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An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove.

机译：d（CTACTGCTTTAG）的NMR和分子模型分析。 d（CTAAAGCAGTAG）揭示了TpA台阶的特殊行为与其在主要凹槽中其碱基对的边对边接触有关。

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摘要

In a previous NMR study we detected the presence of particular motions and hydration properties within the DNA fragment d(CTACTGCTTTAG).d(CTAAAGCAGTAG). Now, we report on an NMR and molecular modelling analysis of this sequence focusing our attention on the biologically important TpA steps. NOe and coupling constant restraints were introduced in three different modelling protocols: X-PLOR and JUMNA used with Flex and AMBER94 as force-fields. Despite their differences the protocols produce similar mean B-DNA structures (r.m.s.d. <1 A). The new information confirms our previous experimental results on the narrowing of the minor groove along the T8T9T10/A17A16A15 run and the sudden widening at the T10pA11 step ending this run. It is further shown that this step displays a large positive roll with its T10:A15 and A11:T14 base-pairs likely stabilised by amino-amino and amino-carbonyl interactions in the major groove. A relationship between roll values and amino-amino and amino-carbonyl distances strongly suggests that electrostatics or bifurcated hydrogen-bonds could be responsible for induction of positive rolls in TpA steps. Such edge-to-edge interactions could explain the slower motions shown by the adenine A15. The influence of these interactions on the stabilisation of particular DNA conformers is discussed using our data and those provided by the recent literature.

机译：在先前的NMR研究中，我们检测到DNA片段d（CTACTGCTTTAG）.d（CTAAAGCAGTAG）中存在特定的运动和水合特性。现在，我们报告了该序列的NMR和分子模型分析，重点是生物学上重要的TpA步骤。在三种不同的建模协议中引入了NOe和耦合常数约束：X-PLOR和JUMNA与Flex和AMBER94用作力场。尽管它们之间存在差异，但方案产生的平均B-DNA结构相似（r.m.s.d. <1 A）。新信息证实了我们先前的实验结果，即沿着T8T9T10 / A17A16A15运行的小凹槽变窄以及在结束该运行的T10pA11步骤突然变宽。进一步表明，该步骤显示出大的正向滚动，其T10：A15和A11：T14碱基对可能通过主沟中的氨基-氨基和氨基-羰基相互作用而稳定。滚动值与氨基-氨基和氨基-羰基距离之间的关系强烈表明，静电或分叉的氢键可能是导致TpA步骤中正滚动的原因。这样的边缘到边缘的相互作用可以解释腺嘌呤A15显示的较慢的运动。这些相互作用对特定DNA构象异构体稳定的影响使用我们的数据和最新文献提供的数据进行了讨论。

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期刊名称 Nucleic Acids Research
作者
S Leporc; O Mauffret; G Tevanian; E Lescot; M Monnot; S Fermandjian;
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作者单位

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年(卷),期 1999(27),24
年度 1999
页码 4759–4767
总页数 9
原文格式 PDF
正文语种
中图分类分子生物学;
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1. An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove. [J] . Leporc S, Mauffret O, Tevanian G, Nucleic Acids Research . 1999,第24期

机译：d（CTACTGCTTTAG）的NMR和分子模型分析。 d（CTAAAGCAGTAG）揭示了TpA台阶的特殊行为与其在主要凹槽中的碱基对的边对边接触有关。
2. An NMR and molecular modelling analysis of d(CTACTGCTTTAG)·d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove [J] . E. Lescot, G. Tevanian, M. Monnot, Nucleic acids research . 1999,第24期

机译：d（CTACTGCTTTAG）·d（CTAAAGCAGTAG）的NMR和分子模型分析表明，TpA台阶的特殊行为与其在主要凹槽中碱基对的边对边接触有关
3. An NMR study of d(CTACTGCTTTAG).d(CTAAAGCAGTAG) showing hydration water molecules in the minor groove of a TpA step. [J] . Leporc S, Mauffret O, El-Antri S, Journal of Biomolecular Structure and Dynamics . 1998,第3期

机译：d（CTACTGCTTTAG）.d（CTAAAGCAGTAG）的NMR研究显示TpA步骤的小沟中存在水合水分子。
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机译：分子动力学正确地模拟了GAGU RNA内部环的异常主要构象并通过NMR揭示了异常的次要构象
7. An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove. [O] . Leporc, S, Mauffret, O, Tevanian, G, 1999

机译：d（CTACTGCTTTAG）的NMR和分子模型分析。 d（CTAAAGCAGTAG）揭示了TpA台阶的特殊行为与其在主要凹槽中其碱基对的边对边接触有关。
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An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove.

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