Results 11 to 20 of about 1,985,752 (333)

Facilitated diffusion of DNA-binding proteins [PDF]

Physical Review Letters, 2005
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space
A. Jeltsch, Chen-Xu Wu, Holger Merlitz, Jörg Langowski, K. Klenin, Konstantin V. Klenin, M. Ptashne   +6 more
core   +6 more sources

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins [PDF]

Nucleic Acids Research, 2003
A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting ...
Berman, Helen M, Jones, Susan, Shanahan, Hugh P, Thornton, Janet M   +3 more
core   +13 more sources

DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins [PDF]

Nature Communications
Single-stranded DNA-binding proteins (SSBs) protect transiently exposed ssDNA, yet how DNA polymerase (DNAp) displaces them during replication remains unclear.
Longfu Xu, Shikai Jin, Mia Urem, Seung-Joo Lee, Meindert H. Lamers, Xun Chen, Peter G. Wolynes, Gijs J. L. Wuite   +7 more
doaj   +3 more sources

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments [PDF]

Cell Reports: Methods, 2023
Summary: Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay
Miranda Molina, Lindsey E. Way, Zhongqing Ren, Qin Liao, Bianca Guerra, Brandon Shields, Xindan Wang, HyeongJun Kim   +7 more
doaj   +2 more sources

Blood Plasma Exosomes Contain Circulating DNA in Their Crown

Diagnostics, 2022
It is known that circulating DNA (cirDNA) is protected from nuclease activity by proteins that form macromolecular complexes with DNA. In addition, it was previously shown that cirDNA can bind to the outer surface of exosomes.
Oleg Tutanov, Tatiana Shtam, Alina Grigor’eva, Alexey Tupikin, Yuri Tsentalovich, Svetlana Tamkovich   +5 more
doaj   +1 more source

Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

Frontiers in Molecular Biosciences, 2021
DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic ...
Kiyoto Kamagata
doaj   +1 more source

Prediction of DNA-Binding Protein–Drug-Binding Sites Using Residue Interaction Networks and Sequence Feature

Frontiers in Bioengineering and Biotechnology, 2022
Identification of protein–ligand binding sites plays a critical role in drug discovery. However, there is still a lack of targeted drug prediction for DNA-binding proteins. This study aims at the binding sites of DNA-binding proteins and drugs, by mining
Wei Wang, Wei Wang, Yu Zhang, Dong Liu, Dong Liu, HongJun Zhang, XianFang Wang, Yun Zhou   +7 more
doaj   +1 more source

Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models. [PDF]

PLoS Computational Biology, 2014
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA.
Tadashi Ando, Jeffrey Skolnick
doaj   +1 more source

DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers [PDF]

, 2010
Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric
A. Sawasdichai, A. Shukla, A. Soufi, Bess, Butcher, C. Smith, Cai, Cairns, Crompton, D'Elia, Dafforn, de Los Rios, Desjobert, Galande, Gaston, Gaston, Gaston, Goldman, Jennings, K. Gaston, Katsani, Larquet, Lennard, Luger, Luijsterburg, Martino, Mohd-Sarip, P. Noy, P.-S. Jayaraman, Puppin, Sekiya, Song, Soufi, Soufi, Soufi, T. Dafforn, Tanny, Thaw, Topisirovic, Vernon, Williams, Yasui   +41 more
core   +6 more sources

21 Fluorescent Protein-Based DNA Staining Dyes

Molecules, 2022
Fluorescent protein–DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope.
Yurie Tehee Kim, Hyesoo Oh, Myung Jun Seo, Dong Hyeun Lee, Jieun Shin, Serang Bong, Sujeong Heo, Natalia Diyah Hapsari, Kyubong Jo   +8 more
doaj   +1 more source