BENDING AND CURVATURE CALCULATIONS IN B-DNA
BENDING AND CURVATURE CALCULATIONS IN B-DNA
复制标题
DOI：
10.1093/nar/22.24.5497
复制
发表时间：
1994-12-11
影响因子：
14.9
通讯作者：
DICKERSON, RE
中科院分区：
文献类型：
--
作者：
GOODSELL, DS;DICKERSON, RE
一个简单的程序，BEND，已经被编写来计算局部弯曲和宏观曲率的大小在每个点沿着任意的B-DNA序列，使用任何所需的弯曲模型，指定值的扭曲，滚动和倾斜作为序列的函数。该程序已被用来评估六种不同的DNA弯曲模型在三个类别。两个是弯曲的非A束模型：（a）基于Satchwell等人1986（J. Mol. Biol. 191，659-675），（B）Calladine等1988（J. Mol. Biol. 201，127-137）。三个是弯曲的A-道模型：（c）Bolshoy在al 1991年的楔形模型（Proc. Natl. Acad. Sci. USA 88，2312-2316），（d）Cacchione等人1989年的模型（Biochem.28，8706-8713），（e）模型（B）的反向版本。最后一个是结模型：（d）Koo和Crothers 1988（Proc. Natl. Acad. Sci. USA 85，1763-1767）。虽然他们有广泛不同的假设和扭曲，滚动和倾斜的值，所有六个模型正确预测实验A-道曲率所测量的凝胶阻滞和环化动力学，但只有新的核小体定位模型是成功的，在预测曲率的地区包含阶段GGGCCC序列。该模型-显示局部弯曲在混合序列DNA，强弯曲在序列GGC，和直，刚性的A-tracts-是唯一的模型与两个解决方案的数据从凝胶阻滞和环化动力学和结构数据从X-射线晶体学一致。
A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categories. Two are bent non-A-tract models: (a) A new model based on the nucleosome positioning data of Satchwell al al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 127-137). Three are bent A-tract models: (c) The wedge model of Bolshoy at al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione at al 1989 (Biochem. 28, 8706-8713), (e) A reversed version of model (b). The last is a junction model: (d) The model of Koo and Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although they have widely different assumptions and values for twist, roll and tilt, all six models correctly predict experimental A-tract curvature as measured by gel retardation and cyclization kinetics, but only the new nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model - showing local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts - is the only model consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.