Computer simulation of DNA supercoiling in a simple elastomechanical approximation

✍ Scribed by Pavla Šelepová; Jaroslav Kypr

• Publisher: Wiley (John Wiley & Sons)
• Year: 1985
• Tongue: English
• Weight: 769 KB
• Volume: 24
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360240510

✦ Synopsis

Synopsis

DNA supercoiling is both an interesting problem from the theoretical point of view and an important phenomenon affecting DNA functions in viuo. Experimentally, however, hardly more than the overall hydrodynamic shape, superhelical density, and enzymic or chemical reactivity of the parameters that are in some way related to DNA secondary and tertiary structure in the superhelical state can be determined. Consequently, it is highly desirable to build up models of DNA supercoiling that, on the one hand, match the above type of global data and, on the other, take advantage of the knowledge about DNA structure at lower levels of complexity, i.e., with linear DNA molecules and its synthetic models. One possible approach, presented here, deals with an extension of Fuller's and Benham's general ideas concerning an elastomechanical model of DNA supercoiling. We extend their model with an algorithm suitable for numerical calculations and construct a fast computer program, ROPASE, that displays the rod shapes as dependent on its elastic properties and applied stress. Development of this program made inevitable a detailed analysis of the input parameters found to be degenerate in the sense that not all of them should be considered variable to generate the whole set of possible solutions of the model. Many calculations were performed using ROPASE to test its properties and the properties of the elastomechanical model. Representative DNA shapes are presented.