Construction of Arabidopsis Transcription Factor ORFeome Collections and Identification of Protein–DNA Interactions by High-Throughput Yeast One-Hybrid Screens

2018 ◽  
pp. 151-182 ◽  
Author(s):  
S. Earl Kang ◽  
Ghislain Breton ◽  
Jose L. Pruneda-Paz
Keyword(s):  
Transcription Factor ◽  
High Throughput ◽  
Dna Interactions ◽  
Protein Dna Interactions

scholarly journals DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level

Applied Nano ◽  
2022 ◽  
Vol 3 (1) ◽  
pp. 16-41
Author(s):  
Aurimas Kopūstas ◽  
Mindaugas Zaremba ◽  
Marijonas Tutkus
Keyword(s):  
High Throughput ◽  
Single Molecule ◽  
Dna Interaction ◽  
Dna Interactions ◽  
Ensemble Averaging ◽  
Target Search ◽  
Single Molecule Level ◽  
Protein Dna Interactions ◽  
Long Time

Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms.

scholarly journals A high throughput molecular force assay for protein–DNA interactions

Lab on a Chip ◽  
2011 ◽  
Vol 11 (5) ◽  
pp. 856 ◽  
Author(s):  
Philip M. D. Severin ◽  
Dominik Ho ◽  
Hermann E. Gaub
Keyword(s):  
High Throughput ◽  
Dna Interactions ◽  
Molecular Force ◽  
Protein Dna Interactions

Nanoscale “Curtain Rods”: High-Throughput Tools for Studying DNA-Protein Interactions

2008 ◽  
Vol 1138 ◽  
Author(s):  
Teresa Fazio ◽  
Mari-Liis Visnapuu ◽  
Shalom J. Wind ◽  
Eric Greene
Keyword(s):  
Data Acquisition ◽  
Real Time ◽  
Lipid Bilayer ◽  
High Throughput ◽  
Single Molecule ◽  
Protein Interactions ◽  
Massively Parallel ◽  
Dna Interactions ◽  
Parallel Data ◽  
Protein Dna Interactions

AbstractIn this work, we combine nanoscale engineering with single-molecule biology to probe the biochemical interactions between individual proteins and DNA. This approach, a vast improvement over previous methods, constructs a platform to observe thousands of protein-DNA interactions in real time with unprecedented detail. A key challenge in these experiments involves collecting enough statistically relevant data in order to analyze reactions which are designed to be probed individually. “DNA curtains” are formed by flowing the DNA tethered to a lipid bilayer across nanopatterned barriers, facilitating massively parallel data acquisition.

scholarly journals Molecular dynamics studies on the DNA-binding process of ERG

2016 ◽  
Vol 12 (12) ◽  
pp. 3600-3610 ◽  
Author(s):  
Matthias G. Beuerle ◽  
Neil P. Dufton ◽  
Anna M. Randi ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factor ◽  
Dna Binding ◽  
Sequence Specificity ◽  
Dna Interactions ◽  
Binding Process ◽  
Protein Dna Interactions

Molecular dynamics study elucidating the mechanistic background of the DNA-binding process and the sequence specificity of the transcription factor ERG. Along with the biological findings the capabilities of unbiased DNA-binding simulations in combination with various means of analysis in the field of protein DNA-interactions are shown.

scholarly journals ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

Methods ◽  
2009 ◽  
Vol 48 (3) ◽  
pp. 240-248 ◽  
Author(s):  
Dominic Schmidt ◽  
Michael D. Wilson ◽  
Christiana Spyrou ◽  
Gordon D. Brown ◽  
James Hadfield ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Interactions ◽  
Protein Dna Interactions
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