Conformation and Energetics of Supercoiled DNA: Experimental and Theoretical Studies
Although DNA supercoiling has been known for years to be intimately associated with many aspects of transcription, replication, and recombination, the structure of superhelical DNA in solution has only recently begun to be understood. Because significant supercoiling requires a DNA molecule at least 1kb in size, high-resolution techniques such as X-ray diffraction and NMR spectroscopy are not applicable. Much of the classical information about the structure of supercoiled DNA comes from hydro-dynamic and related techniques such as sedimentation, light-, X-ray-, and neutron-scattering. These techniques are sensitive to the large-scale polymer behavior of macromolecules reflected in quantities such as the mean chain radius, but give little insight into details of structure without a model for polymer-chain organization. Electron microscopy (EM) has been frequently used as a semiquantitative tool for examining the structure of supercoiled DNA; however, the images of superhelical molecules visualized by electron microscopy have only recently been quantitatively analyzed and reconciled with theoretical models (Boles et al. 1990). The interpretation of EM data requires assumptions about effects of heavy-metal staining, dehydration, shadowing, and the interaction of DNA with the grid surface, all of which are difficult to test. Gel electrophoresis is one potentially powerful technique that is highly sensitive to the topological state of a DNA molecule; however, the effect of supercoiling on electrophoretic mobility remains poorly understood.
KeywordsHelical Twist Molecular Dynamic Technique Molecular Mechanic Model Bend Locus Trial Conformation
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