Giessner-Prettre C, Ribas Prado F, Pullman B, Kan L, Kast J R, Ts'o P O
Comput Programs Biomed. 1981 Sep-Dec;13(3-4):167-83. doi: 10.1016/0010-468x(81)90096-9.
A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.
介绍了一个名为SHIFTS的FORTRAN计算机程序。通过SHIFTS，可以计算已知序列和预定构象的单链和双链核酸质子共振的核磁共振化学位移。该程序可以处理由6种碱基类型（A、U、G、C、I和T）中的4种组成的任意序列的RNA和DNA。有A-、A'-、B-、D-和S-构象的几何参数数据文件。使用SEQ程序[1]的修改版本计算所有原子的位置。然后，基于此定义的几何结构，分别计算相邻核苷酸的原子对每个单体单元质子施加的三种化学位移效应：环电流屏蔽效应；局部原子磁化率效应（包括抗磁和顺磁项）；以及极化或电场效应。将该程序的结果与γ（ApApGpCpUpU）2螺旋双链体的实验结果以及基于A'-型和B-型模型构建以及评估环电流效应的图形程序对同一螺旋的计算结果进行了比较。
