Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides
Language English Country Germany Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
- Keywords
- RNA, catalysis, molecular dynamics, oligonucleotides, ribozymes,
- MeSH
- Catalysis MeSH
- Kinetics MeSH
- Oligonucleotides chemical synthesis chemistry MeSH
- RNA, Catalytic chemistry MeSH
- Base Sequence MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Oligonucleotides MeSH
- RNA, Catalytic MeSH
The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.
References provided by Crossref.org
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
