Results 1 to 10 of about 1,342,407 (165)

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

DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues.

PLoS ONE, 2016
DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years.
Xin Ma, Jing Guo, Xiao Sun
doaj   +2 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

Facilitated Diffusion of DNA-Binding Proteins [PDF]

Physical Review Letters, 2006
4 pages, 2 figures Nov 22 2005 - accepted for ...
Klenin, K. V., Merlitz, H., Langowski, J., Wu, C. X.   +3 more
openaire   +4 more sources

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

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

Protein–DNA binding in high-resolution [PDF]

Critical Reviews in Biochemistry and Molecular Biology, 2015
Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events. For example, the ChIP-exo protocol precisely characterizes protein-DNA cross-linking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion.
Shaun, Mahony, B Franklin, Pugh
openaire   +2 more sources