The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural selection for the first functional sequences. Fitness landscapes are the subject of much speculation, but their structure is essentially unknown. Here we describe a comprehensive map of a fitness landscape, exploring nearly all of sequence space, for short RNAs surviving selection in vitro. With the exception of a small evolutionary network, we find that fitness peaks are largely isolated from one another, highlighting the importance of historical contingency and indicating that natural selection would be constrained to local exploration in the RNA world.T he nucleotide sequence of an organism's genome determines its fitness in a given selective environment. All possible sequences of length L constitute a discrete sequence space containing 4 L points. Including fitness as another variable creates a "landscape" in sequence space, in which highly fit sequences occupy peaks (1, 2). Evolution can be thought of as a random walk on this landscape with a bias toward climbing peaks (3). Knowledge of the fitness landscape is a fundamental prerequisite for a quantitative understanding of evolution. Although several models of theoretical landscapes have been proposed (reviewed in refs. 4 and 5), there is a lack of empirical data. Landscapes based on RNA secondary structure have been explored computationally, but the relationship to function is unknown (6-10). Experimental efforts at determining a comprehensive fitness landscape are generally stymied by the astronomical size of sequence space, but synthesis of nearly every variant is feasible for relatively short sequences (i.e., RNAs with length L <30 nucleotides). Therefore, complete landscapes for short RNAs could be mapped in principle. Such landscapes are of particular interest for understanding evolution in the RNA world of early life (11)(12)(13)(14).Limited fitness landscapes localized around known functional sequences have been explored for proteins (15-17), viruses (18, 19), and functional nucleic acids, including ribozymes and ribosomal RNA (20-24). The local fitness landscape around a known RNA ligase ribozyme (L = 54) was mapped using highthroughput sequencing (25). However, random sampling of RNA and DNA sequence space can be done by in vitro selection, or SELEX, for de novo discovery of functional molecules (26)(27)(28)(29). Such studies generally take very sparse samples of sequence space, owing to their focus on obtaining functional, and therefore longer, sequences. Thorough sampling techniques have been used to explore all possible DNA targets for a known DNAbinding protein (30). Such studies illuminate the biology of extant organisms but do not address the initial evolution of macromolecular activity. The entirety of a macromolecular fitness landscape has not yet been explored. Therefore, fundamental questions about the shape of fitn...

Non-enzymatic, template-directed synthesis of nucleic acids is a paradigm for self-replicating systems. The evolutionary dynamics of such systems depend on several factors, including the mutation rates, relative replication rates, and sequence characteristics of mutant sequences. We measured the kinetics of correct and incorrect monomer insertion downstream of a primer-template mismatch (mutation), using a range of backbone structures (RNA, DNA, and LNA templates and RNA and DNA primers) and two types of 5′-activated nucleotides (oxyazabenzotriazolides and imidazolides, i.e., nucleoside 5’-phosphorimidazolides). Our study indicated that for all systems studied, an initial mismatch was likely to be followed by another error (54-75% of the time) and extension after a single mismatch was generally 10-100 times slower than extension without errors. If the mismatch was followed by a matched base pair, the extension rate recovered to nearly normal levels. Based on these data, we simulated nucleic acid replication in silico, which indicated that a primer suffering an initial error would lag behind properly extended counterparts due to a cascade of subsequent errors and kinetic stalling, with the typical mutational event consisting of several consecutive errors. Our study also included different sequence contexts, which suggest the presence of cooperativity among monomers affecting both absolute rate (by up to two orders of magnitude) and fidelity. The results suggest that molecular evolution in enzyme-free replication systems would be characterized by large ‘leaps’ through sequence space rather than isolated point mutations, perhaps enabling rapid exploration of diverse sequences. The findings may also be useful for designing self-replicating systems combining high fidelity with evolvability.

Many approaches to the origin of life focus on how the molecules found in biology might be made in the absence of biological processes, from the simplest plausible starting materials. Another approach could be to view the emergence of the chemistry of biology as process whereby the environment effectively directs “primordial soups” toward structure, function, and genetic systems over time. This does not require the molecules found in biology today to be made initially, and leads to the hypothesis that environment can direct chemical soups toward order, and eventually living systems. Herein, we show how unconstrained condensation reactions can be steered by changes in the reaction environment, such as order of reactant addition, and addition of salts or minerals. Using omics techniques to survey the resulting chemical ensembles we demonstrate there are distinct, significant, and reproducible differences between the product mixtures. Furthermore, we observe that these differences in composition have consequences, manifested in clearly different structural and functional properties. We demonstrate that simple variations in environmental parameters lead to differentiation of distinct chemical ensembles from both amino acid mixtures and a primordial soup model. We show that the synthetic complexity emerging from such unconstrained reactions is not as intractable as often suggested, when viewed through a chemically agnostic lens. An open approach to complexity can generate compositional, structural, and functional diversity from fixed sets of simple starting materials, suggesting that differentiation of chemical ensembles can occur in the wider environment without the need for biological machinery.

Research on prebiotic chemistry and the origins of nucleic acids and proteins has traditionally been focussed on only one or the other. However, if nucleotides and amino acids co-existed on the early Earth, their mutual interactions and reactivity should be considered explicitly. Here we set out to investigate nucleotide/nucleoside formation by simple dehydration reactions of constituent building blocks (sugar, phosphate, and nucleobase) in the presence of different amino acids. We demonstrate the simultaneous formation of glycosidic bonds between ribose, purines, and pyrimidines under mild conditions without catalysts or activated reagents, as well as nucleobase exchange, in addition to the simultaneous formation of nucleotide and nucleoside isomers from several nucleobases. Clear differences in the distribution of glycosylation products are observed when glycine is present. This work demonstrates that reaction networks of nucleotides and amino acids should be considered when exploring the emergence of catalytic networks in the context of molecular evolution.