title: NMR structure of a gemcitabine-substituted model Okazaki fragment.
abstract: Gemcitabine (2'-deoxy-2',2'-difluorodeoxycytidine; dFdC) is a potent anticancer drug that exerts cytotoxic activity, in part, through incorporation of the nucleoside triphosphate dFdCTP into DNA and perturbations to DNA-mediated processes. The structure of a model Okazaki fragment containing a single dFdC substitution, [GEM], was determined using NMR spectroscopy and restrained molecular dynamics to understand structural distortions that may be induced in replicating DNA resulting from dFdC substitution. The electrostatic surface of [GEM] was also computed to determine how the geminal difluoro group of dFdC perturbs DNA electrostatics. The stability of [GEM] was investigated using temperature-dependent UV spectroscopy. dFdC adopted a C3'-endo conformation in [GEM] and decreased the melting temperature of the duplex by 4.3 degrees C. dFdC substitution did not decrease helical stacking among adjacent purines in the DNA duplex region. dFdC substitution substantially altered the electrostatic properties of the model Okazaki fragment, with increased electron density in the vicinity of the geminal difluoro group. The results are consistent with dFdC substitution altering the structural, electrostatic, and thermodynamic properties of DNA and interfering in DNA-mediated processes. Interference in DNA-mediated processes due to dFdC substitution likely contributes to the anticancer activity of dFdC.
authors.affiliation: Graduate Group in Biophysics and Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA.
authors.forename: David
authors.initials: D
authors.lastname: Konerding
authors.forename: Thomas L
authors.initials: TL
authors.lastname: James
authors.forename: Eric
authors.initials: E
authors.lastname: Trump
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Soto
authors.forename: Luis A
authors.initials: LA
authors.lastname: Marky
authors.forename: William H
authors.initials: WH
authors.lastname: Gmeiner
mesh_terms: D000964:Antimetabolites, Antineoplastic; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004261:DNA Replication; D003841:Deoxycytidine / Q000031:analogs & derivatives*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D055672:Static Electricity; D013816:Thermodynamics; D000093542:Gemcitabine
chemical_list: D000964:Antimetabolites, Antineoplastic; C022262:Okazaki fragments; D009838:Oligodeoxyribonucleotides; D003841:Deoxycytidine; D004247:DNA; D000093542:Gemcitabine