DNA persistence length revisited
DNA persistence length revisited
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DOI：
10.1002/bip.10151
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发表时间：
2001-01-01
期刊：
影响因子：
2.9
通讯作者：
Stellwagen, NC
中科院分区：
文献类型：
--
作者：
Lu, YJ;Weers, B;Stellwagen, NC
在4℃到43℃的不同温度下，用瞬变电双折射(TEB)测量了长度从79到789碱基对的DNA限制性片段。DNA片段不包含连续四个或更多的腺嘌呤残基，并且在聚丙烯酰胺凝胶中以正常的电泳迁移率迁移，这表明它们本身并不弯曲或弯曲。用于测量的低离子、强度的缓冲液含有1 mm Tris Cl。PH 8.0、EDTA和不同浓度的Na+或Mg2+离子。用非线性最小二乘法对TEB场无场衰变信号进行了拟合，得到了转动弛豫时间；双折射的衰变对于碎片是单指数的：S的长度是241个碱基对(BP)，对于更大的碎片是多指数的。然后利用末端弛豫时间(DNA分子的末端对末端旋转的特征)来确定DNA的持续长度(P)和流体动力学半径(R)作为温度和离子强度的函数，使用几种不同的流体动力学模型。获得的p和r的特定值取决于模型。P.J.Hagerman和B.H.Zimm的蠕虫链模型(BiPolmers1981，Vol.20，pp.1481-1502)与修订的Broersma方程(J.Newman等人，Journal of Mol Biol 1997，Vol.116，pp.593-606)相结合，似乎最适合描述DNA在低离子强度溶液中的柔性。由该方程的全局最小二乘拟合得到的p和r值与DNA长度无关，并且个体值与平均值的偏差相当小。DNA在含有1 mM Tris缓冲液的各种低离子强度溶液中计算的共识r值为14.7+/-0.4埃(20℃)，共识p值从814下降到564埃(在含有1 mm Tris缓冲液和0.2-1 mMNaC l的溶液中)，并进一步减小到440埃(在含有0.2 mm镁离子的溶液中)，持续长度在20℃时表现出一个浅的最大值，并且随着温度的升高或降低而缓慢下降，无论使用何种模型来拟合数据。相比之下，流体动力学半径的共同值与温度无关。计算的持续长度和流体动力学半径与文献中的其他数据进行了比较。(C)2002年威利期刊公司。
DNA restriction fragments ranging from 79 to 789 base pairs in length have been characterized by transient electric birefringence (TEB) measurements at various temperatures between 4 and 43degreesC. The DNA fragments do not contain runs of four or more adenine residues in a row and migrate with normal electrophoretic mobilities in polyacrylamide gels, indicating that they are not intrinsically curved or bent. The low ionic, strength buffers used for the measurements contained 1 mM Tris Cl. pH 8.0, EDTA, and variable concentrations of Na+ or Mg2+ ions. The rotational relaxation times were obtained by fitting the TEB field-free decay signals with a nonlinear least-squared fitting program; the decay of the birefringence was monoexponential for fragments :S 241 base pair (bp) in length and multiexponential for larger fragments. The terminal relaxation times, characteristic of the end-over-end rotation of the DNA molecules, were then used to determine the persistence length (p) and hydrodynamic radius (r) of DNA as a function of temperature and ionic strength, using several different hydrodynamic models. The specific values obtained for p and r are model dependent. The wormlike chain model of P. J. Hagerman and B. H. Zimm (Biopolymers 1981, Vol. 20, pp. 1481-1502) combined with the revised Broersma equation (J. Newman et al., Journal of Mol Biol 1997, Vol. 116, pp, 593-606) appears to be the most suitable for describing the flexibility of DNA in low ionic strength solutions. The values of p and r obtained from the global least squares fitting of this equation are independent of DNA length, and the deviations of the, individual values from the average are reasonably small. The consensus r value calculated for DNA in various low ionic strength solutions containing 1 mM Tris buffer is 14,7 +/- 0.4 Angstrom at 20degreesC, The consensus p values decrease from 814 similar to 564 Angstrom in solutions containing 1 mM Tris buffer plus 0.2-1 mM NaCl and decrease still further to 440 A in solutions containing 0.2 mM Mg2+ ions, The persistence length exhibits a shallow maximum at 20degreesC and decreases slowly upon either increasing or decreasing the temperature, regardless of the model used to fit the data. By contrast, the consensus values of the hydrodynamic radius are independent of temperature. The calculated persistence lengths and hydrodynamic radii are compared with other data in the literature. (C) 2002 Wiley Periodicals, Inc.