A computer-generated supercoiled model of the pUC19 plasmid

• Published in: European biophysics journal Vol. 34; no. 1; pp. 13 - 18
• Main Authors: Kümmerle, E A, Pomplun, E
• Format: Journal Article
• Language: English
• Published: Germany Springer Nature B.V 01.02.2005
• Subjects: Algorithms; Computer Simulation; Deoxyribonucleic acid; DNA; Models, Chemical; Models, Molecular; Monte Carlo Method; Monte Carlo simulation; Motion; Nucleic Acid Conformation; Nucleic Acid Denaturation; Plasmids - chemistry; Plasmids - ultrastructure; Temperature
• ISSN: 0175-7571; 1432-1017
• DOI: 10.1007/s00249-004-0431-2

DNA models have become a powerful tool in the simulation of radiation-induced molecular damage. Here, a computer code was developed which calculates the coordinates of individual atoms in supercoiled plasmid DNA. In this prototype study, the known base-pair sequence of the pUC19 plasmid has been utilized. The model was built in a three-step process. Firstly, a Monte Carlo simulation was performed to shape a segment chain skeleton. Checks on elastic energy, distance and unknotting were applied. The temperature was considered in two different ways: (1) it was kept constant at 293 K and (2) it was gradually reduced from 350 K to less than 10 K. Secondly, a special smoothing procedure was introduced here to remove the edges from the segment chain without changing the total curve length while avoiding the production of overshooting arcs. Finally, the base pair sequence was placed along the smoothed segment chain and the positions of all the atoms were calculated. As a first result, a few examples of the supercoiled plasmid models will be presented, demonstrating the strong influence of appropriate control of the system temperature.