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Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

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Chemical Triphosphorylation of Oligonucleotides
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Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.

Julie Puyo-Fourtine1, Yanan Du1, Erika McCarthy1

  • 1Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.

Journal of the American Chemical Society
|July 15, 2026
PubMed
Summary

This study reveals key design principles for programmable RNA catalysts (SAMURI) by analyzing molecular dynamics and simulations. Understanding conformational and electronic factors enhances RNA alkylation efficiency for therapeutic applications.

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Area of Science:

  • Biochemistry and Molecular Biology
  • RNA Catalysis and Engineering
  • Computational Chemistry

Background:

  • Programmable RNA catalysts are crucial for advancing RNA therapeutics and functional applications.
  • The SAM analogue-utilizing ribozyme (SAMURI) facilitates site-specific RNA alkylation but its catalytic determinants are not fully understood.
  • Existing knowledge gaps hinder the rational design of more efficient RNA alkyltransferases.

Purpose of the Study:

  • To elucidate the molecular determinants governing the reactivity and efficiency of the SAMURI ribozyme.
  • To characterize the interplay between conformational dynamics and electronic factors in SAMURI-catalyzed RNA alkylation.
  • To provide a framework for designing improved programmable RNA alkyltransferases.

Main Methods:

  • Integrated computational approaches including molecular dynamics (MD), 3D-RISM solvation analysis, and alchemical free energy calculations.
  • Quantum pKa shift predictions and ab initio QM/MM free energy simulations were employed to analyze catalytic mechanisms.
  • Characterization of near-attack configurations (NACs) and cofactor electronic properties.

Main Results:

  • SAMURI exhibits stable global fold, but catalytically competent NACs are rare, with observed rates depending on the fraction of reactive conformations (f_react).
  • A Mg2+ binding site and a specific hydrogen bond involving the cofactor amine and U8:O2 were identified to enrich f_react.
  • ProSeDMA shows higher reactivity than SAM due to superior leaving group properties, enhancing intrinsic rate (k_int); A52 substitutions modulate pKa, nucleophilicity, and k_int.

Conclusions:

  • SAMURI catalysis is governed by a synergistic combination of conformational preorganization and electronic effects.
  • The study provides critical insights into the structure-function relationships of RNA alkyltransferases.
  • Findings offer a rational basis for designing novel, highly efficient programmable RNA catalysts for therapeutic applications.