Yathindra N, Sundaralingam M
Proc Natl Acad Sci U S A. 1974 Sep;71(9):3325-8. doi: 10.1073/pnas.71.9.3325.
The possible backbone phosphodiester conformations in a dinucleoside monophosphate and a dinucleoside triphosphate have been investigated by semiempirical energy calculations. Conformational energies have been computed as a function of the rotations omega' and omega about the internucleotide P-O(3') and P-O(5') linkages, with the nucleotide residues themselves assumed to be in one of the preferred [C(3')-endo] conformations. The terminal phosphates in a dinucleoside triphosphate greatly limit the possible conformations for the backbone (in a polynucleotide) compared to a dinucleoside monophosphate. There appear to be two major types of conformations that are favored for the backbone. The phosphodiester conformation (omega',omega) approximately (290 degrees ,290 degrees ) characteristic of helical structures is one of them, indicating that the polynucleotide backbone shows an inherent tendency for the helical conformation. The other favored conformation is centered at (omega',omega) approximately (190 degrees ,300 degrees ) and results in an extended backbone structure with unstacked bases. A third possible conformation centered at (omega', omega) approximately (200 degrees , 60 degrees ) and the (190 degrees , 300 degrees ) conformation appear to be important for the folding of a polynucleotide chain. The conformation (omega',omega) approximately (80 degrees ,80 degrees ), observed in a dinucleoside monophosphate and believed to be a candidate for producing an abrupt turn in a polynucleotide chain, is found to be stereochemically unfavorable in a dinucleoside triphosphate and a polynucleotide.
通过半经验能量计算研究了单磷酸二核苷和三磷酸二核苷中可能的主链磷酸二酯构象。构象能量是作为围绕核苷酸间P - O(3')和P - O(5')键的旋转ω'和ω的函数来计算的，假定核苷酸残基本身处于优选的[C(3')-内型]构象之一。与单磷酸二核苷相比，三磷酸二核苷中的末端磷酸极大地限制了（多核苷酸中）主链的可能构象。主链似乎有两种主要的有利构象类型。螺旋结构特有的磷酸二酯构象（ω'，ω）约为（290度，290度）是其中之一，表明多核苷酸主链具有形成螺旋构象的内在趋势。另一种有利构象以（ω'，ω）约为（190度，300度）为中心，导致碱基未堆积的伸展主链结构。以（ω'，ω）约为（200度，60度）为中心的第三种可能构象和（190度，300度）构象似乎对多核苷酸链的折叠很重要。在单磷酸二核苷中观察到的（ω'，ω）约为（80度，80度）的构象，被认为是多核苷酸链中产生突然转折的候选构象，发现在三磷酸二核苷和多核苷酸中在立体化学上是不利的。
