title: Influence of an 8-oxoadenine lesion on the structural and dynamic features of a 30-mer DNA fragment with and without a mismatch.
abstract: OBJECTIVE
  To elucidate the influence of the oxidative lesion 7,8-dihydro-8-oxoadenine (8-oxoA) on the structural and dynamic features of a 30-mer DNA fragment, and to understand if differences occur when C is positioned opposite 8-oxoA instead of T.
  
  
  METHODS
  Two 30-mer DNA oligomers with or without the 8-oxoA and two complementary oligomers with C or T base opposite the lesion site were synthesized and annealed. Duplexes named AT, A*T, AC and A*C were characterized by means of circular dichroism and UV denaturation measurements. gamma-Ray footprinting experiments were performed to give insight into their fine three-dimensional structure. Elastic torsional constants were derived by following the decay of the fluorescence polarization anisotropy (FPA) of the ethidium-DNA complexes measured by multifrequency-phase fluorometry.
  
  
  RESULTS
  The introduction of one oxidative lesion in a 30-mer DNA oligomer with and without a mismatch did not cause relevant changes in their overall conformation and slightly modified their elastic properties. Small energetic differences were revealed by thermodynamic analysis in the sample bearing both the oxidative lesion and the mismatch. Minor variations in the cleavage pattern due to the hydroxyl radicals in the A*T sample were observed and present along the entire DNA fragment length. In the A*C sample, by contrast, there was a major modification in the cleavage pattern extending for about 11 bases around the lesion, especially towards the 5'-end.
  
  
  CONCLUSIONS
  Differences in the fine structure and in the elastic properties between the A*T and A*C samples were observed, while their overall conformation was unchanged. The results are consistent with the hypothesis that the observed local changes of the double helix structure in A*C are due to the pairing of the oxidized adenine in a syn conformation with the cytosine.
authors.affiliation: Laboratorio di Fisica, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Rome, Italy. barone@iss.it
authors.forename: F
authors.initials: F
authors.lastname: Barone
authors.forename: L
authors.initials: L
authors.lastname: Cellai
authors.forename: C
authors.initials: C
authors.lastname: Giordano
authors.forename: G
authors.initials: G
authors.lastname: La Sala
authors.forename: F
authors.initials: F
authors.lastname: Mazzei
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives* / Q000633:toxicity*; D016880:Anisotropy; D020137:Base Pair Mismatch; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000187:drug effects*; D004249:DNA Damage; D005720:Gamma Rays; D006863:Hydrogen-Ion Concentration; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D010100:Oxygen / Q000378:metabolism; D011487:Protein Conformation; D013050:Spectrometry, Fluorescence; D014466:Ultraviolet Rays
chemical_list: D009841:Oligonucleotides; C002992:8-hydroxyadenine; D004247:DNA; D000225:Adenine; D010100:Oxygen