title: Fluorescence probing of aminofluorene-induced conformational heterogeneity in DNA duplexes.
abstract: Fluorescence spectroscopy was used to study carcinogen-induced conformational heterogeneity in DNA duplexes. The fluorophore 2-aminopurine (AP) was incorporated adjacent (5') to the lesion (G*) in eight different DNA duplexes [d(5'-CTTCT PG* NCCTC-3'):d(5'-GAGGN XTAGAAG-3'), G* = FAF adduct, P = AP, N = G, A, C, T, and X = C, A] modified by FAF [ N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene], a fluorine-tagged model DNA adduct derived from the potent carcinogen 2-aminofluorene. Steady-state measurements showed that fluorescence intensity and Stern-Volmer constants ( Ksv) derived from acrylamide quenching experiments decreased for all carcinogen-modified duplexes relative to the controls, which suggests greater AP stacking in the duplex upon adduct formation. Conformation-specific stacking of AP with the neighboring adduct was evidenced by a sequence-dependent variation in fluorescence intensity, position of emission maximum, degree of emission quenching by acrylamide, and temperature-dependent spectral changes. The magnitude of stacking was in the order of FAF residue in base-displaced stacked (S) > minor groove wedged (W) > major groove B type (B). This work represents a novel utility of AP in probing adduct-induced conformational heterogeneities in DNA duplexes.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences and Physics, University of Rhode Island, Kingston, RI 02881, USA.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Jain
authors.forename: Yana K
authors.initials: YK
authors.lastname: Reshetnyak
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: D015075:2-Aminopurine / Q000737:chemistry; D020106:Acrylamide / Q000737:chemistry; D002273:Carcinogens / Q000737:chemistry*; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D018736:DNA Adducts / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D005449:Fluorenes / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods
chemical_list: D002273:Carcinogens; D018736:DNA Adducts; D005449:Fluorenes; D020106:Acrylamide; C012177:2-aminofluorene; D015075:2-Aminopurine