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Facilitated diffusion on DNA

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https://www.readbyqxmd.com/read/29629148/surface-immobilized-and-self-shaped-dna-hydrogels-and-their-application-in-biosensing
#1
Xiaoxia Mao, Guifang Chen, Zihan Wang, Yuanguang Zhang, Xiaoli Zhu, Genxi Li
Hydrogels are of great interest in the field of biosensing for their good biocompatibility, plasticity, and capability of providing 3D scaffolds. Nevertheless, the application of hydrogels has not been linked with broad surface biosensing systems yet. To overcome the limitations, here for the first time, surface-immobilized pure DNA hydrogels were synthesized using a surficial primer-induced strategy and adopted for biosensing applications. The DNA hydrogel 3D scaffold is successfully constructed on a transparent ITO electrode, which facilitates both colourimetric and electrochemical measurements...
January 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29584872/sliding-of-a-single-lac-repressor-protein-along-dna-is-tuned-by-dna-sequence-and-molecular-switching
#2
Alessia Tempestini, Carina Monico, Lucia Gardini, Francesco Vanzi, Francesco S Pavone, Marco Capitanio
In any living cell, genome maintenance is carried out by DNA-binding proteins that recognize specific sequences among a vast amount of DNA. This includes fundamental processes such as DNA replication, DNA repair, and gene expression and regulation. Here, we study the mechanism of DNA target search by a single lac repressor protein (LacI) with ultrafast force-clamp spectroscopy, a sub-millisecond and few base-pair resolution technique based on laser tweezers. We measure 1D-diffusion of proteins on DNA at physiological salt concentrations with 20 bp resolution and find that sliding of LacI along DNA is sequence dependent...
March 23, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29504083/an-ultrasensitive-hollow-silica-based-biosensor-for-pathogenic-escherichia-coli-dna-detection
#3
Eda Yuhana Ariffin, Yook Heng Lee, Dedi Futra, Ling Ling Tan, Nurul Huda Abd Karim, Nik Nuraznida Nik Ibrahim, Asmat Ahmad
A novel electrochemical DNA biosensor for ultrasensitive and selective quantitation of Escherichia coli DNA based on aminated hollow silica spheres (HSiSs) has been successfully developed. The HSiSs were synthesized with facile sonication and heating techniques. The HSiSs have an inner and an outer surface for DNA immobilization sites after they have been functionalized with 3-aminopropyltriethoxysilane. From field emission scanning electron microscopy images, the presence of pores was confirmed in the functionalized HSiSs...
March 5, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29428720/effects-of-pre-incubation-with-c-type-natriuretic-peptide-on-nuclear-maturation-mitochondrial-behavior-and-developmental-competence-of-sheep-oocytes
#4
Tong Zhang, Xiaomei Fan, Ruilan Li, Chunqiang Zhang, Jiaxin Zhang
In vitro produced mammalian embryos suffer from developmental failure, with a large proportion showing embryonic retardation, degradation, or apoptosis. This failure is due, in part, to incomplete oocyte cytoplasmic maturation. C-type natriuretic peptide (CNP) has been reported to act as a meiotic inhibitor. Here we explored the potential effects of CNP pre-treatment sheep oocytes on nuclear maturation, changes in mitochondrial behavior and developmental competence of in vitro fertilized embryos. Sheep cumulus-oocyte complexes (COCs) were aspirated from abattoir-derived ovaries...
February 8, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29364650/biological-nanopores-confined-spaces-for-electrochemical-single-molecule-analysis
#5
Chan Cao, Yi-Tao Long
Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules...
January 24, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29339733/role-of-macromolecular-crowding-on-the-intracellular-diffusion-of-dna-binding-proteins
#6
Pinki Dey, Arnab Bhattacherjee
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, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29333542/acceleration-of-bursty-multiprotein-target-search-kinetics-on-dna-by-colocalisation
#7
Prathitha Kar, Andrey G Cherstvy, Ralf Metzler
Proteins are capable of locating specific targets on DNA by employing a facilitated diffusion process with intermittent 1D and 3D search steps. Gene colocalisation and coregulation-i.e. the spatial proximity of two communicating genes-is one factor capable of accelerating the target search process along the DNA. We perform Monte Carlo computer simulations and demonstrate the benefits of gene colocalisation for minimising the search time in a model DNA-protein system. We use a simple diffusion model to mimic the search for targets by proteins, produced initially in bursts of multiple proteins and performing the first-passage search on the DNA chain...
