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1. Full Text Genomic footprinting
by Vierstra, Jeff and Stamatoyannopoulos, John A
Nature Methods, ISSN 1548-7091, 02/2016, Volume 13, Issue 3, pp. 213 - 221
The advent of DNA footprinting with DNase I more than 35 years ago enabled the systematic analysis of protein-DNA interactions, and the technique has been... 
TRANSCRIPTION FACTORS | DNA-BINDING | GLUCOCORTICOID-RECEPTOR | PROTEIN | SPECIFICITY | CHROMATIN | IN-VIVO | DEOXYRIBONUCLEIC ACID | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | DYNAMICS | DNA - genetics | Algorithms | Chromosome Mapping - methods | Humans | High-Throughput Nucleotide Sequencing - methods | DNA Footprinting - methods | Genome, Human - genetics | Analysis | Genomics | Protein binding | Proteins | Genomes | Deoxyribonucleic acid--DNA
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2. Full Text Functional footprinting of regulatory DNA
by Vierstra, Jeff and Reik, Andreas and Chang, Kai-Hsin and Stehling-Sun, Sandra and Zhou, Yuanyue and Hinkley, Sarah J and Paschon, David E and Zhang, Lei and Psatha, Nikoletta and Bendana, Yuri R and O'Neil, Colleen M and Song, Alexander H and Mich, Andrea K and Liu, Pei-Qi and Lee, Gary and Bauer, Daniel E and Holmes, Michael C and Orkin, Stuart H and Papayannopoulou, Thalia and Stamatoyannopoulos, George and Rebar, Edward J and Gregory, Philip D and Urnov, Fyodor D and Stamatoyannopoulos, John A
Nature Methods, ISSN 1548-7091, 09/2015, Volume 12, Issue 10, pp. 927 - 930
Regulatory regions harbor multiple transcription factor (TF) recognition sites; however, the contribution of individual sites to regulatory function remains... 
CELLS | HUMAN GENOME | BIOCHEMICAL RESEARCH METHODS | NUCLEASES | Erythropoiesis | Humans | Regulatory Sequences, Nucleic Acid | DNA Breaks, Double-Stranded | DNA Footprinting - methods | Transcription Factors - metabolism | Carrier Proteins - genetics | Enhancer Elements, Genetic | Base Sequence | DNA Repair | Erythrocytes - physiology | Mutation | Genome, Human | Genomics - methods | Nuclear Proteins - genetics | Binding Sites | Physiological aspects | Transcription factors | Genomics | DNA | Methods | Genomes | Deoxyribonucleic acid--DNA
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3. Full Text Ultrasonic Footprinting
by Grokhovsky, S L
Molecular Biology, ISSN 0026-8933, 7/2018, Volume 52, Issue 4, pp. 609 - 620
Ligand binding influences the dynamics of the DNA helix in both the binding site and adjacent regions. This, in particular, is reflected in the changing... 
Life Sciences | Biochemistry, general | Human Genetics | actinomycin D | footrpinting | Life Sciences, general | DNA conformation | DNA cleavage | ultrasound | DRUG | MULTIPLE COMPLEXES | ACID | ACTINOMYCIN-D-BINDING | BIOCHEMISTRY & MOLECULAR BIOLOGY | SINGLE-STRANDED-DNA | CLEAVAGE | NMR | SEQUENCE | SITES | B-DNA | Usage | Ultrasonic waves | Genetic research | Genetic aspects | Research | Dactinomycin | DNA-ligand interactions | Deoxyribonuclease | Footprinting | Ultrasonic imaging | Phosphodiester bonds | Nucleotide sequence | Genomes | Chromophores | Ultrasound | Binding sites | Sugar | Deoxyribonucleic acid--DNA | Conformation
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4. Ultrasonic Footprinting
by Grokhovsky, S.L
Molekuliarnaia biologiia, ISSN 0026-8984, 07/2018, Volume 52, Issue 4, pp. 705 - 717
actinomycin D | footrpinting | DNA conformation | DNA cleavage | ultrasound
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5. Footprinting of nucleic acid-protein complexes
by Revzin, Arnold
1993, Separation, detection, and characterization of biological macromolecules., ISBN 0125865007, xxi, 193
DNA-protein interactions | Research | RNA-protein interactions | Laboratory manuals
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6. Full Text SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
by Das, Rhiju and Laederach, Alain and Pearlman, Samuel M and Herschlag, Daniel and Altman, Russ B
RNA, ISSN 1355-8382, 03/2005, Volume 11, Issue 3, pp. 344 - 354
Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding... 
