Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization [PDF]
RNA, 2005 We have used a compartmentalized in vitro selection method to directly select for ligase ribozymes that are capable of acting on and turning over separable oligonucleotide substrates. Starting from a degenerate pool, we selected a trans-acting variant of the Bartel class I ligase which statistically may have been the only active variant in the starting
Karl E. Griswold +2 more
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Ribozyme activity modulates the physical properties of RNA–peptide coacervates [PDF]
, 2023 Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology.
Ghosh, Basusree +4 more
core
Redesign of an Artificial Ligase Ribozyme Based on the Analysis of Its Structural Elements [PDF]
RNA Biology, 2005 The catalytic and folding properties of "DSL ribozyme" were investigated. This artificial ligase ribozyme was constructed by installing a catalytic unit to a designed self-folding RNA. The self-folding RNA was composed of three helices connected via two tertiary interactions that served as scaffolding in the molecular design.
Tan Inoue +3 more
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Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: variations on a theme [PDF]
, 1999 Viroids and viroid-like satellite RNAs from plants, and the human hepatitis delta virus (HDV) RNA share some properties that include small size, circularity and replication through a rolling-circle mechanism.
Flores, Ricardo +5 more
core +1 more source
The effect of cytidine on the structure and function of an RNA ligase ribozyme
RNA, 2001 A cytidine-free ribozyme with RNA ligase activity was obtained by in vitro evolution, starting from a pool of random-sequence RNAs that contained only guanosine, adenosine, and uridine. This ribozyme contains 74 nt and catalyzes formation of a 3',5'-phosphodiester linkage with a catalytic rate of 0.016 min(-1).
Gerald F. Joyce, Jeff Rogers
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Machine Learning Guided Exploration of an Empirical Ribozyme Fitness Landscape [PDF]
, 2023 Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyFitness landscape of a biomolecule is a representation of its activity as a function of its sequence.
Rotrattanadumrong, Rachapun
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Beyond seek and destroy: How to generate allelic series using genome editing tools [PDF]
, 2020 Genome editing tools have greatly facilitated the functional analysis of genes of interest by targeted mutagenesis. Many usable genome editing tools, including different site-specific nucleases and editor databases that allow single-nucleotide ...
Bes, Martine +10 more
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The secondary structure and sequence optimization of an RNA ligase ribozyme
Nucleic Acids Research, 1995 In vitro selection can generate functional sequence variants of an RNA structural motif that are useful for comparative analysis. The technique is particularly valuable in cases where natural variation is unavailable or non-existent. We report the extension of this approach to a new extreme--the identification of a 112 nt ribozyme secondary structure ...
David P. Bartel, Eric H. Ekland
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Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection” [PDF]
Molecules, 2010 In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A
Hiroyuki Furuta +3 more
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In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole–activated substrates [PDF]
Proceedings of the National Academy of Sciences, 2020 Significance Current models for the origin of life include an earlier period when prebiotic chemistry dictated the nonenzymatic copying of RNA polymers, followed by a period of ribozyme-catalyzed reactions using nucleoside-5′-triphosphate (NTP) substrates. Our study addresses the transition from nonenzymatic to ribozyme-catalyzed RNA template
Travis Walton +4 more
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