DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method.
Sign Up to like & getrecommendations! Published in 2021 at "Analytical biochemistry"
DOI: 10.1016/j.ab.2021.114298
Abstract: To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an… read more here.
Keywords: target search; dna facilitated; biosensor; dna ... See more keywords
Argonaute Target Search is Facilitated by Long Distance Diffusion
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.1701
Abstract: Argonaute proteins have a variety of functions ranging from post transcriptional gene silencing in eukaryotes to host defence in prokaryotic systems. Despite the well-established functional understanding of Argonautes, the biophysical understanding of its targeting mechanism… read more here.
Keywords: target search; argonaute; diffusion; long distance ... See more keywords
Shedding Light on Cas9 Target Search
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2016.11.427
Abstract: The CRISPR/Cas adaptive immune system provides prokaryotes with a defensive mechanism against invading viruses and plasmids. The invading viral DNA fragments are incorporated into the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus in the… read more here.
Keywords: system; crispr; dna; cas9 target ... See more keywords
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.
Sign Up to like & getrecommendations! Published in 2019 at "Biophysical journal"
DOI: 10.1016/j.bpj.2019.05.007
Abstract: Dynamics of nuclear proteins in crowded chromatin has only been poorly understood. Here, we address the diffusion, target search, and structural dynamics of three proteins in a model chromatin using coarse-grained molecular simulations run on… read more here.
Keywords: diffusion; chromatin; target search; density ... See more keywords
Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Cell"
DOI: 10.1016/j.molcel.2021.01.039
Abstract: Summary Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Toward identifying universal mechanisms of the target search,… read more here.
Keywords: binding proteins; dna; transient non; target search ... See more keywords
Multi-AUV cooperative target search and tracking in unknown underwater environment
Sign Up to like & getrecommendations! Published in 2018 at "Ocean Engineering"
DOI: 10.1016/j.oceaneng.2017.12.037
Abstract: Abstract For target search and tracking in unknown underwater environment, an integrated algorithm for a cooperative team of multiple autonomous underwater vehicles (Multi-AUV) is proposed by combining the Glasius bio-inspired neural network (GBNN) and bio-inspired… read more here.
Keywords: search; multi auv; unknown underwater; target search ... See more keywords
Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA.
Sign Up to like & getrecommendations! Published in 2021 at "Nature communications"
DOI: 10.1038/s41467-021-21144-0
Abstract: Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we… read more here.
Keywords: small rna; target; target search; base ... See more keywords
Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-18933-3
Abstract: Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors,… read more here.
Keywords: search; dna; target search; role macromolecular ... See more keywords
Spatial heterogeneity can facilitate the target search of self-propelled particles.
Sign Up to like & getrecommendations! Published in 2017 at "Soft matter"
DOI: 10.1039/c6sm02679f
Abstract: A numerical investigation of the target search dynamics of self-propelled particles (SPPs) in heterogeneous environments is presented in this work. We show that the spatial heterogeneity has a dramatic effect on the target search dynamics… read more here.
Keywords: target search; spatial heterogeneity; self propelled; target ... See more keywords
Nonspecific interactions between Cas12a and dsDNA located downstream of the PAM mediate target search and assist AsCas12a for DNA cleavage
Sign Up to like & getrecommendations! Published in 2023 at "Chemical Science"
DOI: 10.1039/d2sc05463a
Abstract: Cas12a is one of the most commonly used Cas proteins for genome editing and gene regulation. The first key step for Cas12a to fulfill its function is to search for its target among numerous nonspecific… read more here.
Keywords: ascas12a; diffusion; search; target search ... See more keywords
Nonequilibrium Strategy for Fast Target Search on the Genome.
Sign Up to like & getrecommendations! Published in 2020 at "Physical review letters"
DOI: 10.1103/physrevlett.124.198101
Abstract: Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis," the dynamics of… read more here.
Keywords: target; target search; nonequilibrium strategy; fast target ... See more keywords