DETERMINATION OF THE EXTENT OF DNA BENDING BY AN ADENINE THYMINE TRACT
DETERMINATION OF THE EXTENT OF DNA BENDING BY AN ADENINE THYMINE TRACT
复制标题
DOI：
10.1021/bi00469a027
复制
发表时间：
1990-05-01
期刊：
影响因子：
2.9
通讯作者：
CROTHERS, DM
中科院分区：
文献类型：
--
作者：
KOO, HS;DRAK, J;CROTHERS, DM
我们通过测量含有定相 A 束的 DNA 寡核苷酸的环化速率来确定腺嘌呤-胸腺嘧啶束在 DNA 中诱导的弯曲程度。由 21 bp 长的合成双链脱氧寡核苷酸制备一系列具有 2 bp 单链末端的线性多聚体，其中 (A.cntdot.T)6 束由 CG2-3C 序列分隔，并交替间隔 10 和 11 bp。在DNA连接酶存在下测量多聚体(105-210 bp)的环化率和84 bp长多聚体的双分子缔合率。根据环化和双分子缔合反应的速率常数，获得多聚体的闭环概率。通过蒙特卡罗方法模拟系统弯曲的分子，并计算给定的一组连接弯曲角度的闭环概率。通过将闭环概率的计算值与实验值进行比较并调整连接处弯曲角度以适合实验值，确定了连接处的弯曲程度（或腺嘌呤束的弯曲程度）。
We determined the magnitude of the bend induced in DNA by an adenine-thymine tract by measuring the rate of cyclization of DNA oligonucleotides containing phased A tracts. A series of linear multimers with 2-bp single-stranded ends, in which the (A.cntdot.T)6 tracts are separated by CG2-3C sequences and are positioned 10 and 11 bp apart alternately, were prepared from 21 bp long synthetic duplexed deoxyoligonucleotides. The cyclization rates of the multimers (105-210 bp) and the bimolecular association rate of the 84 bp long multimer were measured in the presence of DNA ligase. From the rate constants of the cyclization and bimolecular association reactions, ring closure probabilities were obtained for the multimers. The systematically bent molecules were simulated by Monte Carlo methods, and the ring closure probabilities were calculated for a given set of junction bend angles. By comparing the calculated values of ring closure probabilities to experimental values and adjusting the junction bend angles to fit experimental values, the extent of bending at the junctions (or the extent of bending for an adenine tract) was determined.