title: Base sequence-dependent bends in site-specific benzo[a]pyrene diol epoxide-modified oligonucleotide duplexes.
abstract: The site specifically modified oligonucleotides 5'-d(TCCTCCTG1G2CCTCTC) (I) and 5'-d(CTATG1G2G3TATC) (II) were synthesized with single modified guanine residues at positions G1, G2, or G3, derived from the covalent binding reaction of 7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene ((+)-anti-BPDE) with the exocyclic amino groups of the guanine residues. In denaturing 20% polyacrylamide gels, the electrophoretic mobilities of the (+)-anti-BPDE-modified oligonucleotides I and II are slower than the mobilities of the respective unmodified oligonucleotides and independent of the positions of the BPDE-modified guanines. However, in the double-stranded forms in native 8% polyacrylamide gels, the electrophoretic mobilities of the duplexes with lesions at G2 or G3 are remarkably slower (reductions in mobilities up to approximately 40%) than to duplexes with lesions at G1 and are attributed to physical bends or flexible hinge joints at the sites of the BPDE lesions. These sequence-dependent mobility effects occur whenever the BPDE-modified guanine residues with (+)-trans-stereochemistry are flanked by unmodified G's on the 5'-side. These retarded electrophoretic mobilities are attributed to bending induced by steric hindrance effects involving the bulky 5'-flanking guanines and the pyrenyl residues that are known to point into the 5'-direction relative to the modified G [Cosman, M., et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1914-1918]. These anomalous electrophoretic mobility effects are not observed in the case of (-)-anti-BPDE-modified sequences I with trans-(-)-anti-BPDE-N2-dG adduct stereochemistry.
authors.affiliation: Chemistry Department, New York University 10003, USA.
authors.forename: T
authors.initials: T
authors.lastname: Liu
authors.forename: J
authors.initials: J
authors.lastname: Xu
authors.forename: H
authors.initials: H
authors.lastname: Tsao
authors.forename: B
authors.initials: B
authors.lastname: Li
authors.forename: R
authors.initials: R
authors.lastname: Xu
authors.forename: C
authors.initials: C
authors.lastname: Yang
authors.forename: S
authors.initials: S
authors.lastname: Amin
authors.forename: M
authors.initials: M
authors.lastname: Moriya
authors.forename: N E
authors.initials: NE
authors.lastname: Geacintov
mesh_terms: D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / Q000737:chemistry / Q000633:toxicity*; D001483:Base Sequence / Q000187:drug effects; D002942:Circular Dichroism; D018736:DNA Adducts / Q000187:drug effects; D004249:DNA Damage; D003854:Deoxyribonucleotides / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D006147:Guanine / Q000737:chemistry; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000187:drug effects*; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry / Q000302:isolation & purification
chemical_list: D018736:DNA Adducts; D003854:Deoxyribonucleotides; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide; D006147:Guanine