Fig. 2: Determinants of an efficient amino acid-catalysed oligomerisation of nucleoside-2′,3′-cyclic phosphates.

a pH dependence of the cNMP (10 mM) oligomerisation without amino acid (black) and with valine (blue), glycine (olive) and lysine (orange) (50 mM) are presented for the pH range 3−12. The chemical structures of nucleotides and amino acids are given as insets with pK_a or pK_aH values (red) of the (de)protonatable groups⁶⁰. b The rate of cCMP (10 mM) oligomerisation in the absence and presence of valine (50 mM) is plotted. c Valine concentration-dependence (0−50 mM) of the cCMP (10 mM) oligomerisation is plotted at pH 9−12 to get insights into the mechanism of the amino acid-catalysed RNA oligomerisation. d Proposed mechanism of amino acid-catalysed RNA oligomerisation. In the dry state, due to the proximity and orientation effects, the amine group of the amino acid (1) may act as a general base to facilitate proton transfer from the 5′−OH of the nucleotide, which attacks the cyclic phosphate of a second nucleotide whilst the ammonium moiety of zwitterionic amino acid (1*, protonated form of 1), may act as a general acid to facilitate proton transfer to the 2′−OH or 3′−OH. Acid-base catalysis can also be achieved by nucleobases, such as guanine (2 and its protonated form 2*) or uracil, as they both have pK_a values close to the amine pK_aH of the amino acids. The mechanism in the opposite direction can be followed for acid-base-catalysed RNA fragmentation¹³. e Proposed transition state complex of the reaction of valine-catalysed cCMP oligomerisation based on quantum chemical calculations using a simplified model (Fig. S20); colour codes: C—grey, N—blue, O—red, H—white, P—orange; H-bonds are shown in green dotted lines. All the experiments were performed at 25 °C. Isotope fits for the molecules in (a−c) are given in Supplementary Data 2. Source data are available for panels (a−c).