ArticleNucleic acids research2018
Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 33 citations in OpenAlex.
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- Mechanistic studies of small molecule ligands selective to RNA single G bulges.Nucleic acids research · 2025Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells.Nucleic acids research · 2025Article
- A general strategy for engineering GU base pairs to facilitate RNA crystallization.Nucleic acids research · 2025Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- Structure of saguaro cactus virus 3' translational enhancer mimics 5' cap for eIF4E binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers.Molecular therapy. Nucleic acids · 2023Article
- Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.International journal of molecular sciences · 2023Review
- Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling.Chemical science · 2023Article
- Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.Nature communications · 2023Article
- ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes.Nucleic acids research · 2023Article
- Article
- Discovery of small molecules that target a tertiary-structured RNA.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
- Thermodynamic characterization of naturally occurring RNA pentaloops.RNA (New York, N.Y.) · 2022Article
- Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.Nature chemical biology · 2022Article
- Structural basis of R-loop recognition by the S9.6 monoclonal antibody.Nature communications · 2022Article
- Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.Nucleic acids research · 2021Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3-6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5'-GNGACCC-3' consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab-RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.