ArticleBiochemistry2007
Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence.
Article in Biochemistry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 46 citations in OpenAlex.
- New insights into the structure and dynamics of the epigenetic modifications on DNA.RSC chemical biology · 2025Article
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation.Nucleic acids research · 2019Article
- Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium.Nucleic acids research · 2018Article
- Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.Frontiers in chemistry · 2016Review
- Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine.RNA (New York, N.Y.) · 2015Article
- Folding and unfolding pathways of the human telomeric G-quadruplex.Journal of molecular biology · 2014Article
- Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle.The journal of physical chemistry letters · 2014Article
- Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.Journal of the American Chemical Society · 2012Article
- Sequence length dictates repeated CAG folding in three-way junctions.Biochemistry · 2011Article
- Loop and stem dynamics during RNA hairpin folding and unfolding.RNA (New York, N.Y.) · 2010Article
- Context dependence of trinucleotide repeat structures.Biochemistry · 2010Article
- Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence.Biochemistry · 2010Article
- 2-aminopurine as a probe for quadruplex loop structures.Methods in molecular biology (Clifton, N.J.) · 2010Article
- Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence.Methods (San Diego, Calif.) · 2009Article
- Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.Biophysical journal · 2009Article
- Structural studies of a trinucleotide repeat sequence using 2-aminopurine.Biochemistry · 2009Article
- Laser-induced temperature jump infrared measurements of RNA folding.Methods in enzymology · 2009Article
- Local RNA conformational dynamics revealed by 2-aminopurine solvent accessibility.Biochemistry · 2008Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The fluorescent base analogue 2-aminopurine (2-AP) is commonly used to study specific conformational and protein binding events involving nucleic acids. Here, combinations of steady-state and time-resolved fluorescence spectroscopy of 2-AP were employed to monitor conformational transitions within a model hairpin RNA from diverse structural perspectives. RNA substrates adopting stable, unambiguous secondary structures were labeled with 2-AP at an unpaired base, within the loop, or inside the base-paired stem. Steady-state fluorescence was monitored as the RNA hairpins made the transitions between folded and unfolded conformations using thermal denaturation, urea titration, and cation-mediated folding. Unstructured control RNA substrates permitted the effects of higher-order RNA structures on 2-AP fluorescence to be distinguished from stimulus-dependent changes in intrinsic 2-AP photophysics and/or interactions with adjacent residues. Thermodynamic parameters describing local conformational changes were thus resolved from multiple perspectives within the model RNA hairpin. These data provided energetic bases for construction of folding mechanisms, which varied among different folding-unfolding stimuli. Time-resolved fluorescence studies further revealed that 2-AP exhibits characteristic signatures of component fluorescence lifetimes and respective fractional contributions in different RNA structural contexts. Together, these studies demonstrate localized conformational events contributing to RNA folding and unfolding that could not be observed by approaches monitoring only global structural transitions.
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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.