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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 available in a repository.
This paper is available in a repository.

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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.