Hydrogen exchange as a probe of the dynamic structure of DNA: I. General acid-base catalysis☆

摘要: Abstract In this paper it is shown that positively-charged proton transfer agents can catalyze the exchange-out from native DNA of hydrogens involved in internucleotide hydrogen-bonding. The negatively-charged catalysts tested did not increase rate exchange. effectiveness hydronium ion catalysis decreased by increasing concentrations sodium ion, while hydroxide increased. measured rates presence various be quantitatively accounted for terms a Bronsted-type relationship involving pK′A values both catalyst and titratible sites DNA, plus superimposed electrostatic effect phosphates which decreases facilitates species. two types chemically distinct exchange (amino imino groups), do participate independently exchange, since addition affects all kinetic classes equally. These results support hypothesis (Printz & von Hippel, 1968) interchain proceeds via local, transiently-open (non-hydrogen bonded) conformational state maintained (“propped” open) (at acid pH) or no alkaline at locus NH … N hydrogen bond. over-all process appears to depend on product equilibrium constant formation open (propped) sites, initial protons exposed process.