ArticleNucleic acids research2006
The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- Electrochemical DNA hairpin sensors for differentiating small molecule intercalation from minor groove binding.Sensors & diagnostics · 2026Article
- Capillary Electrophoresis Can Detect the Simultaneous Presence of Hairpins and Self-Dimers in Non-Symmetric, Single-Stranded DNA Oligomers.Electrophoresis · 2025Article
- Evidence of a Three-State Mechanism in DNA Hairpin Folding.Journal of the American Chemical Society · 2025Article
- DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects.The journal of physical chemistry. A · 2024Article
- A molecular assessment of the practical potential of DNA-based computation.Current opinion in biotechnology · 2023Review
- Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.The journal of physical chemistry letters · 2021Article
- Stacking-induced fluorescence increase reveals allosteric interactions through DNA.Nucleic acids research · 2018Article
- Quantifying Release from Lipid Nanocarriers by Fluorescence Correlation Spectroscopy.ACS omega · 2018Article
- Persistence Length and Cooperativity Estimation of Single Stranded DNA using FCS Combined with HYDRO Program.Journal of fluorescence · 2017Article
- Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.Angewandte Chemie (International ed. in English) · 2015Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- Different fluorophore labeling strategies and designs affect millisecond kinetics of DNA hairpins.Molecules (Basel, Switzerland) · 2014Article
- Differentiation and distributions of DNA/cisplatin crosslinks by liquid chromatography-electrospray ionization-infrared multiphoton dissociation mass spectrometry.Journal of the American Society for Mass Spectrometry · 2014Article
- Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.Biophysical journal · 2013Article
- Probing mercury(II)-DNA interactions by nanopore stochastic sensing.The journal of physical chemistry. B · 2013Article
- Non-Markovian polymer reaction kinetics.Nature chemistry · 2012Article
- Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics.Biophysical journal · 2012Article
- Domain orientation in the N-Terminal PDZ tandem from PSD-95 is maintained in the full-length protein.Structure (London, England : 1993) · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC-dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC-dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC-dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides.
Indexed as
Identifiers
What OpenQuestion holds
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.