Pohorille A, Loew G H
Biophys Chem. 1985 Jun;22(1-2):37-51. doi: 10.1016/0301-4622(85)80024-7.
Base-pairing properties of O-methylated nucleic-acid bases have been systematically investigated using both semi-empirical quantum-mechanical methods and a second-order perturbation formalism. The energetic, steric and electronic properties of (a) the individual methylated bases, (b) possible base-pairs formed between O-methylated and normal bases, and (c) mini-helices incorporating O-methylated bases were calculated. Two types of base-paired complexes were obtained: Those involving classical linear hydrogen bonds, and those involving bifurcated hydrogen-donor-hydrogen-acceptor interactions. In most complexes the presence of mispairs in the helical structure of nucleic acids is expected to create a local perturbation in the structure of the helix. Even though the most stable planar configurations of the mispairs may deviate markedly from those in the regular double helix, the induced deformations in the structure of the backbone are relatively small. Internal energies and geometries of mispairs are strongly affected by the conformation of the exocyclic group of the methylated bases. Another important contribution to the stability of various base-pairing schemes comes from stacking interactions.
已使用半经验量子力学方法和二阶微扰形式体系，对O - 甲基化核酸碱基的碱基配对特性进行了系统研究。计算了以下各项的能量、空间和电子特性：(a) 单个甲基化碱基；(b) O - 甲基化碱基与正常碱基之间可能形成的碱基对；(c) 包含O - 甲基化碱基的小螺旋。得到了两种类型的碱基配对复合物：一种涉及经典的线性氢键，另一种涉及分叉的氢供体 - 氢受体相互作用。在大多数复合物中，核酸螺旋结构中错配的存在预计会在螺旋结构中产生局部扰动。尽管错配的最稳定平面构型可能与规则双螺旋中的构型明显不同，但主链结构中的诱导变形相对较小。错配的内能和几何形状受甲基化碱基环外基团构象的强烈影响。各种碱基配对方案稳定性的另一个重要贡献来自堆积相互作用。
