title: Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties.
abstract: Circular dichroism (CD) and UV-melting experiments were conducted with 16 oligodeoxynucleotides modified by the carcinogen 2-aminofluorene, whose sequence around the lesion was varied systematically [d(CTTCTNG[AF]NCCTC), N = G, A, C, T], to gain insight into the factors that determine the equilibrium between base-displaced stacked (S) and external B-type (B) duplex conformers. Differing stabilities among the duplexes can be attributed to different populations of S and B conformers. The AF modification always resulted in sequence-dependent thermal (T(m)) and thermodynamic (-DeltaG degrees ) destabilization. The population of B-type conformers derived from eight selected duplexes (i.e. -AG*N- and -CG*N-) was inversely proportional to the -DeltaG degrees and T(m) values, which highlights the importance of carcinogen/base stacking in duplex stabilization even in the face of disrupted Watson-Crick base pairing in S-conformation. CD studies showed that the extent of the adduct-induced negative ellipticities in the 290-350 nm range is correlated linearly with -DeltaG degrees and T(m), but inversely with the population of B-type conformations. Taken together, these results revealed a unique interplay between the extent of carcinogenic interaction with neighboring base pairs and the thermodynamic properties of the AF-modified duplexes. The sequence-dependent S/B heterogeneities have important implications in understanding how arylamine-DNA adducts are recognized in nucleotide excision repair.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA.
authors.forename: Srinivasa Rao
authors.initials: SR
authors.lastname: Meneni
authors.forename: Rhijuta
authors.initials: R
authors.lastname: D'Mello
authors.forename: Gregory
authors.initials: G
authors.lastname: Norigian
authors.forename: Gregory
authors.initials: G
authors.lastname: Baker
authors.forename: Lan
authors.initials: L
authors.lastname: Gao
authors.forename: M Paul
authors.initials: MP
authors.lastname: Chiarelli
authors.forename: Bongsup P
authors.initials: BP
authors.lastname: Cho
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D018736:DNA Adducts / Q000737:chemistry*; D005092:Exonucleases / Q000378:metabolism; D005449:Fluorenes / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D021241:Spectrometry, Mass, Electrospray Ionization; D013816:Thermodynamics
chemical_list: C052668:2-aminofluorene-DNA complex; D018736:DNA Adducts; D005449:Fluorenes; D009838:Oligodeoxyribonucleotides; D005092:Exonucleases