用非弹性小角 X 射线散射技术对 DNA 周围的离子进行计数。
Counting ions around DNA with anomalous small-angle X-ray scattering.
机构信息
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States.
出版信息
J Am Chem Soc. 2010 Nov 24;132(46):16334-6. doi: 10.1021/ja107259y. Epub 2010 Nov 3.
Abstract
The majority of charge-compensating ions around nucleic acids form a diffuse counterion "cloud" that is not amenable to investigation by traditional methods that rely on rigid structural interactions. Although various techniques have been employed to characterize the ion atmosphere around nucleic acids, only anomalous small-angle X-ray scattering (ASAXS) provides information about the spatial distribution of ions. Here we present an experimentally straightforward extension of ASAXS that can be used to count the number of ions around nucleic acids.
摘要
大多数在核酸周围的电荷补偿离子形成一个弥散的抗衡离子“云”，这是不容易用传统的方法来研究，传统方法依赖于刚性的结构相互作用。虽然已经采用了各种技术来描绘核酸周围的离子环境，但只有异常小角 X 射线散射 (ASAXS) 提供了关于离子空间分布的信息。在这里，我们提出了一个实验上简单的 ASAXS 扩展，可以用来计算核酸周围的离子数量。
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本文引用的文献
1
Using anomalous small angle X-ray scattering to probe the ion atmosphere around nucleic acids.利用反常小角X射线散射探测核酸周围的离子氛围。
Methods Enzymol. 2009;469:391-410. doi: 10.1016/S0076-6879(09)69019-4. Epub 2009 Nov 17.
2
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA.与双链DNA相比，螺旋拓扑结构和抗衡离子分布都有助于双链RNA中更有效的电荷屏蔽。
Nucleic Acids Res. 2009 Jul;37(12):3887-96. doi: 10.1093/nar/gkp257. Epub 2009 Apr 24.
3
Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye.使用荧光染料直接定量镁离子与RNA的相互作用。
Methods Enzymol. 2009;455:71-94. doi: 10.1016/S0076-6879(08)04203-1.
4
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.核酸周围离子氛围的定量与全面分解
J Am Chem Soc. 2007 Dec 5;129(48):14981-8. doi: 10.1021/ja075020g. Epub 2007 Nov 9.
5
Metal ions and RNA folding: a highly charged topic with a dynamic future.金属离子与RNA折叠：一个充满活力且前景广阔的热门话题。
Curr Opin Chem Biol. 2005 Apr;9(2):104-9. doi: 10.1016/j.cbpa.2005.02.004.
6
A guide to ions and RNA structure.离子与RNA结构指南。
RNA. 2004 Mar;10(3):335-43. doi: 10.1261/rna.5205404.
7
Counterion distribution around DNA probed by solution X-ray scattering.通过溶液X射线散射探测DNA周围的抗衡离子分布。
Phys Rev Lett. 2003 May 9;90(18):188103. doi: 10.1103/PhysRevLett.90.188103. Epub 2003 May 8.
8
Salt effects on nucleic acids.盐对核酸的影响。
Curr Opin Struct Biol. 1995 Jun;5(3):323-8. doi: 10.1016/0959-440x(95)80093-x.
9
Ion effects on ligand-nucleic acid interactions.离子对配体 - 核酸相互作用的影响。
J Mol Biol. 1976 Oct 25;107(2):145-58. doi: 10.1016/s0022-2836(76)80023-x.
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