Examination of prebiotic adaptor models

Abstract

Some models of the prebiotic protein synthesizing mechanism involve hairpin helices as adaptor molecules (Hopfield, 1978: Kuhn and Waser, 1981: Crothers, 1982). We examined the feasibility of hairpin strands to act as primitive adaptor molecules (Kuhn and Waser, 1981). Both right and left handed helices were used in the analysis of the stereochemical feasibility of the simultaneous recognition of the anticodon by the codons on messenger RNA and peptide condensation between two amino acids carried by adjacent hairpin strands. Initially right handed hairpin helices were constructed using the anticodon loop of the crystal structure of tRNA (Sussman et al., 1978). A complex of two such hairpin strands aligned on a messenger RNA was constructed, such that the anticodons recognize the codons by the normal Watson-Crick base pairing scheme. The dihedral angles in the junction region of the nucleotide chain between the two codons were varied to bring the two hairpin strands together for peptide bond condensation. The conformation corresponding to the closest approach of the two hairpin helices corresponds to a distance between the 2'hydroxyl oxygens on the 3'-end nucleotides in the two hairpins, (where the amino acid gets attached) of 26.5A. It is evident that if two amino acids are attached to the 2' oxygens of the adjacent hairpin helices, peptide bond condensation between the two amino acids is not possible. In the second instance, we examined the feasibility of hairpin strands with left handed helices making use of the crystal structure of Z-DNA (Wang et al., 1979). Kuhn and his co-workers in a series of papers (Kuhn and Waser, 1981: Lehmann and Kuhn, 1984) suggest a sequence of three (anticodon) nucleotides to be in the loop region of the hairpin helices. Gralla and Crothers (1973) suggest that a hairpin loop of three nucleotides is destabilizing thermodynamically. They further propose that a loop of three nucleotides will exist when the bases flanking the loop are not in a base pairing configuration. Marky and Olson (1982) suggest that even a loop length of four will be possible only when there is a lot of flexibility in the chain. From energy minimization studies of dApdApdAp, Ponnuswamy and