March 28, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29329560/overexpression-of-the-double-homeodomain-protein-dux4c-interferes-with-myofibrillogenesis-and-induces-clustering-of-myonuclei
#8
Céline Vanderplanck, Alexandra Tassin, Eugénie Ansseau, Sébastien Charron, Armelle Wauters, Céline Lancelot, Kelly Vancutsem, Dalila Laoudj-Chenivesse, Alexandra Belayew, Frédérique Coppée
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is associated with DNA hypomethylation at the 4q35 D4Z4 repeat array. Both the causal gene DUX4 and its homolog DUX4c are induced. DUX4c is immunodetected in every myonucleus of proliferative cells, while DUX4 is present in only 1/1000 of myonuclei where it initiates a gene deregulation cascade. FSHD primary myoblasts differentiate into either atrophic or disorganized myotubes. DUX4 expression induces atrophic myotubes and associated FSHD markers...
January 12, 2018: Skeletal Muscle
https://www.readbyqxmd.com/read/29216364/energetic-funnel-facilitates-facilitated-diffusion
#9
Massimo Cencini, Simone Pigolotti
Transcription factors (TFs) are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism-dubbed facilitated diffusion. By studying a collection of TF binding sites of Escherichia coli from the RegulonDB database and of Bacillus subtilis from DBTBS, we reveal a funnel in the binding energy landscape around the target sequences...
January 25, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155710/dna-nanotubes-as-a-versatile-tool-to-study-semiflexible-polymers
#10
Jörg Schnauß, Martin Glaser, Jessica S Lorenz, Carsten Schuldt, Christin Möser, Martin Sajfutdinow, Tina Händler, Josef A Käs, David M Smith
Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes...
October 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29121337/parp1-changes-from-three-dimensional-dna-damage-searching-to-one-dimensional-diffusion-after-auto-parylation-or-in-the-presence-of-ape1
#11
Lili Liu, Muwen Kong, Natalie R Gassman, Bret D Freudenthal, Rajendra Prasad, Stephanie Zhen, Simon C Watkins, Samuel H Wilson, Bennett Van Houten
PARP1-dependent poly-ADP-ribosylation (PARylation) participates in the repair of many forms of DNA damage. Here, we used atomic force microscopy (AFM) and single molecule fluorescence microscopy to examine the interactions of PARP1 with common DNA repair intermediates. AFM volume analysis indicates that PARP1 binds to DNA at nicks, abasic (AP) sites, and ends as a monomer. Single molecule DNA tightrope assays were used to follow the real-time dynamic behavior of PARP1 in the absence and presence of AP endonuclease (APE1) on AP DNA damage arrays...
December 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28871786/fast-background-free-dna-paint-imaging-using-fret-based-probes
#12
Alexander Auer, Maximilian T Strauss, Thomas Schlichthaerle, Ralf Jungmann
DNA point accumulation in nanoscale topography (DNA-PAINT) enables super-resolution microscopy by harnessing the predictable, transient hybridization between short dye-labeled "imager" and complementary target-bound "docking" strands. DNA-PAINT microscopy allows sub-5 nm spatial resolution, spectrally unlimited multiplexing, and quantitative image analysis. However, these abilities come at the cost of nonfluorogenic imager strands, also emitting fluorescence when not bound to their docking strands. This has thus far prevented rapid image acquisition with DNA-PAINT, as the blinking rate of probes is limited by an upper-bound of imager strand concentrations, which in turn is dictated by the necessity to facilitate the detection of single-molecule binding events over the background of unbound, freely diffusing probes...
