SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2 - ADJACENT G-A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND B(II) PHOSPHATE GROUPS
SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2 - ADJACENT G-A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND B(II) PHOSPHATE GROUPS
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DOI：
10.1016/0022-2836(92)90497-8
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发表时间：
1992-11-05
影响因子：
5.6
通讯作者：
REID, BR
中科院分区：
文献类型：
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作者：
CHOU, SH;CHENG, JW;REID, BR
利用二维核磁共振（2D-NMR）和距离几何方法确定了一种相当不寻常的b型双相[d(ATGAGCGAATA)]2的溶液结构。该序列形成了一个稳定的10碱基对b型双链，具有3 '悬垂和两对相邻的G: a错配，通过剪切氢键方案配对。所有非交换质子，包括3G和7G残基的立体特异性h - 5s / H-5'R，都通过2D-NMR进行了分配。磷光谱是用H-3′和H-4′的异核相关来分配的。完整的分配揭示了相邻G:A错配对及其相邻核苷酸的几种不寻常的核Overhauser增强（NOEs）和不寻常的化学位移。从随时间变化的noe中得到质子间距离，用于生成初始结构，并通过二维核Overhauser增强谱的迭代反算进一步改进；根据改进的距离边界计算了22个最终结构。所有这些最终结构都表现出完全缠绕的螺旋结构，对于精确的距离界限具有较小的惩罚值和较小的成对均方根偏差值（通常为0.5 Å至0.9 Å）。这两条螺旋状链在两个G:A错配位点交换碱基堆叠，导致碱基堆叠在每一侧，而不是在扭曲双链的每一条上。在G:A错配步骤处发现了非常大的扭转角（77°）。所有的最终结构都在相邻的G:A错配位点具有BIIphosphate构象，与观察到的向下31p化学位移和蒙特卡罗构象搜索结果一致。我们的结果支持了31p化学位移与骨干扭角有关的假设。在相邻的G:A错配步骤中的这些BIIphosphate构象表明G:A对G- nh2与附近的磷酸氧原子之间不太可能形成氢键。这种不寻常的双链结构可以通过强链间和链内的碱基堆叠来稳定，正如在不匹配堆叠中优异的碱基重叠所表明的那样。
The solution structure of a rather unusualB-form duplex [d(ATGAGCGAATA)]2has been determined using two-dimensional nuclear magnetic resonance (2D-NMR) and distance geometry methods. This sequence forms a stable ten base-pairB-form duplex with 3′ overhangs and two pairs of adjacent G:A mismatches pairedviaa sheared hydrogen-bonding scheme. All non-exchangeable protons, including the stereo-specific H-5′S/H-5′R of the 3G and 7G residues, were assigned by 2D-NMR. The phosphorus spectrum was assigned using heteronuclear correlation with H-3′ and H-4′ resonances. The complete assignments reveal several unusual nuclear Overhauser enhancements (NOEs) and unusual chemical shifts for the neighboring G:A mismatch pairs and their adjacent nucleotides. Inter-proton distances were derived from time-dependent NOEs and used to generate initial structures, which were further refined by iterative back-calculation of the two-dimensional nuclear Overhauser enhancement spectra; 22 final structures were calculated from the refined distance bounds. All these final structures exhibit fully wound helical structures with small penalty values against the refined distance bounds and small pair-wise root-mean-square deviation values (typically 0.5 Å to 0.9 Å). The two helical strands exchange base stacking at both of the two G:A mismatch sites, resulting in base stacking down each side rather than down each strand of the twisted duplex. Very large twist angles (77 °) were found at the G:A mismatch steps. All the final structures were found to have BIIphosphate conformations at the adjacent G:A mismatch sites, consistent with observed downfield31P chemical shifts and Monte-Carlo conformational search results. Our results support the hypothesis that31P chemical shifts are related to backbone torsion angles. These BIIphosphate conformations in the adjacent G:A mismatch step suggest that hydrogen bonding of the G:A pair G-NH2to a nearby phosphate oxygen atom is unlikely. The unusual structure of the duplex may be stabilized by strong interstrand base stacking as well as intrastrand stacking, as indicated by excellent base overlap within the mismatch stacks.