Excess counterion binding and ionic stability of kinked and branched DNA
Excess counterion binding and ionic stability of kinked and branched DNA
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DOI：
10.1016/s0301-4622(98)00171-9
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发表时间：
1998-08-24
影响因子：
3.8
通讯作者：
Olson, WK
中科院分区：
文献类型：
--
作者：
Fenley, MO;Manning, GS;Olson, WK
我们计算与扭结和分支的DNA，这些结构的离子稳定性作为链长和钠盐和镁盐浓度的函数，使用数值counterion凝聚理论的抗衡离子的过量数量。DNA结构被建模为两个或多个有限的磷酸盐电荷线从扭结或结中心辐射。围绕（40-90度）扭结双链体的过量抗衡离子的数量非常小（最多4个）。相比之下，在含有低至中等NaCl浓度的溶液中，大的三向和四向DNA连接（每个臂具有> 50个碱基对）的几何形状积累了大量过量的钠离子（> 20），但不超过15个镁抗衡离子。扭结的线性链和分支的DNA结构周围的抗衡离子的过量数量保持不变或随链长而增加，趋于达到平台值。在所考虑的整个盐浓度范围内（10（-5）-10（-1）M NaCl或MgCl 2），开放构型，例如平面Y形三通接头（具有三个120度臂间角）和90度十字形四通接头，比紧凑几何形状例如金字塔形三通接头和X形四通接头在离子上更稳定。致密形式的离子稳定性随着盐浓度的增加而增加，并且在高盐下（特别是当镁是支持盐时）变得与扩展几何形状的离子稳定性相当。(C)1998年由Elsevier Science B. V.出版，版权所有。
We compute the excess number of counterions associated with kinked and branched DNA, and the ionic stabilities of these structures as a function of chain length and both sodium and magnesium salt concentration, using numerical counterion condensation theory. The DNA structures are modeled as two or more finite lines of phosphate charges radiating from the kink or junction center. The number of excess counterions around the (40-90 degrees) kinked duplex is very small (at most four). The geometries of large three- and four-way DNA junctions (with > 50 base pairs per arm) in solutions containing low to moderate NaCl concentrations, by contrast, accumulate a substantial number of excess sodium ions (> 20) but no more than 15 magnesium counterions. The excess number of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped three-way junction (with three 120 degrees inter-arm angles) and the 90 degrees cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal three-way junctions and X-shaped four-way junctions, over the entire range of salt concentration considered (10(-5)-10(-1) M NaCl or MgCl2). The ionic stabilities of the compact forms increase with increasing salt concentration and become comparable to those of the extended geometries at high salt (especially when magnesium is the supporting salt). (C) 1998 Published by Elsevier Science B.V. All rights reserved.