Molecular informatics: Hydrogen-bonding, error-coding, and genetic replication

In the error-coding approach to nucleotide alphabet composition, the recognition features of nucleotides are mapped to 4-bit numbers, capturing the hydrogen acceptor/donor patterns (3-bits) and the purine/pyrimidine size motif (1-bit). From the perspective of fidelity, optimal alphabets are composed of nucleotides in which nucleotide size is related to the hydrogen acceptor/donor pattern as a parity bit. The natural alphabet appears to be a subset of one of two optimal solutions, constrained by a combination of chemical and coding-theory factors. This study reviews the validity of this approach, which depends on how reasonably the interaction energies of potentially associating hydrogen donor/acceptor patterns may be interpreted in terms of logic functions applied to corresponding binary interpretations of the patterns. Some physicochemical challenges and limitations of hydrogen D/A patterns as templates for molecularly encoded information are also considered. These have implications not just for our understanding of the genetic alphabet, but also for the enormous variety of molecular systems exploiting hydrogen D/A patterns for the purpose of recognition and assembly, and which offer, at least in principle, the potential for an alternative basis for encoding and transmitting molecular information.