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Todisco, M.

Publications and source records attributed to Todisco, M..

6 recordsLinked to original sources

Stereoselectivity of Aminoacyl-RNA Loop-closing Ligation

The origin of amino acid homochirality remains an unresolved question in the origin of life. The requirement of enantiopure nucleotides for nonenzymatic RNA copying strongly suggests that homochirality of nucleotides and RNA arose early. However, this leaves open the question of whether and how homochiral RNA subsequently imposed biological homochirality on other metabolites including amino acids. Previous studies have reported moderate stereoselectivity for various aminoacyl-RNA transfer reactions. Here we examine aminoacyl-RNA loop-closing ligation, a reaction that captures aminoacylated RNA in a stable phosphoramidate product, such that the amino acid bridges two nucleotides in the RNA backbone. We find that the rate of this reaction is much higher for RNA aminoacylated with L-amino acids than D-amino acids. We present an RNA sequence that near-exclusively captures L-amino acids in loop-closing ligation. Finally, we demonstrate that ligation of aminoacyl-L-RNA results in inverse stereoselectivity for D-amino acids. The observed stereochemical link between D-RNA and L-amino acids in the synthesis of RNA stem-loops containing bridging amino acids constitutes a stereoselective structure building process. We suggest that this process led to a selection for the evolution of aminoacyl-RNA synthetase ribozymes that were selective for L-amino acids, thereby setting the stage for the subsequent evolution of homochiral peptide and ultimately protein synthesis.

biochemistry↗

Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ribozyme

Autocatalytic reactions driving the self-assembly of biological polymers are important for the origin of life, yet few experimental examples of such reactions exist. Here we report an autocatalytic assembly pathway that generates a chimeric, amino acid-bridged aminoacyl-RNA synthetase ribozyme. The noncovalent complex of ribozyme fragments initiates low level aminoacylation of one of the fragments, which after loop-closing ligation generates a highly active covalently-linked chimeric ribozyme. The generation of this ribozyme is increasingly efficient over time due to the autocatalytic assembly cycle that sustains the ribozyme over indefinite cycles of serial dilution. Due to its trans activity, this ribozyme also assembles ribozymes distinct from itself, such as the hammerhead, suggesting that RNA aminoacylation, coupled with nonenzymatic ligation, could have facilitated the emergence and propagation of ribozymes.

biochemistry↗

RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends

Multiple RNA strands can interact in solution and assume a large variety of configurations dictated by their potential for base pairing. Although duplex formation from two complementary oligonucleotides has been studied in detail, we still lack a systematic characterization of the behavior of higher order complexes. Here we focus on the thermodynamic and kinetic effects of an upstream oligonucleotide on the binding of a downstream oligonucleotide to a common template, as we vary the sequence and structure of the contact interface. We show that coaxial stacking in RNA is well correlated with but much more stabilizing than helix propagation over an analogous intact double helix step (median {Delta} {Delta} G37{degrees}C {approx} 1.7 kcal/mol). Consequently, approximating coaxial stacking in RNA with the helix propagation term leads to large discrepancies between predictions and our experimentally determined melting temperatures, with an offset of {approx} 10{degrees}C. Our kinetic study reveals that the hybridization of the downstream probe oligonucleotide is impaired (lower kon) by the presence of the upstream oligonucleotide, with the thermodynamic stabilization coming entirely from an extended lifetime (lower koff) of the bound downstream oligonucleotide, which can increase from seconds to months. Surprisingly, we show that the effect of nicks is dependent on the length of the stacking oligonucleotides, and we discuss the binding of ultrashort (1 [~] 4 nt) oligonucleotides that are relevant in the context of the origin of life. The thermodynamic and kinetic data obtained in this work allow for the prediction of the formation and stability of higher order multi-stranded complexes. Graphic entry for the Table of Contents (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/589350v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@8b11d3org.highwire.dtl.DTLVardef@3f55c6org.highwire.dtl.DTLVardef@185703org.highwire.dtl.DTLVardef@1f8a9e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Structure-guided aminoacylation and assembly of chimeric RNAs

Coded ribosomal peptide synthesis could not have evolved unless its sequence and amino acid specific aminoacylated tRNA substrates already existed. We therefore wondered whether aminoacylated RNAs might have served some primordial function prior to their role in protein synthesis. Here we show that specific RNA sequences can be nonenzymatically aminoacylated and ligated to produce amino acid-bridged stem-loop RNAs. We used deep sequencing to identify RNAs that undergo highly efficient glycine aminoacylation followed by loop-closing ligation. The crystal structure of one such glycine-bridged RNA hairpin reveals a compact internally stabilized structure with the same eponymous T-loop architecture found in modern tRNA. We demonstrate that the T-loop assisted amino acid bridging of RNA oligonucleotides enables the rapid template-free assembly of a chimeric version of an aminoacyl-RNA synthetase ribozyme. We suggest that the primordial assembly of such chimeric ribozymes would have allowed the greater functionality of amino acids to contribute to enhanced ribozyme catalysis, providing a driving force for the evolution of sequence and amino acid specific aminoacyl-RNA synthetase enzymes prior to their role in protein synthesis.

biochemistry↗

Transient States During Oligonucleotides Hybridization: Insights from Annealing Kinetics of Mismatches and Bulges

Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully vs. partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.

biochemistry↗

Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides

Hybridization and strand displacement kinetics determine the evolution of the base-paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt - 12nt) as simple functions of oligonucleotide length, CG content, {Delta}G of hybridization and {Delta}G of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.

biochemistry↗