ArticleAnalytical chemistry2013
Influence of dimethylsulfoxide on RNA structure and ligand binding.
Article in Analytical chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 43 citations in OpenAlex.
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- High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates forbioRxiv : the preprint server for biology · 2023Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- A toolkit for the identification of NEAT1_2/paraspeckle modulators.Nucleic acids research · 2022Article
- Using DMS-MaPseq to uncover the roles of DEAD-box proteins in ribosome assembly.Methods (San Diego, Calif.) · 2022Article
- Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex.International journal of molecular sciences · 2022Article
- A high-throughput assay for directly monitoring nucleolar rRNA biogenesis.Open biology · 2022Article
- Assembly of long L-RNA by native RNA ligation.Chemical communications (Cambridge, England) · 2021Article
- A New Specific and Sensitive RT-qPCR Method Based on Splinted 5' Ligation for the Quantitative Detection of RNA Species Shorter than microRNAs.Non-coding RNA · 2021Article
- Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes.RNA (New York, N.Y.) · 2021Article
- Optimization and evaluation of fluorescence in situ hybridization chain reaction in cleared fresh-frozen brain tissues.Brain structure & function · 2021Article
- Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry.Chemical communications (Cambridge, England) · 2020Article
- Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats.Journal of molecular cell biology · 2019Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough analysis of how lower concentrations (<10%) of DMSO typically used in binding assays affects RNA structure and ligand binding has not been undertaken. Here, we use NMR and 2-aminopurine fluorescence spectroscopy to examine how DMSO affects the structure, dynamics, and ligand binding properties of two flexible hairpin RNAs: the transactivation response element from HIV-1 and bacterial ribosomal A-site. In both cases, 5-10% DMSO decreased stacking interactions and increased local disorder in noncanonical residues within bulges and loops and resulted in 0.3-4-fold reduction in the measured binding affinities for different small molecules, with the greatest reduction observed for an intercalating compound that binds RNA nonspecifically. Our results suggest that, by competing for hydrophobic interactions, DMSO can have a small but significant effect on RNA structure and ligand binding. These effects should be considered when developing ligand binding assays and high throughput screens.
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Registered trials
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.