ArticleNature protocols2013
Exploring protein-DNA interactions in 3D using in situ construction, manipulation and visualization of individual DNA dumbbells with optical traps, microfluidics and fluorescence microscopy.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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.
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Who cites it
26 citing papers in PubMed.
- Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability.RSC advances · 2024Article
- A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint.Nature communications · 2023Article
- Strain-induced self-rolled-up microtubes for multifunctional on-chip microfluidic applications.Biomicrofluidics · 2023Review
- BRCA2 chaperones RAD51 to single molecules of RPA-coated ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Use of Dual Optical Tweezers and Microfluidics for Single-Molecule Studies.Journal of visualized experiments : JoVE · 2022Article
- Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging.Nucleic acids research · 2022Article
- Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement.Nature communications · 2022Article
- Self-assembled microtubular electrodes for on-chip low-voltage electrophoretic manipulation of charged particles and macromolecules.Microsystems & nanoengineering · 2022Article
- DNA replication origins retain mobile licensing proteins.Nature communications · 2021Article
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- Microfluidics for core-shell drug carrier particles - a review.RSC advances · 2020Review
- How p53 Molecules Solve the Target DNA Search Problem: A Review.International journal of molecular sciences · 2020Review
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- Additive manufacturing of laminar flow cells for single-molecule experiments.Scientific reports · 2019Article
- Microfluidic epigenomic mapping technologies for precision medicine.Lab on a chip · 2019Review
- Article
- RecA: Regulation and Mechanism of a Molecular Search Engine.Trends in biochemical sciences · 2016Review
- DNA Sequence Alignment during Homologous Recombination.The Journal of biological chemistry · 2016Review
- Analysis of single nucleic acid molecules in micro- and nano-fluidics.Lab on a chip · 2016Review
- Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases.Methods in enzymology · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In this protocol, we describe a procedure to generate 'DNA dumbbells'-single molecules of DNA with a microscopic bead attached at each end-and techniques for manipulating individual DNA dumbbells. We also detail the design and fabrication of a microfluidic device (flow cell) used in conjunction with dual optical trapping to manipulate DNA dumbbells and to visualize individual protein-DNA complexes by single-molecule epifluorescence microscopy. Our design of the flow cell enables the rapid movement of trapped molecules between laminar flow channels and a flow-free reservoir. The reservoir provides the means to examine the formation of protein-DNA complexes in solution in the absence of external flow forces while maintaining a predetermined end-to-end extension of the DNA. These features facilitate the examination of the role of 3D DNA conformation and dynamics in protein-DNA interactions. Preparation of flow cells and reagents requires 2 days each; in situ DNA dumbbell assembly and imaging of single protein-DNA complexes require another day.
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Registered trials
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