October 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28867292/single-molecule-imaging-reveals-how-mre11-rad50-nbs1-initiates-dna-break-repair
#13
Logan R Myler, Ignacio F Gallardo, Michael M Soniat, Rajashree A Deshpande, Xenia B Gonzalez, Yoori Kim, Tanya T Paull, Ilya J Finkelstein
DNA double-strand break (DSB) repair is essential for maintaining our genomes. Mre11-Rad50-Nbs1 (MRN) and Ku70-Ku80 (Ku) direct distinct DSB repair pathways, but the interplay between these complexes at a DSB remains unclear. Here, we use high-throughput single-molecule microscopy to show that MRN searches for free DNA ends by one-dimensional facilitated diffusion, even on nucleosome-coated DNA. Rad50 binds homoduplex DNA and promotes facilitated diffusion, whereas Mre11 is required for DNA end recognition and nuclease activities...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28858629/selective-expression-of-the-transcription-elongation-factor-ell3-in-b-cells-prior-to-ell2-drives-proliferation-and-survival
#14
Lou-Ella M M Alexander, January Watters, Jessica A Reusch, Michelle Maurin, Brook S Nepon-Sixt, Katerina Vrzalikova, Mark G Alexandrow, Paul G Murray, Kenneth L Wright
B cell activation is dependent on a large increase in transcriptional output followed by focused expression on secreted immunoglobulin as the cell transitions to an antibody producing plasma cell. The rapid transcriptional induction is facilitated by the release of poised RNA pol II into productive elongation through assembly of the super elongation complex (SEC). We report that a SEC component, the Eleven -nineteen Lysine-rich leukemia (ELL) family member 3 (ELL3) is dynamically up-regulated in mature and activated human B cells followed by suppression as B cells transition to plasma cells in part mediated by the transcription repressor PRDM1...
November 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28668123/next-generation-dna-curtains-for-single-molecule-studies-of-homologous-recombination
#15
Michael M Soniat, Logan R Myler, Jeffrey M Schaub, Yoori Kim, Ignacio F Gallardo, Ilya J Finkelstein
Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28468829/fluorescence-and-nmr-spectroscopy-together-with-molecular-simulations-reveal-amphiphilic-characteristics-of-a-burkholderia-biofilm-exopolysaccharide
#16
Michelle M Kuttel, Paola Cescutti, Marco Distefano, Roberto Rizzo
Biofilms are a collective mode of bacterial life in which a self-produced matrix confines cells in close proximity to each other. Biofilms confer many advantages, including protection from chemicals (including antibiotics), entrapment of useful extracellular enzymes and nutrients, as well as opportunities for efficient recycling of molecules from dead cells. Biofilm matrices are aqueous gel-like structures composed of polysaccharides, proteins, and DNA stabilized by intermolecular interactions that may include non-polar connections...
June 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28465594/crowding-facilitated-macromolecular-transport-in-attractive-micropost-arrays
#17
Fan-Tso Chien, Po-Keng Lin, Wei Chien, Cheng-Hsiang Hung, Ming-Hung Yu, Chia-Fu Chou, Yeng-Long Chen
Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium...
May 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28107006/facilitated-diffusion-of-transcription-factor-proteins-with-anomalous-bulk-diffusion
#18
Lin Liu, Andrey G Cherstvy, Ralf Metzler
What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found...
February 7, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28062036/inserting-extrahelical-structures-into-long-dna-substrates-for-single-molecule-studies-of-dna-mismatch-repair
#19
M W Brown, A de la Torre, I J Finkelstein
The DNA mismatch repair (MMR) system corrects errors that occur during DNA replication. MMR needs the coordinated and highly dynamic assembly of repair enzymes at the site of the lesion. By visualizing transient intermediates of these assemblies, single-molecule approaches have shed critical insights into the mechanisms of MMR. These studies frequently require long (>20kb) DNA substrates with lesions and other extrahelical structures inserted at defined positions. DNA derived from bacteriophage λ (λ-DNA) is a high quality long (48...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28012548/facilitated-dissociation-kinetics-of-dimeric-nucleoid-associated-proteins-follow-a-universal-curve
#20
Katelyn Dahlke, Charles E Sing
Recent experimental work has demonstrated facilitated dissociation of certain nucleoid-associated proteins that exhibit an unbinding rate that depends on the concentration of freely diffusing proteins or DNA in solution. This concentration dependence arises due to binding competition with these other proteins or DNA. The identity of the binding competitor leads to different qualitative trends, motivating an investigation to understand observed differences in facilitated dissociation. We use a coarse-grained simulation that takes into account the dimeric nature of many nucleoid-associated proteins by allowing an intermediate binding state...
February 7, 2017: Biophysical Journal
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