对双链DNA进行的核磁共振亚氨基质子交换实验主要监测嘌呤碱基的打开情况。
NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.
作者信息
Priyakumar U Deva, Mackerell Alexander D
机构信息
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.
出版信息
J Am Chem Soc. 2006 Jan 25;128(3):678-9. doi: 10.1021/ja056445a.
Abstract
Molecular dynamics simulations were performed to investigate GC and AT base opening events in DNA. Calculated equilibrium constants between the base open (or flipped) and closed states were shown to be in good agreement with experimental data from NMR imino proton exchange experiments. Analysis of the computed results indicates that the equilbrium constants are dominated by the opening of the A and G bases in the AT and GC base pairs, respectively. Thus, the present results predict that NMR imino proton exchange experiments of base opening are primarily monitoring the opening of purine bases.
摘要
进行分子动力学模拟以研究DNA中的GC和AT碱基打开事件。计算得到的碱基打开（或翻转）状态与关闭状态之间的平衡常数与核磁共振亚氨基质子交换实验的实验数据显示出良好的一致性。对计算结果的分析表明，平衡常数分别主要由AT碱基对中的A碱基和GC碱基对中的G碱基的打开所主导。因此，目前的结果预测，碱基打开的核磁共振亚氨基质子交换实验主要监测嘌呤碱基的打开。
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本文引用的文献
1
Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.含GCGC的DNA十二聚体中的碱基翻转：核酸力场CHARMM、AMBER和BMS性能的比较研究。
J Chem Theory Comput. 2006 Jan;2(1):187-200. doi: 10.1021/ct0501957.
2
Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.蛋白质与DNA相互作用的特异性：来自嗜热栖热菌的（胞嘧啶-C5）-甲基转移酶的能量识别
J Mol Biol. 2005 Jan 14;345(2):265-74. doi: 10.1016/j.jmb.2004.10.042.
3
Sequence-dependence of the energetics of opening of at basepairs in DNA.DNA中碱基对打开能量学的序列依赖性。
Biophys J. 2004 Oct;87(4):2545-51. doi: 10.1529/biophysj.104.045179.
4
Atomistic view of base flipping in DNA.DNA中碱基翻转的原子水平视图。
Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1439-60. doi: 10.1098/rsta.2004.1383.
5
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.B-DNA内的碱基对打开：来自伞形抽样模拟的GC和AT碱基对的自由能路径
Nucleic Acids Res. 2003 Mar 1;31(5):1434-43. doi: 10.1093/nar/gkg239.
6
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.胞嘧啶-5-甲基转移酶介导的DNA中蛋白质促进的碱基翻转
Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):68-73. doi: 10.1073/pnas.0135427100. Epub 2002 Dec 27.
7
Role of base flipping in specific recognition of damaged DNA by repair enzymes.碱基翻转在修复酶对损伤DNA的特异性识别中的作用。
J Mol Biol. 2002 Nov 8;323(5):823-34. doi: 10.1016/s0022-2836(02)00999-3.
8
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J Am Chem Soc. 2002 Jun 26;124(25):7272-3. doi: 10.1021/ja025980x.
9
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.含DNA GCGC序列中碱基翻转的自由能和结构路径
J Mol Biol. 2002 May 24;319(1):141-60. doi: 10.1016/S0022-2836(02)00194-8.
10
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Biochemistry. 2000 Jan 25;39(3):607-15. doi: 10.1021/bi991863b.
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