Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation

Abstract

We have recently shown that 2-aminoimidazole is a superior nucleotide activating group for nonenzymatic RNA copying. Here we describe a prebiotic synthesis of 2-aminoimidazole that shares a common mechanistic pathway with that of 2-aminooxazole, a previously described key intermediate in prebiotic nucleotide synthesis. In the presence of glycolaldehyde, cyanamide, phosphate and ammonium ion, both 2-aminoimidazole and 2-aminooxazole are produced, with higher concentrations of ammonium ion and acidic pH favoring the former. Given a 1:1 mixture of 2-aminoimidazole and 2-aminooxazole, glyceraldehyde preferentially reacts and cyclizes with the latter, forming a mixture of pentose aminooxazolines, and leaving free 2-aminoimidazole available for nucleotide activation. The common synthetic origin of 2-aminoimidazole and 2-aminooxazole and their distinct reactivities are suggestive of a reaction network that could lead to both the synthesis of RNA monomers and to their subsequent chemical activation.

Scheme 1. Common Prebiotic Synthetic Pathway for 2-Aminooxazole (2NH₂Ox) and 2-Aminoimidazole (2NH₂Im)

P_i: inorganic phosphate.

Figure 1

(a) Possible mechanism for the synthesis of 2NH₂Ox and 2NH₂Im. The initial formation of α-aminoacetaldehyde is thought to be a potential intermediate on the path to 2NH₂Im, although this exchange reaction may also occur after addition of cyanamide. (b) Partial ¹H NMR spectrum (400 MHz, D₂O) showing the H4/H5 aromatic resonances for 2NH₂Ox (red) and 2NH₂Im (blue) after reaction of glycolaldehyde, cyanamide, sodium phosphate and ammonium chloride, all at 1 M, for 3 h at pH 7 and 60 °C.

Figure 2

Bar graph displaying the ratios of 2NH₂Im to 2NH₂Ox at varying pH and NH₄Cl concentrations. All ratios were determined by ¹H NMR spectroscopy from reactions that were carried out at 60 °C with 1 M sodium phosphate, and monitored over a period of 3 h.

Figure 3

Selective cyclization of rac-glyceraldehyde with 2NH₂Ox in the presence of 2NH₂Im. The reaction was carried out at 1 M of each component and was monitored by high-resolution (Q-TOF) LC-MS using a C₁₈ column. All traces are extracted ion chromatograms for m/z values that correspond to the [M + H]⁺ ions for 2NH₂Ox (red), 2NH₂Im (blue) and the mixture of aminooxazoline stereoisomers (green). All chromatograms were extracted with a tolerance ±0.1 Da. The 24 h chromatograms have been displayed offset by ∼10 s for clarity.

Scheme 2. Synthesis of Cytidine-5′-phosphoro-(2-aminoimidazole) Making Use of N-cyano-2-aminoimidazole