Prebiotic RNA Engineering in a Clay Matrix: Molecular Modeling Rationale and Mechanistic Proposals for Explaining Helicity, Antiparallelism and Prebiotic Replication of Nucleic Acids
DOI:
https://doi.org/10.37155/2972-449X-vol1(2)-75Keywords:
Antiparallel stacking, Auto-intercalation, Clay matrix, Montmorillonite, Nucleic acids helicity, Origin of life, RNA replication, Tetraplexes, ViroidsAbstract
In the last few years, a renewed interest has been devoted to the origin of life. Nucleic acids have a central role in biogenesis and prebiotic synthesis of ribose, purines and pyrimidines has been described. Particularly attractive is the idea that life on Earth was first founded on simple and autocatalytic RNA molecules (RNA world). RNA duplexes are formed by helical and antiparallel chains, but the rationale for these features is not yet known. An inverted (antiparallel) stacking of purine rings from guanosine and other nucleosides has been found in crystallographic studies. Molecular modeling also supports an inverted conformation, and this preferential stacking occurs when they are aggregated within a clay (montmorillonite) matrix, which is confirmed by spectral studies. Thus, crystallography, spectroscopy and molecular modeling allow proposing a “zipper” model in which antiparallel nucleosides stack within the clay matrix, and then high-energy polyphosphates form auto-intercalated single RNA chains. Unstacking and strand separation result in the shortening and inclination of the ribose-phosphate chains, leading to helicity, antiparallelism and base pairing by H-bonding, with formation of typical RNA structures such as hairpins, cloverleaves, hammerheads, dumbbells, circular viroids and virusoids. A “tetris” model for the prebiotic self-replication mechanism of these simple RNA duplexes, involving the formation of an RNA tetraplex, is also proposed.
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