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

Content Provider	Springer Nature Link
Author	Kanavarioti, Anastassia Lee, Lynn F. Gangopadhyay, Sumana
Copyright Year	1999
Abstract	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.
Starting Page	473
Ending Page	487
Page Count	15
File Format	PDF
ISSN	01696149
Journal	Origins of Life and Evolution of Biospheres
Volume Number	29
Issue Number	5
e-ISSN	15730875
Language	English
Publisher	Kluwer Academic Publishers
Publisher Date	1999-01-01
Publisher Place	Dordrecht
Access Restriction	Subscribed
Subject Keyword	Organic Chemistry Geochemistry Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Ecology, Evolution, Behavior and Systematics Space and Planetary Science

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