RNA folding | Footprinting | Electrophoresis | Software | Hydroxyl radical | Gel | footprinting | software | PROTEIN-DNA INTERACTIONS | P4-P6 DOMAIN | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | electrophoresis | QUANTITATIVE-ANALYSIS | gel | hydroxyl radical | TETRAHYMENA RIBOZYME | LAMBDA-PHAGE REPRESSOR | GEL IMAGES | MONOVALENT | CATALYTIC RNA MOLECULE | BINDING | Thermodynamics | Automation | Algorithms | Kinetics | RNA - chemistry | Method
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7. Full Text Dissecting neural differentiation regulatory networks through epigenetic footprinting
by Ziller, Michael J and Edri, Reuven and Yaffe, Yakey and Donaghey, Julie and Pop, Ramona and Mallard, William and Issner, Robbyn and Gifford, Casey A and Goren, Alon and Xing, Jeffrey and Gu, Hongcang and Cacchiarelli, Davide and Tsankov, Alexander M and Epstein, Charles and Rinn, John L and Mikkelsen, Tarjei S and Kohlbacher, Oliver and Gnirke, Andreas and Bernstein, Bradley E and Elkabetz, Yechiel and Meissner, Alexander
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7539, pp. 355 - 359
Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal... 
TRANSCRIPTION FACTORS | STEM-CELLS | HUMAN ES | HUMAN GENOME | CHIP DATA | COUP-TFI | RNA-SEQ | DNA | MULTIDISCIPLINARY SCIENCES | PARTIAL LEAST-SQUARES | EXPRESSION | Embryonic Stem Cells - metabolism | RNA, Small Interfering - genetics | Reproducibility of Results | Embryonic Stem Cells - cytology | Humans | RNA, Small Interfering - analysis | Neural Stem Cells - cytology | Transcription Factors - metabolism | Cell Differentiation - genetics | Epigenomics - methods | Epigenesis, Genetic - genetics | Transcription, Genetic - genetics | Binding Sites | Neural Stem Cells - metabolism | Cell Lineage - genetics | Epigenetic inheritance | Neural circuitry | Stem cells | Genetic research | Genetic aspects | Research | Cell differentiation | Neurological research | Transcription factors | Neurons | Genes | DNA methylation | Epigenetics | Genomes | Alzheimers disease | Binding sites
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8. Full Text Genome-wide footprinting: Ready for prime time?
by Sung, Myong-Hee and Baek, Songjoon and Hager, Gordon L
Nature Methods, ISSN 1548-7091, 02/2016, Volume 13, Issue 3, pp. 222 - 228
High-throughput sequencing technologies have allowed many gene locus-level molecular biology assays to become genome-wide profiling methods. DNA-cleaving... 
GLUCOCORTICOID-RECEPTOR BINDING | ANDROGEN RECEPTOR | CELLS | TRANSCRIPTION FACTOR-BINDING | CHROMATIN ACCESSIBILITY | DNA INTERACTIONS | PROTEIN | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | SITES | INTRANUCLEAR DYNAMICS | DNA - genetics | Algorithms | Chromosome Mapping - methods | Humans | High-Throughput Nucleotide Sequencing - methods | DNA Footprinting - methods | Genome, Human - genetics | Analysis | Genomes | Molecular biology | Technology | Deoxyribonucleic acid--DNA
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9. Chemical Generation of Hydroxyl Radical for Oxidative 'Footprinting'
by Leser, Micheal and Chapman, Jessica R and Chapman, Jessica R and Khine, Michelle and Pegan, Jonathan and Law, Matt and Law, Matt and El Makkaoui, Mohammed and Makkaoui, Mohammed El and Ueberheide, Beatrix M and Ueberheide, Beatrix M and Brenowitz, Michael and Brenowitz, Michael
Protein and Peptide Letters, ISSN 0929-8665, 2019, Volume 26, Issue 1, pp. 61 - 69
Background: For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of... 
Footprinting | Fenton reaction | Structure mapping | Mass spectrometry | Hydroxyl radical | Protein | footprinting | RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | RADIOLYTIC MODIFICATION | structure mapping | NUCLEIC-ACIDS | OXYGEN | hydroxyl radical | ACCESSIBLE SURFACE-AREAS | PEPTIDES | FOLDING PATHWAY | DNA | protein | mass spectrometry | AMINO-ACID-RESIDUES
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10. Full Text Analysis of computational footprinting methods for DNase sequencing experiments
by Gusmao, Eduardo G and Allhoff, Manuel and Zenke, Martin and Costa, Ivan G
Nature Methods, ISSN 1548-7091, 03/2016, Volume 13, Issue 4, pp. 303 - 309
DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I... 
