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首页> 美国卫生研究院文献>Biophysical Journal >Conformational characteristics of the dimeric subunits of DNA from energy minimization studies. Mixed sugar-puckered dApdA dApdT dTpdA and dTpdT.
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Conformational characteristics of the dimeric subunits of DNA from energy minimization studies. Mixed sugar-puckered dApdA dApdT dTpdA and dTpdT.

机译：来自能量最小化研究的DNA二聚体亚基的构象特征。混合起皱的dApdAdApdTdTpdA和dTpdT。

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摘要

An extensive investigation on the conformational characteristics of four deoxydinucleoside monophosphates, namely, dApdA, dApdT, dTpdA, and dTpdT was carried through calculation of the classical potential energy of the systems. The four major types of sugar-pucker sequences, namely, 3E-3E, 3E-2E, 2E-3E, 2E-2E, were included in the study. For each of the units, energies were computed for 96 starting conformations that resulted from the consideration of all possible low energy regions for the relevant seven dihedral angles and the four sugar-pucker sequences, and minimized by permitting all the seven dihedral angles to vary simultaneously. The number and the order of preference of low energy conformations obtained were found to be characteristic of the base sequence of the unit considered. The conformational states close to the A-DNA, B-DNA, C-DNA, and Watson-Crick DNA structures are noted to be preferred for all the units except dTpdT. The 3E-2E sugar-pucker sequence is the most favored and the 2E-3E sequence is the least favored state in terms of the associated number of local minima. For each unit, there exists a set of specific conformational states with more or less equal stabilities but different sugar-pucker sequences. The mixed sugar-pucker states 2E-3E and 3E-2E, when incorporated, in the conventional A-DNA and B-DNA conformational states, respectively, have energies that allow them to act as intermediates in the B form in equilibrium with A form transitions. Such transitions are most likely to occur at sites with a Thymine-Adenine base sequence. Available experimental results were interpreted in terms of their stabilities.
机译：通过计算系统的经典势能，对四种脱氧二核苷单磷酸（dApdA，dApdT，dTpdA和dTpdT）的构象特征进行了广泛的研究。研究包括糖折叠序列的四种主要类型，即3E-3E，3E-2E，2E-3E，2E-2E。对于每个单元，计算了96个起始构象的能量，这些构象是由于考虑了相关的七个二面角和四个糖褶序列的所有可能的低能区域而产生的，并通过允许所有七个二面角同时变化来最小化。发现获得的低能构象的数目和优先顺序是所考虑单元的基本序列的特征。注意到除了dTpdT以外，所有单位都优选接近A-DNA，B-DNA，C-DNA和Watson-Crick DNA结构的构象状态。就局部极小值的相关数目而言，最受青睐的是3E-2E糖折叠序列，最受青睐的是2E-3E序列。对于每个单元，存在一组特定的构象状态，其具有或多或少相等的稳定性，但糖折叠序列不同。掺入糖的折叠状态2E-3E和3E-2E分别以常规的A-DNA和B-DNA构象态结合时具有的能量使其能够以与A形式平衡的形式充当B形式的中间体过渡。这种转变最有可能发生在具有胸腺嘧啶-腺嘌呤碱基序列的位点。可用的实验结果根据其稳定性进行了解释。

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