Diepoxybutane and epibromohydrin bend DNA towards the major groove
Document Type Dissertation/Thesis
Diepoxybutane (DEB) and epibromohydrin (EBH) are small organic molecules that can form cross links between strands of DNA. DEB and EBH form covalent bonds between the deoxyguanosines in complementary 5'-GNC sequences (N=any base). We investigated possible bending of cross-linked DNA oligomers from 30-42 bp in length. After the oligomers were cross-linked, labeled, and ligated, polyacrylamide gels were used to quantitatively determine the degree of bending. Because A-tracts (5 successive adenine residues on a single strand) are known to bend DNA towards the minor groove (Koo et al 1990), oligomers with A-tracts positioned either a whole or half helical turn away from the cross-linking site were used to determine the direction of the induced bend. The DNA samples were compared to normal DNA strands of the same complementarity with a retarded electrophoretic mobility indicating bending. Analyses of native polyacrylamide gels revealed that DEB and EBH bend DNA towards the major groove. The degree of bending calculated from the differences in actual versus apparent base pair lengths was an average of 33? per helical turn for both epoxides.