Gervais V, Cognet J A, Guy A, Cadet J, Téoule R, Fazakerley G V
Département de Biologie Cellulaire et Moléculaire, CEA Saclay, Gif-sur-Yvette, France.
Biochemistry. 1998 Jan 27;37(4):1083-93. doi: 10.1021/bi971202j.
The presence of a N-(2-deoxy-D-erythro pentofuranosyl)urea (henceforth referred to as deoxyribosylurea) residue, ring fragmentation product of a thymine, in a frameshift situation in the sequence 5'd(AGGACCACG).d(CGTGGurTCCT) has been studied by 1H and 31P nuclear magnetic resonance and molecular dynamics. At equilibrium, two species are found in slow exchange. We observe that the deoxyribosylurea residue can be either intra- or extrahelical within structures which otherwise do not deviate strongly from that of a B-DNA as observed by NMR. Our study suggests that this is determined by the nature and number of hydrogen bonds which this residue can form as a function of two possible isomers. There are two possible structures for the urea side chain, either cis or trans for the urido bond which significantly changes the hydrogen bonding geometry of the residue. In the intrahelical species, the cis isomer can form two good hydrogen bonds with the bases on the opposite strand in the intrahelical species, A4 and C5, which is not the case for the trans isomer. This results in a kink in the helical axis. For the major extrahelical species, the situation is reversed. The trans isomer is able to form two good hydrogen bonds, with G13 on the same strand and A7 on the opposite strand. For the extrahelical species, the cis isomer can form only one hydrogen bond. In this major structure the NMR data show that the bases which are on either side of the deoxyribosylurea residue in the sequence, G14 and T16, are stacked over each other in a way similar to a normal B-DNA structure. This requires the formation of a loop for the backbone between these two residues. This loop can belong to one of two families, right- or left-handed. In a previous study of an abasic frameshift [Cuniasse et al. (1989) Biochemistry 28, 2018-2026], a left-handed loop was observed, whereas in this study a right-handed loop is found for the first time in solution. The deoxyribosylurea residue lies in the minor groove and can form both an intra- and an interstrand hydrogen bond.
通过¹H和³¹P核磁共振以及分子动力学研究了在序列5'd(AGGACCACG).d(CGTGGurTCCT)移码情况下胸腺嘧啶环断裂产物N-(2-脱氧-D-赤藓糖戊呋喃糖基)脲（以下简称脱氧核糖基脲）残基的存在情况。在平衡状态下，发现两种物种处于缓慢交换状态。我们观察到，脱氧核糖基脲残基在结构中可以是螺旋内或螺旋外的，否则通过核磁共振观察到的结构与B-DNA的结构差异不大。我们的研究表明，这取决于该残基作为两种可能异构体的函数所能形成的氢键的性质和数量。脲侧链有两种可能的结构，即尿苷键的顺式或反式，这会显著改变残基的氢键几何结构。在螺旋内物种中，顺式异构体可以与螺旋内物种中相反链上的碱基A4和C5形成两个良好的氢键，而反式异构体则不然。这导致螺旋轴出现扭结。对于主要的螺旋外物种，情况则相反。反式异构体能够与同一条链上的G13和相反链上的A7形成两个良好的氢键。对于螺旋外物种，顺式异构体只能形成一个氢键。在这种主要结构中，核磁共振数据表明，序列中脱氧核糖基脲残基两侧的碱基G14和T16以类似于正常B-DNA结构的方式相互堆积。这需要在这两个残基之间的主链形成一个环。这个环可以属于两个家族之一，右手或左手。在先前对无碱基移码的研究中[Cuniasse等人（1989年）《生物化学》28卷，2018 - 2026页]，观察到一个左手环，而在本研究中首次在溶液中发现了一个右手环。脱氧核糖基脲残基位于小沟中，并且可以形成链内和链间氢键。
