Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
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DOI：
10.1093/nar/gkr031
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发表时间：
2011-05
影响因子：
14.9
通讯作者：
Cheatham TE 3rd
中科院分区：
文献类型：
--
作者：
Cang X;Šponer J;Cheatham TE 3rd
富含鸟嘌呤的DNA序列倾向于形成四链g -四重结构。沿g链的典型糖苷构象模式，如在Oxytricha nova端粒g - four - plexes中观察到的5 ' -syn-anti-syn-anti模式，已经被很好地记录下来。然而，对这些特征糖苷模式的解释尚未出现。本文对简化的双四重唱[d(GG)]4模型进行了MD模拟和自由能分析，并表明四种碱基对阶进模式具有截然不同的相对稳定性：syn-anti > -anti > -syn > syn-syn。这表明了以下规则：当折叠时，反平行g -四联体倾向于最大化反同步步骤的数量，并避免不利的反同步和反同步步骤。这一规律与蛋白质数据库（PDB）中大多数反平行g -四重结构一致。g -四联体的结构多态性与这些糖苷构象模式和g束的长度有关。G2-和g4 -链的折叠拓扑结构不是很多态，因为每条链都倾向于填充稳定的syn-anti - repeat。另一方面，g3束不能在每个g束上呈现这种重复模式。这导致不同几何形状之间的能量差异较小，并有助于解释人类端粒g -四联体的极端结构多态性。
Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5′-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)]4 models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.
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