Conversion of a Ribozyme to a Deoxyribozyme through In Vitro Evolution

Paul, Natasha; Springsteen, Greg; Joyce, Gerald F.

doi:10.1016/j.chembiol.2006.01.007

Cited by 40 publications

(24 citation statements)

References 61 publications

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“…Similarly, DNA versions of some in vitro-selected RNA aptamers retain binding activity toward their targets (39). Additionally, a ribozyme ligase sequence was evolved into an active deoxyribozyme by only a few mutations (40). Finally, classical studies of various DNA-RNA chNA versions of the hammerhead ribozyme have demonstrated that some DNA substitutions can increase (41) or decrease activity (42).…”

Section: Discussionmentioning

confidence: 99%

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

Trevino

Zhang

Elenko

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Multiple lines of evidence support the hypothesis that the early evolution of life was dominated by RNA, which can both transfer information from generation to generation through replication directed by base-pairing, and carry out biochemical activities by folding into functional structures. To understand how life emerged from prebiotic chemistry we must therefore explain the steps that led to the emergence of the RNA world, and in particular, the synthesis of RNA. The generation of pools of highly pure ribonucleotides on the early Earth seems unlikely, but the presence of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone heterogeneity. We suggest that homogeneous monomers might not have been necessary if populations of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible, function would have to be maintained despite the repeated scrambling of backbone chemistry from generation to generation. We have tested this possibility in a simplified model system, by using a T7 RNA polymerase variant capable of transcribing nucleic acids that contain an approximately 1∶1 mixture of deoxy-and ribonucleotides. We readily isolated nucleotide-binding aptamers by utilizing an in vitro selection process that shuffles the order of deoxy-and ribonucleotides in each round. We describe two such RNA/DNA mosaic nucleic acid aptamers that specifically bind ATP and GTP, respectively. We conclude that nonheritable variations in nucleic acid backbone structure may not have posed an insurmountable barrier to the emergence of functionality in early nucleic acids.abiogenesis | genetic takeover | RNA progenitor | origin of life G iven that RNA is likely to have played a key role early in the evolution of life (1), understanding the origins of the RNAbased biosphere is a critical aspect of understanding the origin of life. The difficulties associated with the prebiotic synthesis of a macromolecule as complicated and fragile as RNA have stimulated interest in the hypothesis that RNA was preceded by simpler and/or more stable progenitor nucleic acids (2-4). The systematic exploration of nucleic acids that are structurally related to RNA has revealed that the formation of stable WatsonCrick base-paired, antiparallel duplex structures is compatible with a surprising degree of variation in the sugar-phosphate backbone (5). These studies imply that many distinct nucleic acids are in principle capable of mediating the inheritance of genetic information. On the other hand, recent advances in the prebiotic chemistry leading to the pyrimidine ribonucleotides (6) have revived the prospects of the RNA-first model, with the attendant advantage of avoiding a difficult genetic takeover. Both RNAfirst and RNA-late models assume that life began with a single, well-defined genetic polymer. Perhaps the greatest problem implicit in this assumption is the challenge of explaining the origin of pure nucleotide monomers on the early Earth. Indeed, the supp...

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Section: Discussionmentioning

confidence: 99%

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

Trevino

Zhang

Elenko

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…The core octamer of the ribosomal peptidyl transferase is also the favored binding site sequence adjacent to a transition state analog for peptide bond formation (Yarus and Welch 2000). This implies that this core peptidyl transferase sequence came from selection on a molecule very like modern RNA (because RNA activities are usually disrupted by minor modification of their nucleotides [Paul et al 2006]). Similarly, in all four cases so far examined, successively squeezed selection shows that the simplest binding sites for Ile (Lozupone et al 2003), Trp , His , and Arg (Janas et al 2010) contain essential cognate coding triplets.…”

Section: Rna Chemistry and Evolutionary Questionsmentioning

confidence: 99%

Chiral histidine selection by D-ribose RNA

Illangasekare

Turk²,

Peterson³

et al. 2010

RNA

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The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L-and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/ requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four-to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.

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“…Although there is no known example of a deoxyribozyme in nature, catalytic variants selected in vitro to perform peroxidations were observed for hemin aptamers (212). Alternatively, the translation of the catalytic function encoded by a ribozyme with RNA ligase activity into a deoxyribozyme can be obtained by directed in vitro evolution of the translated sequence (161). In this report, Joyce and coworkers demonstrate that the basic chemistry of the ribozyme catalytic activity could be detected in the evolved deoxyribozyme although the value of the catalytic parameters and the stereospecificity were not preserved.…”

Section: Protein Engineeringmentioning

confidence: 97%

Protein Engineering of Redox-Active Enzymes

Saab‐Rincón

Valderrama

2009

Antioxidants & Redox Signaling

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Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.

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Conversion of a Ribozyme to a Deoxyribozyme through In Vitro Evolution

Cited by 40 publications

References 61 publications

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

Chiral histidine selection by D-ribose RNA

Protein Engineering of Redox-Active Enzymes

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