Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling

We have analyzed previously three representative p53 single-point mutations by capillary-electrophoresis single-strand conformation polymorphism (CE-S SCP). In the current study, we compared our CE-SSCP results with the potent ial secondary structures predicted by an RNA/DNA-folding algorithm with DNA , energy rules, used in conjunction with a computer analysis workbench call ed STRUCTURELAB. Each of these mutations produces measurable shifts in CE m igration times relative to wild type. Using computerized folding analysis, each of the mutations was found to have a conformational difference relativ e to wild type, which accounts for the observed differences in CE migration . Additional properties exhibited in the CE electropherograms were also exp lained using the computerized analysis. These include the appearance of sec ondary peaks and the temperature dependence of the electrophoretic patterns . The results yield insight into the mechanism of SSCP and how the conditio ns of this measurement, especially temperature, may be optimized to improve the sensitivity of the SSCP method. The results may also impact other diag nostic methods, which would benefit by a better understanding of DNA single -strand conformation polymorphisms to optimize conditions for enzymatic cle avage and DNA hybridization reactions.