Bending and flexibility of methylated and unmethylated EcoRI DNA
Bending and flexibility of methylated and unmethylated EcoRI DNA
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DOI：
10.1006/jmbi.2001.5247
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发表时间：
2002-02-08
影响因子：
5.6
通讯作者：
Crothers, DM
中科院分区：
文献类型：
--
作者：
Nathan, D;Crothers, DM
我们使用环化动力学实验和Monte Carlo模拟来确定含有EcoRI限制性位点的DNA十聚体的结构模型。我们的研究结果与最近的EcoRl十二聚体的晶体和NMR结构一致，其中七度的整体弯曲对称地分布在分子上。Monte Carlo模拟表明，该序列具有更高的灵活性“假设是各向同性的，相比“通用”的DNA序列。该模型被用作研究胞嘧啶甲基化对DNA弯曲和柔性的影响的起点。虽然甲基化不影响弯曲的幅度或方向，但它导致甲基化核苷酸的弯曲柔性和欠缠绕的降低。我们证明，我们的方法可以通过添加有关序列的全局结构和灵活性的信息来增强对DNA结构和动力学的理解。我们还表明，环化动力学可以用来研究修饰的核苷酸的性质。(C)2002 Elsevier Science Ltd.
We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRl restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRl dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility' assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methytation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides. (C) 2002 Elsevier Science Ltd.