子组装通过结晶状态的碱基核酸碱基
3. Higher-order structure of nucleic acids in the gas phase: Top-down analysis of base-pairing interactions [J] . Fabris D., Kellersberger K.A., Wilhide J.A. International journal of mass spectrometry . 2012,第Null期

机译：气相中核酸的高级结构：碱基配对相互作用的自上而下分析
4. PNAB: Prediction of protein-nucleic acid binding affinity using heterogeneous ensemble models [C] . Wenyi Yang, Lei Deng IEEE International Conference on Bioinformatics and Biomedicine . 2019

机译：PNAB：使用异类集成模型预测蛋白质-核酸结合亲和力
5. Affinity purification of nucleic acids and protein - nucleic acid complexes using biotinylated nucleotide probes. [D] . Welcher, Andrew Avery. 1987

机译：使用生物素化的核苷酸探针亲和纯化核酸和蛋白质-核酸复合物。
6. Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions [O] . D. Fabris, K.A. Kellersberger, J.A. Wilhide -1

机译：气相中核酸高阶结构：基础配对相互作用的自上而下分析
7. Higher-order structure of nucleic acids in the gas phase: Top-down analysis of base-pairing interactions [O] . D. Fabris, K.A. Kellersberger, J.A. Wilhide 2012

机译：气相中核酸高阶结构：基础配对相互作用的自上而下分析

Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation.

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