title: Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides.
abstract: 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.
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno (Czech Republic).
authors: Petr
authors: P
authors: Stadlbauer
authors: Jiří
authors: J
authors: Šponer
authors: Giovanna
authors: G
authors: Costanzo
authors: Ernesto
authors: E
authors: Di Mauro
authors: Samanta
authors: S
authors: Pino
authors: Judit E
authors: JE
authors: Šponer
mesh_terms: D001483:Base Sequence; D002384:Catalysis; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D016337:RNA, Catalytic
keywords: RNA; catalysis; molecular dynamics; oligonucleotides; ribozymes