ArticleBiophysical journal2001
Probing the structure and dynamics of a DNA hairpin by ultrafast quenching and fluorescence depolarization.
Article in Biophysical journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 70 citations in OpenAlex.
- BZ Junctions and Its Application as Probe (2AP) to Detect Z-DNA Formation and Its Effector.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.Nucleic acids research · 2016Article
- Conquering 2-aminopurine's deficiencies: highly emissive isomorphic guanosine surrogate faithfully monitors guanosine conformation and dynamics in DNA.Journal of the American Chemical Society · 2015Article
- Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2013Article
- Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer.Nucleic acids research · 2013Article
- Applying 6-methylisoxanthopterin-enhanced fluorescence to examine protein-DNA interactions in the picomolar range.Biochemistry · 2012Article
- 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
- Specific implications of the HIV-1 nucleocapsid zinc fingers in the annealing of the primer binding site complementary sequences during the obligatory plus strand transfer.Nucleic acids research · 2011Article
- Studies on the site and mode of TMPyP4 interactions with Bcl-2 promoter sequence G-Quadruplexes.Biophysical journal · 2010Article
- Conformational analysis of DNA repair intermediates by time-resolved fluorescence spectroscopy.The journal of physical chemistry. A · 2009Article
- Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.Nucleic acids research · 2009Article
- Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine.Nucleic acids research · 2008Article
- Molecular beacons with intrinsically fluorescent nucleotides.Nucleic acids research · 2006Article
- Fluorescent properties of DNA base analogue tC upon incorporation into DNA--negligible influence of neighbouring bases on fluorescence quantum yield.Nucleic acids research · 2005Article
- Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations.RNA (New York, N.Y.) · 2004Article
- Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA hairpins have been investigated in which individual adenines were replaced by their fluorescent analog 2-aminopurine (2AP). The temperature dependence of the time evolution of polarized emission spectra was monitored with picosecond time resolution. Four isotropic decay components for each oligonucleotide indicated the coexistence of at least four conformations. The fluorescence for three of these was significantly quenched, which is explained by hole transfer from 2AP to guanine(s). An approximately 8-ps component is ascribed to direct hole transfer, the approximately 50-ps and approximately 500-ps components are ascribed to structural reorganization, preceding hole transfer. At room temperature, a fraction remains unquenched on a 10-ns timescale, in contrast to higher temperatures, where the flexibility increases. Besides quenching due to base stacking, a second quenching process was needed to describe the data. Evidence for both intrastrand and interstrand hole transfer was found. The extracted probability for stacking between neighboring bases in double-stranded regions was estimated to be approximately 75% at room temperature and approximately 25% at 80 degrees C, demonstrating structural disorder of the DNA. Fluorescence depolarization revealed both local dynamics of the DNA and overall dynamics of the entire oligonucleotide. Upon raising the temperature, the C-N terminus of the hairpin appears to melt first; the rest of the hairpin denatures above the average melting temperature.
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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.