Kinetic and mechanistic analysis of dinucleotide and oligonucleotide formation from the 5′-phosphorimidazolide of adenosine on Na+-montmorillonite

Article abstract of DOI:10.1021/ja00096a013

The rate constants for the condensation reaction of the 5′-phosphorimidazolide of adenosine (ImpA) to form dinucleotides and oligonucleotides have been measured in the presence of Na⁺-volclay (a Na⁺-montmorillonite) in pH 8 aqueous solution at 25 °C. The rates of the reaction of ImpA with an excess of adenosine 5′-monophosphoramidate (NH₂pA), .P₁,P₂-diadenosine 5′,5′-pyrophosphate (A5′ppA), or adenosine 5′-monophosphate (5′-AMP or pA) in the presence of the montmorillonite to form NH₂pA^3′pA, A^5′ppA^3′pA, and pA^3′pA, respectively, were measured. Only 3′,5′-linked products were observed. The magnitude of the rate constants decrease in the order NH₂pA^3′pA > A^5′-ppA^3′pA > pA^3′pA. The binding of ImpA to montmorillonite was measured, and the adsorption isotherm was determined. The binding of ImpA to montmorillonite and the formation of higher oligonucleotides is not observed in the absence of salts. Mg²⁺ enhances binding and oligonucleotide formation more than Ca²⁺ and Na⁺. The rate constants for the oligonucleotide formation were determined from the reaction products formed from 10 to 40 mM ImpA in the presence of Na⁺-montmorillonite using the computer program SIMFIT. The magnitudes of the rate constants for the formation of oligonucleotides increased in the order 2-mer < 3-mer < 4-mer ? 7-mer. The rate constants for dinucleotide and trinucleotide formation are more than 1000 times larger than those measured in the absence of montmorillonite. The rate constants for the formation of dinucleotide, trinucleotide, and tetranucleotide are 41, 2.6, and 3.7 times larger than those for the formation of oligo(G)s with a poly(C) template. The hydrolysis of ImpA was accelerated 35 times in the presence of the montmorillonite. The catalytic ability of montmorillonite to form dinucleotides and oligonucleotides is quantitatively evaluated and possible pathways for oligo(A) formation are proposed.