Role of helicity in the nonenzymatic template-directed primer extension of DNA

Abstract

A 2-fold (2AI-dA) and 4.5-fold (2AI-dC) increase in nonenzymatic template-directed primer extension of DNA was observed when a conformational shift was induced by RNA binding.

The Impact of Activating Agents on Non‐Enzymatic Nucleic Acid Extension Reactions

“…There is increasing evidence to support the reactivity difference between RNA and DNA being due to a structural difference in the helix and nucleotide conformation adopted by each system. [19,49] rather than the chemical differences between the deoxyribose and ribose sugars. [28] The (deoxy)ribose sugars of DNA and RNA are pentose sugars and so do not sit in a planar conformation in solution.…”

“…This reactivity difference is important as DNA preferentially adopts a B-type helix but can adopt an A-type helix under the influence of solvent conditions [51] or binding factors. [49] However, steric occlusion of the 2'-OH in RNA results in the A-type helix being preferentially adopted.…”

“…[35] The reactivity of DNA could be improved by pushing DNA into the more reactive A-type conformation, either through solvent effects [51] or binding partners. [49] The use of 3'-NH 2 -DNA in which the 3'-hydroxyl has been replaced with a more nucleophilic amine group has been suggested as a more reactive alternative to DNA. [17,21a,24,54] The 3'-NH 2 -DNA is particularly efficient because in addition to the increased nucleophilicity of the amine group they adopt an A-type helix with a strong monomer preference for the C3'-endo conformation.…”