ArticleRNA (New York, N.Y.)2003
Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme.
Article in RNA (New York, N.Y.), 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins.Life (Basel, Switzerland) · 2019Article
- Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction.Nature chemistry · 2019Article
- Extensive libraries of gene truncation variants generated by in vitro transposition.Nucleic acids research · 2017Article
- Many Activities, One Structure: Functional Plasticity of Ribozyme Folds.Molecules (Basel, Switzerland) · 2016Review
- Improving the odds: Influence of starting pools on in vitro selection outcomes.Methods (San Diego, Calif.) · 2016Review
- DNA-catalyzed glycosylation using aryl glycoside donors.Chemical communications (Cambridge, England) · 2016Article
- RNA synthesis by in vitro selected ribozymes for recreating an RNA world.Life (Basel, Switzerland) · 2015Review
- Conversion of biosynthetic precursors of RNA to those of DNA by photoredox chemistry.Journal of molecular evolution · 2014Article
- The origins of the RNA world.Cold Spring Harbor perspectives in biology · 2012Review
- Assembly and activation of a kinase ribozyme.RNA (New York, N.Y.) · 2010Article
- Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure.Journal of the American Chemical Society · 2010Article
- Functional nucleic acid sensors.Chemical reviews · 2009Review
- Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection.Nucleic acids research · 2006Article
- Extensive 3' modification of plant small RNAs is modulated by helper component-proteinase expression.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Ribozyme motif structure mapped using random recombination and selection.RNA (New York, N.Y.) · 2005Article
- An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We previously isolated from random sequences ribozymes able to form a glycosidic linkage between a ribose sugar and 4-thiouracil in a reaction that mimics protein-catalyzed nucleotide synthesis. Here we report on two serial in vitro selection experiments that defined the core motif of one of the nucleotide synthase ribozymes and provided improved versions of this ribozyme. The first selection experiment started from a degenerate sequence pool based on the previously isolated sequence and used a selection-amplification protocol that allowed the sequence requirements at the 3' terminus of the ribozyme to be interrogated. Comparing the active sequences identified in this experiment revealed the complicated secondary structure of the nucleotide synthase ribozyme. A second selection was then performed to remove nonessential sequence from the ribozyme. This selection started with a pool with variation introduced in both the sequence and the length of the nonconserved loops and joining regions. This pool was generated using a partial reblocking/deblocking strategy on a DNA synthesizer, allowing the combinatorial synthesis of both point deletions and point substitutions. The consensus ribozyme motif that emerged was an approximately 71 nt pseudoknot structure with five stems and two important joining segments. Comparative sequence analysis and a cross-linking experiment point to the probable location of nucleotide synthesis. The prototype isolate from the second selection was nearly 35 times more efficient than the initial isolate and at least 10(8) times more efficient than an upper limit of an as-yet undetectable uncatalyzed reaction, supporting the idea that RNA-catalyzed nucleotide synthesis might have been important in an RNA world.
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