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Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution.在水溶液中，二核苷酸单磷酸阴离子的分子内碱基堆积。
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本文引用的文献

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A free energy analysis of nucleic acid base stacking in aqueous solution.水溶液中核酸碱基堆积的自由能分析。
Biophys J. 1995 Oct;69(4):1528-35. doi: 10.1016/S0006-3495(95)80023-8.
2
Contributions of the thymine methyl group to the specific recognition of poly- and mononucleotides: an analysis of the relative free energies of solvation of thymine and uracil.胸腺嘧啶甲基对多核苷酸和单核苷酸特异性识别的贡献：胸腺嘧啶和尿嘧啶溶剂化相对自由能的分析。
Biochemistry. 1994 Mar 15;33(10):3050-4. doi: 10.1021/bi00176a038.
3
Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics.利用分子动力学研究二磷酸鸟苷-3',5'-尿苷的堆积-解堆积过程。
Biophys J. 1994 Aug;67(2):812-24. doi: 10.1016/S0006-3495(94)80541-7.
4
Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects.DNA和RNA螺旋稳定性巨大差异的起源：C-5甲基和2'-羟基效应。
Biochemistry. 1995 Mar 28;34(12):4125-32. doi: 10.1021/bi00012a031.
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The interpretation of protein structures: estimation of static accessibility.蛋白质结构的解读：静态可及性的评估
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Molecular interactions of pyrimidines, purines, and some other heteroaromatic compounds in aqueous media.嘧啶、嘌呤及其他一些杂环芳香化合物在水介质中的分子相互作用。
Biochemistry. 1970 Feb 3;9(3):577-83. doi: 10.1021/bi00805a019.
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An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and inter-strand stacking interaction energy.关于DNA构象序列依赖性的从头算分子轨道研究：链内和链间堆积相互作用能的评估。
J Theor Biol. 1988 Feb 7;130(3):327-35. doi: 10.1016/s0022-5193(88)80032-8.
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Free energy via molecular simulation: applications to chemical and biomolecular systems.通过分子模拟的自由能：在化学和生物分子系统中的应用
Annu Rev Biophys Biophys Chem. 1989;18:431-92. doi: 10.1146/annurev.bb.18.060189.002243.
9
Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.对d(CGCGAATTCGCG)双螺旋进行30皮秒分子动力学的构象和螺旋分析：“曲线”、刻度盘和窗口
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Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.疏水作用在位点特异性蛋白质-DNA复合物稳定性中的作用。
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单链脱氧核糖核苷单磷酸堆积-解堆积过程的平均力计算潜力。

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates.

作者信息

Norberg J, Nilsson L

机构信息

Department of Biosciences at NOVUM, Karolinska Institute, Huddinge, Sweden.

出版信息

Biophys J. 1995 Dec;69(6):2277-85. doi: 10.1016/S0006-3495(95)80098-6.

DOI:10.1016/S0006-3495(95)80098-6
PMID:8599635
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1236466/
Abstract

The free energy of the stacking-unstacking process of deoxyribodinucleoside monophosphates in aqueous solution has been investigated by potential of mean force calculations along a reaction coordinate, defined by the distance between the glycosidic nitrogen atoms of the bases. The stacking-unstacking process of a ribodinucleoside monophosphate was observed to be well characterized by this coordinate, which has the advantage that it allows for a dynamical backbone and flexible bases. All 16 naturally occurring DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in both the 5' and the 3' positions were studied. From the free-energy profiles we observed the deepest minima for the stacked states of the purine-purine dimers, but good stacking was also observed for the purine-pyrimidine and pyrimidine-purine dimers. Substantial stacking ability was found for the dimers composed of a thymine base and a purine base and also for the deoxythymidylyl-3',5'-deoxythymidine dimer. Very poor stacking was observed for the dCpdC dimer. Conformational properties and solvent accessibility are discussed for the stacked and unstacked dimers. The potential of mean force profiles of the stacking-unstacking process for the DNA dimers are compared with the RNA dimers.

摘要

通过沿着由碱基的糖苷氮原子之间的距离定义的反应坐标进行平均力势计算，研究了脱氧核糖核苷单磷酸在水溶液中的堆积-解堆积过程的自由能。观察到核糖核苷单磷酸的堆积-解堆积过程可以很好地用该坐标来表征，其优点是它允许动态的主链和灵活的碱基。研究了所有16种由5'和3'位置的腺嘌呤、胞嘧啶、鸟嘌呤或胸腺嘧啶碱基组成的天然存在的DNA二聚体。从自由能分布中，我们观察到嘌呤-嘌呤二聚体的堆积状态有最深的最小值，但嘌呤-嘧啶和嘧啶-嘌呤二聚体也观察到了良好的堆积。发现由胸腺嘧啶碱基和嘌呤碱基组成的二聚体以及脱氧胸苷酰-3',5'-脱氧胸苷二聚体具有相当大的堆积能力。观察到dCpdC二聚体的堆积非常差。讨论了堆积和未堆积二聚体的构象性质和溶剂可及性。将DNA二聚体的堆积-解堆积过程的平均力势分布与RNA二聚体进行了比较。