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Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand

In the prebiotic RNA world, the self-replication of RNA without enzymes can be achieved through the utilization of 2-aminoimidazole activated nucleotides as efficient substrates. The mechanism of RNA nonenzymatic polymerization has been extensively investigated biophysically and structurally by usin...

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Autores principales: Dantsu, Yuliya, Zhang, Ying, Zhang, Wen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: RSC 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10619131/
https://www.ncbi.nlm.nih.gov/pubmed/37920395
http://dx.doi.org/10.1039/d3cb00137g
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author Dantsu, Yuliya
Zhang, Ying
Zhang, Wen
author_facet Dantsu, Yuliya
Zhang, Ying
Zhang, Wen
author_sort Dantsu, Yuliya
collection PubMed
description In the prebiotic RNA world, the self-replication of RNA without enzymes can be achieved through the utilization of 2-aminoimidazole activated nucleotides as efficient substrates. The mechanism of RNA nonenzymatic polymerization has been extensively investigated biophysically and structurally by using the model of an RNA primer/template complex which is bound by the imidazolium-bridged or triphosphate-bridged diguanosine intermediate. However, beyond the realm of the guanosine substrate, the structural insight into how alternative activated nucleotides bind and interact with the RNA primer/template complex remains unexplored, which is important for understanding the low reactivity of adenosine and uridine substrates in RNA primer extension, as well as its relationship with the structures. Here we use crystallography as a method and determine a series of high-resolution structures of RNA primer/template complexes bound by ApppG, a close analog of the dinucleotide intermediate containing adenosine and guanosine. The structures show that ApppG ligands bind to the RNA template through both Watson–Crick and noncanonical base pairs, with the primer 3′-OH group far from the adjacent phosphorus atom of the incoming substrate. The structures indicate that when adenosine is included in the imidazolium-bridged intermediate, the complexes are likely preorganized in a suboptimal conformation, making it difficult for the primer to in-line attack the substrate. Moreover, by co-crystallizing the RNA primer/template with chemically activated adenosine and guanosine monomers, we successfully observe the slow formation of the imidazolium-bridged intermediate (Ap-AI-pG) and the preorganized structure for RNA primer extension. Overall, our studies offer a structural explanation for the slow rate of RNA primer extension when using adenosine-5′-phosphoro-2-aminoimidazolide as a substrate during nonenzymatic polymerization.
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spelling pubmed-106191312023-11-02 Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand Dantsu, Yuliya Zhang, Ying Zhang, Wen RSC Chem Biol Chemistry In the prebiotic RNA world, the self-replication of RNA without enzymes can be achieved through the utilization of 2-aminoimidazole activated nucleotides as efficient substrates. The mechanism of RNA nonenzymatic polymerization has been extensively investigated biophysically and structurally by using the model of an RNA primer/template complex which is bound by the imidazolium-bridged or triphosphate-bridged diguanosine intermediate. However, beyond the realm of the guanosine substrate, the structural insight into how alternative activated nucleotides bind and interact with the RNA primer/template complex remains unexplored, which is important for understanding the low reactivity of adenosine and uridine substrates in RNA primer extension, as well as its relationship with the structures. Here we use crystallography as a method and determine a series of high-resolution structures of RNA primer/template complexes bound by ApppG, a close analog of the dinucleotide intermediate containing adenosine and guanosine. The structures show that ApppG ligands bind to the RNA template through both Watson–Crick and noncanonical base pairs, with the primer 3′-OH group far from the adjacent phosphorus atom of the incoming substrate. The structures indicate that when adenosine is included in the imidazolium-bridged intermediate, the complexes are likely preorganized in a suboptimal conformation, making it difficult for the primer to in-line attack the substrate. Moreover, by co-crystallizing the RNA primer/template with chemically activated adenosine and guanosine monomers, we successfully observe the slow formation of the imidazolium-bridged intermediate (Ap-AI-pG) and the preorganized structure for RNA primer extension. Overall, our studies offer a structural explanation for the slow rate of RNA primer extension when using adenosine-5′-phosphoro-2-aminoimidazolide as a substrate during nonenzymatic polymerization. RSC 2023-08-30 /pmc/articles/PMC10619131/ /pubmed/37920395 http://dx.doi.org/10.1039/d3cb00137g Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by-nc/3.0/
spellingShingle Chemistry
Dantsu, Yuliya
Zhang, Ying
Zhang, Wen
Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title_full Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title_fullStr Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title_full_unstemmed Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title_short Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand
title_sort insight into the structures of unusual base pairs in rna complexes containing a primer/template/adenosine ligand
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10619131/
https://www.ncbi.nlm.nih.gov/pubmed/37920395
http://dx.doi.org/10.1039/d3cb00137g
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