ArticleMolecules (Basel, Switzerland)2014
Different fluorophore labeling strategies and designs affect millisecond kinetics of DNA hairpins.
Article in Molecules (Basel, Switzerland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Single-Molecule Microfluidics for Membrane Protein Biophysics.The Journal of membrane biology · 2026Review
- An automated single-molecule FRET platform for high-content, multiwell plate screening of biomolecular conformations and dynamics.Nature communications · 2023Article
- Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity.Journal of molecular biology · 2023Article
- "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy.Journal of biological physics · 2022Article
- Flow radiocytometry using droplet optofluidics.Biosensors & bioelectronics · 2021Article
- Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules.Micromachines · 2021Review
- DNA hybridisation kinetics using single-molecule fluorescence imaging.Essays in biochemistry · 2021Review
- A Multichannel Time-Tagged Time-Resolved (TTTR) Model for Quantification of Oligomer Concentrations Based on Antibunching Effect.ACS omega · 2018Article
- Deciphering Design Principles of Förster Resonance Energy Transfer-Based Protease Substrates: Thermolysin-Like Protease fromACS omega · 2018Article
- Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality.Nucleic acids research · 2017Article
- Effects of Fluorophore Attachment on Protein Conformation and Dynamics Studied by spFRET and NMR Spectroscopy.Chemistry (Weinheim an der Bergstrasse, Germany) · 2017Article
- Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A.Biophysical journal · 2017Article
- Special issue: single molecule techniques.Molecules (Basel, Switzerland) · 2015Article
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3 authors.
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Abstract
Changes in molecular conformations are one of the major driving forces of complex biological processes. Many studies based on single-molecule techniques have shed light on conformational dynamics and contributed to a better understanding of living matter. In particular, single-molecule FRET experiments have revealed unprecedented information at various time scales varying from milliseconds to seconds. The choice and the attachment of fluorophores is a pivotal requirement for single-molecule FRET experiments. One particularly well-studied millisecond conformational change is the opening and closing of DNA hairpin structures. In this study, we addressed the influence of base- and terminal-labeled fluorophores as well as the fluorophore DNA interactions on the extracted kinetic information of the DNA hairpin. Gibbs free energies varied from ∆G0 = -3.6 kJ/mol to ∆G0 = -0.2 kJ/mol for the identical DNA hairpin modifying only the labeling scheme and design of the DNA sample. In general, the base-labeled DNA hairpin is significantly destabilized compared to the terminal-labeled DNA hairpin and fluorophore DNA interactions additionally stabilize the closed state of the DNA hairpin. Careful controls and variations of fluorophore attachment chemistry are essential for a mostly undisturbed measurement of the underlying energy landscape of biomolecules.
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