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Original article (peer-reviewed)

Journal CHEMISTRY & BIODIVERSITY
Volume (Issue) 9(9)
Page(s) 2050 - 2063
Title of proceedings CHEMISTRY & BIODIVERSITY

Abstract

Deletion of the substituted pyrimidine ring in purine-2'-deoxynucleoside 5'-monophosphates leads to the artificial nucleotide analogue dImMP2–. This analogue can be incorporated into DNA to yield upon addition of Ag+ ions a molecular wire. Here we measured the acidity constants of H2(dImMP)± having one proton at N3 and one at the PO32– group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N3 is somewhat more basic than PO32– and consequently, the (H•dImMP)– tautomer with the proton at N3 dominates to about 75 %. The calculated micro acidity constants are confirmed by 31P and 1H NMR shift measurements. The here assembled data allow many quantitative comparisons, e.g., the N3-protonated and thus positively charged imidazole residue facilitates deprotonation of the P(O)2(OH)– group by 0.3 pK units. Knowledge of the intrinsic site basicities also allows predictions about metal-ion binding; e.g., Mg2+ and Mn2+ will primarily coordinate to the phosphate group whereas Ni2+ and Cu2+ will preferably bind to N3. Macrochelate formation for these metal ions is also predicted. The micro acidity constant for (N3)H+ deprotonation in the (H•dImMP•H)± species (pka = 6.46) and the Mn+ binding properties are of relevance for understanding the behaviour of dImMP units present in DNA hairpins and metalated duplexes.
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