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Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction.
Biochimica et Biophysica Acta (BBA) - General Subjects ( IF 3 ) Pub Date : 2020-03-14 , DOI: 10.1016/j.bbagen.2020.129600
Satyabrata Maiti 1 , Debasish Mukherjee 2 , Parthajit Roy 3 , Jaydeb Chakrabarti 4 , Dhananjay Bhattacharyya 1
Affiliation  

BACKGROUND Molecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs. METHODS We employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair. RESULTS We noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear. CONCLUSIONS The quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs "tug of war" situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity. GENERAL SIGNIFICANCE We have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.

中文翻译:

在两个剪切的Watson-Crick基对之间叠加几何:基于计算化学和生物信息学的预测。

背景技术使用从晶体结构数据库获得的碱基对参数的最可能值,可以对RNA双螺旋分子进行分子建模。A:A w:wC非规范碱基对,涉及两个顺式腺嘌呤的Watson-Crick边缘,在数据库中非常常见。由于两种不同的H键方案,其剪切力的双峰分布会在分配大多数可能值时造成混乱。当A:A w:wC基本对堆叠在Sheared摆动G:UW:WC基本对上时,其效果就很明显。方法我们采用分子动力学模拟了三个可能的双螺旋,其中心分别具有GAG,UAG和GAU序列基序,并针对堆叠在G:UW:WC碱基对上的非经典A:A w:wC碱基对进行了量子化学计算。结果我们注意到GAG基序具有稳定的结构,其中A:A碱基对的剪切力特别为负,但在A:A w:wC碱基配对中未发现其他基序的稳定性。在二核苷酸步骤序列A:A w:wC :: G:UW:WC和A:A w:wC :: U:GW:WC上的混合DFT-D和MP2堆积能量分析揭示了A:A的可行方向: :G:U首选具有负剪切力的H键合模式之一,该模式由晶体结构数据库支持。然而,A:A :: U:G二核苷酸更喜欢仅具有正剪切力的结构。结论量子化学计算解释了为什么GAG序列基序的MD模拟仅显得稳定。在GAU和UAG主题的情况下,A:A w:wC碱基对的正剪和负剪之间的“拔河”情况引起构象可塑性。
更新日期:2020-03-19
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