title: Digital and analog chemical evolution.
abstract: Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life.  These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment.  The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution.  Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.
authors.affiliation: Center for Fundamental and Applied Molecular Evolution, NSF/NASA Center for Chemical Evolution, Department of Chemistry, Emory University, Atlanta, Georgia, USA.
authors.forename: Jay T
authors.initials: JT
authors.lastname: Goodwin
authors.forename: Anil K
authors.initials: AK
authors.lastname: Mehta
authors.forename: David G
authors.initials: DG
authors.lastname: Lynn
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism; D001704:Biopolymers / Q000737:chemistry / Q000378:metabolism; D019418:Evolution, Chemical; D056004:Molecular Dynamics Simulation; D011685:Purine Nucleotides / Q000737:chemistry / Q000378:metabolism; D011741:Pyrimidine Nucleosides / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism
chemical_list: D016229:Amyloid beta-Peptides; D001704:Biopolymers; D011685:Purine Nucleotides; D011741:Pyrimidine Nucleosides