Relative Reactivity of Ribosyl 2'-OH vs. 3'-OH in Concentrated Aqueous Solutions of Phosphoimidazolide Activated Nucleotides

Details Relative Reactivity of Ribosyl 2'-OH vs. 3'-OH in Concentrated Aqueous Solutions of Phosphoimidazolide Activated Nucleotides Relative Reactivity of Ribosyl 2'-OH vs. 3'-OH in Concentrated Aqueous Solutions of Phosphoimidazolide Activated Nucleotides

Oct 1999

adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1999oleb...29..473k&link_type=abstract

Origins of Life and Evolution of the Biosphere, v. 29, Issue 5, p. 473-487 (1999).

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Scientific paper

Phosphoimidazolide activated ribomononucleotides (*pN, see structure) are useful substrates for the non-enzymatic synthesis of oligonucleotides. In the presence of metal ions, aqueous solutions of *pN yield primarily the two internucleotide-linked (pN^2'pN and pN^3'pN) and the pyrophosphate-linked (N^5'ppN) dimers. Small amounts of cyclic dimers and higher oligomers are also produced. In this study the relative reactivity of 2'-OH vs. 3'-OH was determined from the ratio of the yields of pN^2'pN vs. pN^3'pN. Experiments were performed at 23 °C in the range 7.2 <= pH <= 8.4 with substrates that differ in nucleobase (guanosine (G), cytidine (C), uridine (U), and adenosine (A)) and leaving group (imidazole (Im), 2-methylimidazole (2-MeIm) and 2,4-dimethylimidazole (2,4-diMeIm)). Two metal ions (Mg^2+ or Mn^2+) were employed as catalysts. The conditions used here, i.e. a substrate concentration in the range 0.1 M to 1.0 M and metal ion concentration in the range 0.05 M to 0.2 M, favor base-stacking interactions. The ratio pN^2'pN: pN^3'pN = 2'-5': 3'-5' was found independent of nucleobase and typically varied between 2 to 3 indicating that the 2'-OH is about 2 to 3 times more reactive than the 3'-OH. *pN with Im, compared to 2-MeIm and 2,4-diMeIm leaving group, produce lower yields of internucleotide linked dimers, and a higher pN^2'pN: pN^3'pN ratio. Trends in the data, observed with all three leaving groups, suggest an increase in pN^2'pN: pN^3'pN ratio with decreasing substrate concentration (up to 5.47 with 0.051 M ImpG). The observations are in accord with earlier studies reporting a relative reactivity 2'-5': 3'-5'= 6 to 9 obtained with Im as the leaving group, in dilute nucleotide solutions and under conditions that disfavor stacking. It is speculated that the concentration induced change in the relative reactivity is the result of self-association via base-stacking that enhances selectively the proximity of the 3'-OH of one molecule to the reactive P-N bond of an other molecule. The implication of these conclusions for oligomerization/ligation reactions is discussed.

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