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Wiley, Chemistry and Biodiversity, 9(9), p. 2050-2063, 2012

DOI: 10.1002/cbdv.201100437

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Synthesis and AcidBase Properties of an Imidazole-Containing Nucleotide Analog, 1-(2′-Deoxy-β-D-ribofuranosyl)imidazole 5′-Monophosphate (dImMP2−)

Journal article published in 2012 by Nicole Megger, Silke Johannsen, Jens Müller ORCID, Roland K. O. Sigel
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Deletion of the substituted pyrimidine ring in purine-2'-deoxynucleoside 5'-monophosphates leads to the artificial nucleotide analog dImMP(2-) . This analog can be incorporated into DNA to yield, upon addition of Ag(+) ions, a molecular wire. Here, we measured the acidity constants of H(2) (dImMP)(±) having one proton at N(3) and one at the PO$\rm{{_{3}^{2-}}}$ group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N(3) is somewhat more basic than PO$\rm{{_{3}^{2-}}}$ and, consequently, the (H⋅ dImMP)(-) tautomer with the proton at N(3) dominates to ca. 75%. The calculated micro acidity constants are confirmed by (31) P- and (1) H-NMR chemical shifts. The assembled data allow many quantitative comparisons, e.g., the N(3)-protonated and thus positively charged imidazole residue facilitates deprotonation of the P(O)(2) (OH)(-) group by 0.3 pK units. Information on the intrinsic site basicities also allows predictions about metal-ion binding; e.g., Mg(2+) and Mn(2+) will primarily coordinate to the phosphate group, whereas Ni(2+) and Cu(2+) will preferably bind to N(3). Macrochelate formation for these metal ions is also predicted. The micro acidity constant for N(3)H(+) deprotonation in the (H ⋅ dImMP⋅H)(±) species (pk(a)  6.46) and the M(n+) -binding properties are of relevance for understanding the behavior of dImMP units present in DNA hairpins and metalated duplexes.