Z-curve: A computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature

作     者：Lee, SS Park, K Kang, CW 

作者机构：Korea Adv Inst Sci & Technol Dept Biol Sci Taejon 305701 South Korea 

出 版 物：《MOLECULES AND CELLS》 (分子与细胞)

年 卷 期：1999年第9卷第4期

页      面：350-357页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 07[理学] 

主　　题：computer program DNA curvature or bendin end-to-end distance gel mobility shift graphics wedge model 

摘      要：In order to predict curvature of DNA fragments, we previously developed a computer program for simply calculating a vectorial sum of all individual roll, tilt and twist wedge angles between the nearest base pairs for a given DNA fragment [Lee et al,, (1991)], Now a new program, called Z-curve, was developed to calculate three-dimensional coordinates of the helical center of each base pair along the DNA, using helical axis deviations from B-form DNA by wedge angles. The output file of the new program was designed to become an input file for a graphics program, Insight II. Thus, we were able to obtain three-dimensional graphic presentations of DNA helical axis curvatures of any length. It visualized spatial details of the DNA curvature, where and how much it curves, and to which direction, It also allowed calculation of the three-dimensional distance between two ends of a DNA fragment, which could provide a measure of its curvature, Here, three DNA fragments, both curved and straight, were subjected to the Z-curve and Insight II programs. The results showed that their curvature details could be visualized to the level of the base pair, whether the DNA fragments contained an oligo(A) track or not. Their estimated curvatures mere consistent with the experimental results of permutation gel mobility assay.