Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation.
The uranyl(VI)-mediated photocleavage of a Drew-Dickerson sequence oligonucleotide (5'-dGATCACGC-GAATTCGCGT) either as the (self-complementary) duplex or cloned into the BamH1 site of pUC19 has been studied. At pH 6.5 in acetate buffer relatively enhanced photocleavage is observed at the 3'-end of the AATT sequence corresponding to maximum cleavage across the minor groove in the A/T tract. Thus maximum cleavage correlates with minimum minor groove width in the crystal structure and also with the largest electronegative potential according to computations. Using plasmid constructs with cloned inserts of the type [CGCG(A/T4)]n, we also analysed all possible sequence combinations of the (A/T)4 tract and in all cases we observed maximum uranyl-mediated photocleavage across the minor groove in the (A/T)4 tract without any significant differences between the various sequences. From these results we infer that DNA double helices of all (A/T)4 sequences share the same narrow minor groove helix conformation.
Sönnichsen
S H
SH
Department of Medical Biochemistry and Genetics, Panum Institute, University of Copenhagen, Denmark.
Nielsen
P E
PE
D001483:Base Sequence; D004492:Edetic Acid / Q000494:pharmacology; D005296:Ferrous Compounds / Q000494:pharmacology; D017665:Hydroxyl Radical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000528:radiation effects; D010777:Photochemistry; D000644:Quaternary Ammonium Compounds / Q000494:pharmacology; D014502:Uranyl Nitrate / Q000494:pharmacology*
D005296:Ferrous Compounds; D009838:Oligodeoxyribonucleotides; D000644:Quaternary Ammonium Compounds; D014502:Uranyl Nitrate; D017665:Hydroxyl Radical; D004492:Edetic Acid; C038178:ammonium ferrous sulfate