Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation

TY - JOUR

T1 - Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation

AU - Sönnichsen, S H

AU - Nielsen, Peter E.

PY - 1996/5/1

Y1 - 1996/5/1

N2 - 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.

AB - 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.

KW - Base Sequence

KW - Edetic Acid/pharmacology

KW - Ferrous Compounds/pharmacology

KW - Hydroxyl Radical

KW - Molecular Sequence Data

KW - Nucleic Acid Conformation

KW - Nucleic Acid Hybridization

KW - Oligodeoxyribonucleotides/chemical synthesis

KW - Photochemistry

KW - Quaternary Ammonium Compounds/pharmacology

KW - Uranyl Nitrate/pharmacology

U2 - 10.1002/(SICI)1099-1352(199605)9:3%3C219::AID-JMR242%3E3.0.CO;2-S

DO - 10.1002/(SICI)1099-1352(199605)9:3%3C219::AID-JMR242%3E3.0.CO;2-S

M3 - Journal article

C2 - 8938594

SN - 0952-3499

VL - 9

SP - 219

EP - 227

JO - Journal of Molecular Recognition

JF - Journal of Molecular Recognition

IS - 3

ER -