Results 21 to 30 of about 2,258,474 (352)

Simulation and analysis of in vitro DNA evolution [PDF]

, 2003
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic simulations of ...
Chao Tang, D. A. Kessler, G. D. Stormo, L. F. Landweber, M. T. Record, Jr., Morten Kloster, T.-K. Man   +6 more
core   +1 more source

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

PLoS ONE, 2014
As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level
Huiying Zhao, Jihua Wang, Yaoqi Zhou, Yuedong Yang   +3 more
doaj   +1 more source

Statistical-mechanical lattice models for protein-DNA binding in chromatin [PDF]

, 2010
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up
Adams C C, Akhrem A A, Bash R C, Gurskii G V, Gurskii G V, Hill T L, Iovanovich B, Karsten Rippe, Lando D Y, Lando D Y, Längst G, Markov A A, Mirny L A, Nechipurenko Y D, Nechipurenko Y D, Nechipurenko Y D, Poland D, Schellman J A, Svaren J, Teif V B, Teif V B, Teif V B, van Holde K E, Vladimir B Teif, Zasedatelev A S   +24 more
core   +2 more sources

Liquid Luminescent DNA-precipitation Assay

Bio-Protocol, 2016
Working on transcription factors requires studying interactions between protein and DNA. After identification of putative binding-sequences and motifs, Electrophoretic Mobility Shift Assay (EMSA) experiment is classically used to determine specific ...
Frédérique Végran, Mélanie Bruchard, Valentin Derangère, François Ghiringhelli   +3 more
doaj   +1 more source

Temperature-sensitive protein–DNA dimerizers [PDF]

, 2005
Programmable DNA-binding polyamides coupled to short peptides have led to the creation of synthetic artificial transcription factors. A hairpin polyamide-YPWM tetrapeptide conjugate facilitates the binding of a natural transcription factor Exd to an ...
Ansari, Aseem Z., Arndt, Hans-Dieter, Dervan, Peter B., Hauschild, Karl E., Metzler, Renee E., Moretti, Rocco, Raffaelle, Marni   +6 more
core   +1 more source

Targeting the Ets Binding Site of the HER2/neu Promoter with Pyrrole-Imidazole Polyamides [PDF]

, 2000
Three DNA binding polyamides (1-3) were synthesized that bind with high affinity (Ka = 8.7·10^9 M^-1 to 1.4·10^10 M^-1) to two 7-base pair sequences overlapping the Ets DNA binding site (EBS; GAGGAA) within the regulatory region of the HER2/neu proximal ...
Beerman, Terry A., Benz, Chris C., Bürli, Roland W., Chiang, Shu-Yuan, Dervan, Peter B., Gawron, Loretta, Scott, Gary K.   +6 more
core   +1 more source

Grafting Miniature DNA Binding Proteins [PDF]

Chemistry & Biology, 2004
Miniature proteins serve as leads for biological and medicinal applications by positioning all amino acids necessary for biomolecular recognition on a compact protein structure. Protein grafting was recently used to create miniature helical proteins with high DNA binding affinity and specificity.
openaire   +2 more sources

ProDFace: A web-tool for the dissection of protein-DNA interfaces

Frontiers in Molecular Biosciences, 2022
Protein-DNA interactions play a crucial role in gene expression and regulation. Identifying the DNA binding surface of proteins has long been a challenge–in comparison to protein-protein interactions, limited progress has been made in the development of ...
Arumay Pal, Pinak Chakrabarti, Sucharita Dey   +2 more
doaj   +1 more source

Multiplexed DNA-Modified Electrodes [PDF]

, 2010
We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets.
Barton, Jacqueline K., Gorodetsky, Alon A., Muren, Natalie B., Slinker, Jason D.   +3 more
core   +2 more sources

Investigating the DNA-Binding Site for VirB, a Key Transcriptional Regulator of Shigella Virulence Genes, Using an In Vivo Binding Tool [PDF]

, 2019
The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood.
Karabachev, Alexander D., Karney, Monika M.A., McKenna, Joy A., Millar, Makensie E., Potoceck, Eliese A., Weatherspoon-Griffin, Natasha, Wing, Helen J.   +6 more
core   +2 more sources