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Synthesis and acid-Base properties of an imidazole-containing nucleotide analog, 1-(2'-Deoxy-B-D-ribofuranosyl)imidazole 5'-monophosphate (dImMP2-)


Megger, N; Johannsen, S; Mueller, J; Sigel, Roland K O (2012). Synthesis and acid-Base properties of an imidazole-containing nucleotide analog, 1-(2'-Deoxy-B-D-ribofuranosyl)imidazole 5'-monophosphate (dImMP2-). International Journal of Chemistry Research, 9(9, SI):2050-2063.

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 PO32- group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N(3) is somewhat more basic than PO32- and, consequently, the (H center dot dImMP)(-) tautomer with the proton at N(3) dominates to ca. 75%. The calculated micro acidity constants are confirmed by P-31- and H-1-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., Mg2+ and Mn2+ will primarily coordinate to the phosphate group, whereas Ni2+ and Cu2+ 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 center dot dImMP center dot H)(+/-) species (pk(a) 6.46) and the Mn+-binding properties are of relevance for understanding the behavior of dImMP units present in DNA hairpins and metalated duplexes.

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 PO32- group by potentiometric pH titrations in aqueous solution. The micro acidity constants show that N(3) is somewhat more basic than PO32- and, consequently, the (H center dot dImMP)(-) tautomer with the proton at N(3) dominates to ca. 75%. The calculated micro acidity constants are confirmed by P-31- and H-1-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., Mg2+ and Mn2+ will primarily coordinate to the phosphate group, whereas Ni2+ and Cu2+ 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 center dot dImMP center dot H)(+/-) species (pk(a) 6.46) and the Mn+-binding properties are of relevance for understanding the behavior of dImMP units present in DNA hairpins and metalated duplexes.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Language:English
Date:2012
Deposited On:05 Mar 2013 11:58
Last Modified:17 Nov 2016 08:58
Publisher:Academic Sciences
ISSN:0976-5689
Publisher DOI:https://doi.org/10.1002/cbdv.201100437
PubMed ID:22976990
Permanent URL: https://doi.org/10.5167/uzh-75257

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