ArticleRNA (New York, N.Y.)2011
Characterization of the B6.61 polymerase ribozyme accessory domain.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Kinetic Effects of β,γ-Modified Deoxynucleoside 5'-Triphosphate Analogues on RNA-Catalyzed Polymerization of DNA.Biochemistry · 2021Article
- Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution.Chemical reviews · 2020Review
- An RNA polymerase ribozyme that synthesizes its own ancestor.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Non-Enzymatic Assembly of a Minimized RNA Polymerase Ribozyme.ChemSystemsChem · 2019Article
- The NTP binding site of the polymerase ribozyme.Nucleic acids research · 2018Article
- Visualizing primer extension without enzymes.eLife · 2018Article
- Transitioning to DNA genomes in an RNA world.eLife · 2017Article
- Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function.Nature chemistry · 2017Article
- Amplification of RNA by an RNA polymerase ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- RNA synthesis by in vitro selected ribozymes for recreating an RNA world.Life (Basel, Switzerland) · 2015Review
- Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides.RNA (New York, N.Y.) · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The "RNA world" hypothesis rests on the assumption that RNA polymerase ribozymes can replicate RNA without the use of protein. In the laboratory, in vitro selection has been used to create primitive versions of such polymerases. The best variant to date is a ribozyme called B6.61 that can extend a RNA primer template by 20 nucleotides (nt). This polymerase has two domains: the recently crystallized Class I ligase core, responsible for phosphodiester bond formation, and the poorly characterized accessory domain that makes polymerization possible. Here we find that the accessory domain is specified by a 37-nt bulged stem-loop structure. The accessory domain is positioned by a tertiary interaction between the terminal AL4 loop of the accessory and the J3/4 triloop found within the ligase core. This docking interaction is associated with an unwinding of the A3 and A4 helixes that appear to facilitate the correct positioning of an essential 8-nt purine bulge found between the two helices. This, together with other constraints inferred from tethering the accessory domain to a range of sites on the ligase core, indicates that the accessory domain is draped over the vertex of the ligase core tripod structure. This geometry suggests how the purine bulge in the polymerase replaces the P2 helix in the Class I ligase with a new structure that may facilitate the stabilization of incoming nucleotide triphosphates.
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