Joint optimization of replication potential and information storage set the letter size of primordial genetic alphabet

TL;DR

This paper explores the evolutionary advantages of a four-letter genetic alphabet over a two-letter one, demonstrating that four-letter sequences are necessary for predictable folding and optimal replication in early RNA/DNA-like molecules.

Contribution

It introduces a model showing that four-letter heteropolymer sequences are essential for stable secondary structure and replication potential, considering asymmetric cooperativity.

Findings

Four-letter sequences enable predictable secondary structure formation.

Palindromic sequences optimize replication potential.

Four-letter alphabet outcompetes two-letter in early evolution scenarios.

Abstract

The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing, given the inherent difficulties in the simultaneous and localized prebiotic synthesis of all four monomers of progenitors of DNA from common precursors on early Earth. Excluding the scenario where a two-letter alphabet genome eventually expanded to include two more letters to code for more amino acids on teleological grounds, we show here that a heteropolymer sequence in the RNA-world-like scenario would have had to be composed of at least four letters in order to predictably fold into a specific secondary structure, and hence must have outcompeted the two-letter alphabet genomes. Using a model that we previously used to demonstrate the evolutionary advantages of unidirectional replication and anti-parallel strand orientation of duplex DNA, we show here that the competing constraints of maximum replicative potential and predictable secondary structure formation can be simultaneously satisfied only by palindromic heteropolymer sequences composed of a minimum of four letters, within the premise of the presence of sequence-dependent asymmetric cooperativity in these RNA/DNA progenitors.