Results 1 to 10 of about 18,298 (211)
A Cytosine Deaminase–Based Genomic Footprinting Assay (cFOOT-seq) for Detecting Transcription Factor Occupancy [PDF]
Bio-ProtocolTranscription factors (TFs) regulate gene expression by binding to cis-regulatory elements in the genome. Understanding transcriptional regulation requires genome-wide characterization of TF occupancy across different chromatin contexts, yet simultaneous
Meng- Yang +6 more
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Interactions of the Streptococcus pneumoniae Toxin-Antitoxin RelBE Proteins with Their Target DNA
Microorganisms, 2021 Type II bacterial toxin-antitoxin (TA) systems are found in most bacteria, archaea, and mobile genetic elements. TAs are usually found as a bi-cistronic operon composed of an unstable antitoxin and a stable toxin that targets crucial cellular functions ...
Inmaculada Moreno-Córdoba +3 more
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Bio-Protocol, 2020 DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate ...
Meng-Lun Hsieh +3 more
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A computational pipeline to visualize DNA-protein binding states using dSMF data
STAR Protocols, 2022 Summary: Here, we present a pipeline to map states of protein-binding DNA in vivo. Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding ...
Satyanarayan Rao, Srinivas Ramachandran
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Site-specific DNA Mapping of Protein Binding Orientation Using Azidophenacyl Bromide (APB)
Bio-Protocol, 2020 The orientation of a DNA-binding protein bound on DNA is determinative in directing the assembly of other associated proteins in the complex for enzymatic action.
Himasha Perera, Michael Trakselis
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Journal of Ovarian Research, 2023 Background Cell-free DNA (cfDNA) is emerging as a potential biomarker for the detection of ovarian cancer (OC). Recently, we reported a method based upon cfDNA whole-genome sequencing data including the nucleosome distribution (nucleosome footprinting NF)
Huimei Zhou +8 more
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Long-Range and Highly Sensitive DNase I Footprinting by an Automated Infrared DNA Sequencer
BioTechniques, 1997 We have shown that an automated DNA sequencer is applicable to fluorescencebased detection of fragments in DNase I footprinting. We demonstrated the potential of long-range and highly sensitive DNase I footprinting taking advantage of an infrared ...
Masayuki Machida +2 more
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Vestige: Maximum likelihood phylogenetic footprinting
BMC Bioinformatics, 2005 Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less ...
Maxwell Peter +2 more
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Bio-Protocol, 2012 The KMnO4 footprinting method offers a rapid and easy way to detect and localize single-stranded regions within a duplex DNA molecule, such as it occurs for instance within an actively transcribing RNA polymerase-DNA complex or during R-loop formation in
Ümit Pul, Reinhild Wurm, Rolf Wagner
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DNA–protein interaction studies: a historical and comparative analysis
Plant Methods, 2021 DNA–protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications, among others.
Ricardo André Campos Ferraz +5 more
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