title: Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy.
abstract: We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag]n+ sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl- and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA>pdA and (pA)n>>(pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity.
authors.affiliation: Laboratoire de Dynamique Interactions et Réactivité, UMR 7075, Université Paris 6 CNRS, 2 rue Henri Dunant, 94320, Thiais, France.
authors.forename: Lydie
authors.initials: L
authors.lastname: Grajcar
authors.forename: Chahrazade
authors.initials: C
authors.lastname: El Amri
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Ghomi
authors.forename: Serge
authors.initials: S
authors.lastname: Fermandjian
authors.forename: Valerie
authors.initials: V
authors.lastname: Huteau
authors.forename: Richard
authors.initials: R
authors.lastname: Mandel
authors.forename: Sophie
authors.initials: S
authors.lastname: Lecomte
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Baron
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D002712:Chlorides / Q000494:pharmacology; D004247:DNA / Q000737:chemistry*; D008274:Magnesium / Q000494:pharmacology; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012964:Sodium / Q000494:pharmacology; D013059:Spectrum Analysis, Raman; D020349:Surface Plasmon Resonance
chemical_list: D002712:Chlorides; D012313:RNA; D004247:DNA; D012964:Sodium; D008274:Magnesium; D000225:Adenine