Seibert Eleanore, Ross J B Alexander, Osman Roman
Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA.
J Mol Biol. 2003 Jul 18;330(4):687-703. doi: 10.1016/s0022-2836(03)00598-9.
Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U wobble base-pairs in two different sequence contexts, TGT/AUA and CGC/GUG. Furthermore, we have investigated the effect of replacing the guanine base in each sequence with a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Our results indicate that each sequence opens spontaneously towards the major groove in the course of the simulations. The TGT/AUA sequence has a greater proportion of structures in the open state than the CGC/GUG sequence. Incorporation of 6MI yields wobble base-pairs that open more readily than their guanine counterparts. In order of increasing open population, the sequences are ordered as CGC<TGT<CMC<TMT, where M represents 6MI. Both members of the base-pair open towards the major groove in a symmetrically coupled motion. Opening results in breakage of the H3(U)-O6(G/6MI) hydrogen bond, and distortion of the H1(G/6MI)-O2(U) hydrogen bond. Structural consequences of the opening include the formation of the H21(G/6MI)-O2(U) hydrogen bond and a change in local solvation in the grooves and particularly near N3-H3 of uracil. Additionally, DNA flexibility is reduced in the open state for bending towards the major groove generating two nearly discrete states: closed unbent and open bent. The observed differences in the local structural and dynamical properties of the G.U base-pair may play an important role in the activity of DNA repair enzymes that initiate base excision by distorting the DNA and flipping the target base from inside the DNA helix.
鸟嘌呤-尿嘧啶（G.U）摆动碱基对是DNA中的一种有害损伤。先前的研究表明，这种摆动碱基对比正常的G.C碱基对更容易发生碱基打开。为了研究碱基对打开的序列依赖性，我们对处于两种不同序列环境（TGT/AUA和CGC/GUG）的G.U摆动碱基对进行了5纳秒的分子动力学模拟。此外，我们还研究了用荧光鸟嘌呤类似物6-甲基异黄蝶呤（6MI）替换每个序列中的鸟嘌呤碱基的效果。我们的结果表明，在模拟过程中，每个序列都自发地向大沟方向打开。TGT/AUA序列处于开放状态的结构比例比CGC/GUG序列更大。掺入6MI产生的摆动碱基对比其鸟嘌呤对应物更容易打开。按开放群体增加的顺序，序列排列为CGC<TGT<CMC<TMT，其中M代表6MI。碱基对的两个成员以对称耦合运动向大沟方向打开。打开导致H3（U）-O6（G/6MI）氢键断裂，以及H1（G/6MI）-O2（U）氢键扭曲。打开的结构后果包括形成H21（G/6MI）-O2（U）氢键，以及沟中特别是尿嘧啶N3-H3附近局部溶剂化的变化。此外，在开放状态下，DNA向大沟弯曲的柔韧性降低，产生两种几乎离散的状态：闭合未弯曲和开放弯曲。观察到的G.U碱基对局部结构和动力学性质的差异可能在DNA修复酶的活性中起重要作用，这些酶通过扭曲DNA并将目标碱基从DNA螺旋内部翻转出来启动碱基切除。
