Diepoxybutane and diepoxyoctane interstrand cross-linking of the 5S DNA nucleosomal core particle

Diepoxyalkanes form interstrand cross-links in DNA oligomers preferentially at 5 ' -GNC sites. We have examined cross-linking by 1,2,3,4-diepoxybutane (DEB) and 1,2,7,8-diepoxyoctane (DEO) within a fragment of the 5S RNA gene of Xenopus borealis in both the free and nucleosomal states. Sites and eff iciencies of interstrand cross-linking were probed through denaturing polya crylamide gel electrophoresis and quantitative phosphorimagery. Both agents targeted 5 ' -GNC sites for cross-linking in the restriction fragment in i ts free state, and DEO also targeted 5 ' -GNNC sites. Monoalkylation occurr ed at all deoxyguanosines. The sites for both monoalkylation and interstran d cross-linking were similar in nucleosomal and free DNA, and cross-linked DNA was cleanly incorporated into the core particle structure. These findin gs suggest that the 5S core particle is able to tolerate any structural abn ormalities induced by diepoxide cross-linking.