High resolution protein-DNA binding energy landscapes via a novel high throughput method

Biopolymers ◽  
2007 ◽  
Vol 85 (5-6) ◽  
pp. vii-viii ◽  
Author(s):  
G. Eric Plum ◽  
David N. Breslauer ◽  
Kenneth J. Breslauer
Keyword(s):  
High Resolution ◽  
Binding Energy ◽  
Dna Binding ◽  
High Throughput ◽  
Energy Landscapes ◽  
High Throughput Method

Describing Delicate Interactions

2007 ◽  
Vol 2007 (369) ◽  
pp. tw24-tw24
Author(s):  
Valda Vinson
Keyword(s):  
Transcription Factors ◽  
Binding Energy ◽  
Dna Binding ◽  
High Throughput ◽  
Biological Networks ◽  
Full Text ◽  
Systems Approach ◽  
Energy Landscapes ◽  
Eukaryotic Transcription ◽  
Link Type

Quantifying the affinities of interactions in biological networks, particularly transient ones, remains a challenge. Maerkl and Quake describe a high-throughput microfluidic platform that allows the measurement of transient and low-affinity interactions and characterize the DNA binding energy landscapes for four eukaryotic transcription factors. In two cases, the binding specificities were used to predict which genes the transcription factors would bind and likely regulate.S. J. Maerkl, S. R. Quake, A systems approach to measuring the binding energy landscapes of transcription factors. Science315, 233-237 (2007). [Abstract][Full Text]

scholarly journals DNB-Based On-Chip Motif Finding (DocMF): a High-Throughput Method to Profile Different Types of Protein-DNA Interactions

2019 ◽  
Author(s):  
Zhuokun Li ◽  
Xiaojue Wang ◽  
Dongyang Xu ◽  
Dengwei Zhang ◽  
Dan Wang ◽  
...  
Keyword(s):  
Dna Binding ◽  
High Throughput ◽  
Motif Finding ◽  
High Coverage ◽  
Protospacer Adjacent Motif ◽  
Highly Sensitive ◽  
Protein Dna Interactions ◽  
High Throughput Method ◽  
On Chip ◽  
Next Generation Sequencing Ngs

ABSTRACTHere we report a highly sensitive DNB-based on-chip Motif Finding (DocMF) system that utilizes high throughput next-generation-sequencing (NGS) chips to profile protein binding or cleaving activity. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer-adjacent-motif (PAM) sequences of different CRISPR systems. Our DocMF platform can simultaneously screen both 5’ and 3’ PAM regions with high coverage using the same NGS library/chip. For the well-studied SpCas9, our DocMF platform identified a small proportion of noncanonical 5’-NAG-3’ (∼5%) and 5’-NGA-3’ (∼1.6%), in addition to its common PAMs, 5’-NGG-3’ (∼89.9%). We also used the DocMF to assay two uncharacterized Cas endonucleases, VeCas9 and BvCpf1. VeCas9 PAMs were not detected by the conventional PAM depletion method. However, DocMF discovered that both VeCas9 and BvCpf1 required broader and more complicated PAM sequences for target recognition. VeCas9 preferred the R-rich motifs, whereas BvCpf1 used the T-rich PAMs. Moreover, after slightly changing the experimental protocol, we observed that dCas9, a DNA-binding protein lacking endonuclease activity, preferably binded to the previously reported PAMs 5’-NGG-3’. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA-binding proteins.

scholarly journals A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors

Science ◽  
2007 ◽  
Vol 315 (5809) ◽  
pp. 233-237 ◽  
Author(s):  
Sebastian J. Maerkl ◽  
Stephen R. Quake
Keyword(s):  
Transcription Factors ◽  
Binding Energy ◽  
High Throughput ◽  
Molecular Interactions ◽  
Biological Networks ◽  
Systems Approach ◽  
Energy Landscapes ◽  
Eukaryotic Transcription ◽  
Network Topologies

A major goal of systems biology is to predict the function of biological networks. Although network topologies have been successfully determined in many cases, the quantitative parameters governing these networks generally have not. Measuring affinities of molecular interactions in high-throughput format remains problematic, especially for transient and low-affinity interactions. We describe a high-throughput microfluidic platform that measures such properties on the basis of mechanical trapping of molecular interactions. With this platform we characterized DNA binding energy landscapes for four eukaryotic transcription factors; these landscapes were used to test basic assumptions about transcription factor binding and to predict their in vivo function.

Multiplex single nucleotide extension (MSNE): a robust and high throughput method for high-resolution HLA-A locus typing

2003 ◽  
Vol 64 (10) ◽  
pp. S92
Author(s):  
Mei Han ◽  
Yue-Qing Tan ◽  
Yanzheng Zhang ◽  
Jeannette Tsai ◽  
Robert Vorhaben ◽  
...  
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
Single Nucleotide ◽  
High Throughput Method

scholarly journals Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

2014 ◽  
Vol 7 (1) ◽  
Author(s):  
Petros Kolovos ◽  
Harmen JG van de Werken ◽  
Nick Kepper ◽  
Jessica Zuin ◽  
Rutger WW Brouwer ◽  
...  
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
Regulatory Elements ◽  
High Throughput Method
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