ArticleNature communications2017
Single molecule high-throughput footprinting of small and large DNA ligands.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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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.
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Who cites it
14 citing papers in PubMed.
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies.Communications biology · 2024Article
- DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules.Biophysics reports · 2022Article
- A Multiplexable Plasmonic Hairpin-DNA Sensor Based On Target-specific Tether Dynamics.ACS sensors · 2021Article
- Dynamics and inhibition of MLL1 CXXC domain on DNA revealed by single-molecule quantification.Biophysical journal · 2021Article
- Profiling selective binding to promoter CpG islands by a single-DNA mechanical footprinting assay.Biophysical journal · 2021Article
- DNA-protein interaction studies: a historical and comparative analysis.Plant methods · 2021Review
- Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold.Nucleic acids research · 2021Article
- Sugar-Pucker Force-Induced Transition in Single-Stranded DNA.International journal of molecular sciences · 2021Article
- Dynamics of TRF1 organizing a single human telomere.Nucleic acids research · 2021Article
- High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments.Nucleic acids research · 2019Article
- High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap.ACS nano · 2018Article
- A single molecule analysis of H-NS uncouples DNA binding affinity from DNA specificity.Nucleic acids research · 2018Article
- Single-molecule multiplexed profiling of protein-DNA complexes using magnetic tweezers.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation.Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.
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Registered trials
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