BIAS | BIOCHEMICAL RESEARCH METHODS | DYNAMICS | RECEPTOR | FACTOR-BINDING SITES | IDENTIFICATION | EXCHANGE | GENOME | HYPERSENSITIVITY | Chromatin - metabolism | Computational Biology - methods | Humans | DNA Footprinting - methods | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Algorithms | Chromatin Immunoprecipitation | K562 Cells | Protein Binding | Software | High-Throughput Nucleotide Sequencing - methods | Binding Sites | Chromatin - genetics | Sequence Analysis, DNA - methods | Genetic research | Nucleases | Research | Nucleotide sequencing | Methods | DNA sequencing | Studies | Analysis | Deoxyribonucleic acid--DNA
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11. Full Text Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
by Zhang, Zhihong and Kuehn, Michael S and Thurman, Robert E and Reynolds, Alex P and Noble, William S and Neph, Shane and Hesselberth, Jay R and Fields, Stanley and Sabo, Peter J and Sandstrom, Richard and Chen, Xiaoyu and Stamatoyannopoulos, John A
Nature Methods, ISSN 1548-7091, 04/2009, Volume 6, Issue 4, pp. 283 - 289
The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of... 
ELEMENTS | SPECIFICITY | CHROMATIN | TRANSCRIPTION | GENES | BIOCHEMICAL RESEARCH METHODS | FACTOR-BINDING-SITES | SACCHAROMYCES-CEREVISIAE | MAP | YEAST GENOME | Amino Acid Sequence | Transcription Factors - chemistry | Molecular Sequence Data | Transcription Factors - genetics | DNA Footprinting - methods | DNA - genetics | Protein Interaction Mapping - methods | DNA - chemistry | Algorithms | Base Sequence | Protein Binding | Binding Sites | Sequence Analysis, DNA - methods | Chromosome mapping | Usage | DNA replication | DNA microarrays | Genomics | Research | Gene expression | Methods | Protein-protein interactions | Proteins | Research methodology | Binding sites | Deoxyribonucleic acid--DNA
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12. Full Text Footprinting protein-DNA complexes using the hydroxyl radical
by Tullius, Thomas D and Jain, Swapan S
Nature Protocols, ISSN 1754-2189, 06/2008, Volume 3, Issue 6, pp. 1092 - 1100
Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA-protein complexes. The high reactivity and lack of base... 
GEL-ELECTROPHORESIS | NUCLEOSOME CORE | NUCLEIC ACID INTERACTIONS | IN-VIVO | RESOLUTION | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | INTERACTION PARAMETERS | MOBILITY SHIFT ASSAY | TRANSCRIPTION FACTOR | BINDING SPECIFICITY | DNA - genetics | Protein Footprinting - methods | Hydroxyl Radical | DNA - chemistry | Proteins - metabolism | Protein Binding | Binding Sites - genetics | DNA - metabolism | Proteins - chemistry | DNA Footprinting - methods | Macromolecular Substances | Physiological aspects | Identification and classification | DNA | Genetic screening | Methods | Binding sites (Biochemistry)
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13. Full Text Pyrite footprinting of RNA
by Schlatterer, Jörg C and Wieder, Matthew S and Jones, Christopher D and Pollack, Lois and Brenowitz, Michael
Biochemical and Biophysical Research Communications, ISSN 0006-291X, 08/2012, Volume 425, Issue 2, pp. 374 - 378
► RNA structure is mapped by pyrite mediated OH footprinting. ► Repetitive experiments can be done in a powdered pyrite filled cartridge. ► High OH reactivity... 
Footprinting | Pyrite | RNA | Hydroxyl radical | CONTACTS | PROTEIN | MOLECULE | BIOCHEMISTRY & MOLECULAR BIOLOGY | EQUILIBRIUM CHANGES | CLEAVAGE | ACCESSIBLE SURFACE | BIOPHYSICS | DIELS-ALDERASE RIBOZYME | PROBE | RNA Folding | Sequence Analysis, RNA - methods | RNA, Catalytic - chemistry | Iron - chemistry | Sulfides - chemistry | Sulfur compounds | Hydroxides | HYDROXYL RADICALS | NUCLEOTIDES | PYRITE | MOLECULAR DYNAMICS METHOD | CUTTING | DNA | ENZYMES | ARCHITECTURE | IRON SULFIDES | CRYSTAL STRUCTURE | 60 APPLIED LIFE SCIENCES
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14. Full Text In vitro DNase I footprinting
by Leblanc, Benoît P and Moss, Tom
Methods in Molecular Biology, ISSN 1064-3745, 09/2015, Volume 1334, pp. 17 - 27
The association of proteins with the DNA double helix can interfere with the accessibility of the latter to nucleases. This is particularly true when using... 
Footprinting | DNase I | Protection | Sequencing | DNA - genetics | DNA - chemistry | Deoxyribonuclease I - chemistry | Deoxyribonuclease I - genetics | DNA-Binding Proteins - genetics | Binding Sites | DNA Footprinting - methods | DNA-Binding Proteins - chemistry | Electrophoresis, Polyacrylamide Gel - methods
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