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https://www.readbyqxmd.com/read/28806726/replication-fork-slowing-and-stalling-are-distinct-checkpoint-independent-consequences-of-replicating-damaged-dna
#1
Divya Ramalingam Iyer, Nicholas Rhind
In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks...
August 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28806521/determination-of-caspase-3-activity-and-its-inhibition-constant-by-combination-of-fluorescence-correlation-spectroscopy-with-a-microwell-chip
#2
Di Su, Xiaocai Hu, Chaoqing Dong, Jicun Ren
Caspase-3 is a key enzyme executing apoptosis during ontogenesis and homeostasis of multicellular organisms, and is a very important and potential drug target in treatment of apoptosis disturbance. So far, no commercial drugs for caspase-3 are available, and it is urgently necessitated to develop an effective method for caspase-3 activity assay and its inhibitor screening. In this paper, we propose a new method for determination of caspase-3 activity and its inhibition constant by combining single molecule fluorescence correlation spectroscopy (FCS) with a microwell chip...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28806075/reversible-on-off-switching-of-a-single-molecule-magnet-via-a-crystal-to-crystal-chemical-transformation
#3
Dong-Qing Wu, Dong Shao, Xiao-Qin Wei, Fu-Xing Shen, Le Shi, David Kempe, Yuan-Zhu Zhang, Kim R Dunbar, Xin-Yi Wang
Dynamic molecular crystals are of great interest due to their potential applications. Herein we report the reversible on-off switching of single-molecule magnet (SMM) behavior in a [Mo(CN)7](4-) based molecular compound. Upon dehydration and rehydration, the trinuclear Mn2Mo molecule [Mn(L)(H2O)]2[Mo(CN)7]·2H2O (1) undergoes reversible crystal-to-crystal transformation to a hexanuclear Mn4Mo2 compound [Mn(L)(H2O)]2[Mn(L)]2[Mo(CN)7]2 (2). This structural transformation involves the breaking and reforming of coordination bonds which leads to significant changes in the color and magnetic properties...
August 14, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28805878/interfacial-entropy-driven-thermophoretic-tweezers
#4
Linhan Lin, Xiaolei Peng, Zhangming Mao, Xiaoling Wei, Chong Xie, Yuebing Zheng
Directed migration of particles and molecules in a temperature gradient field, which is known as thermophoresis or the Soret effect, is of fundamental importance for mass transfer in colloid science and life sciences. However, thermophoretic tweezers that enable versatile particle manipulation have remained elusive due to the complex underlying physical forces in thermophoresis and the lack of general thermophilic particles above room temperature. Herein, we exploit entropic response and permittivity gradient at the particle-solvent interface to optically generated thermal gradient to achieve the thermophoretic trapping and dynamic manipulation of charged particles over an optothermal-responsive substrate...
August 14, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28805818/all-electric-control-of-donor-nuclear-spin-qubits-in-silicon
#5
Anthony J Sigillito, Alexei M Tyryshkin, Thomas Schenkel, Andrew A Houck, Stephen A Lyon
The electronic and nuclear spin degrees of freedom of donor impurities in silicon form ultra-coherent two-level systems that are potentially useful for applications in quantum information and are intrinsically compatible with industrial semiconductor processing. However, because of their smaller gyromagnetic ratios, nuclear spins are more difficult to manipulate than electron spins and are often considered too slow for quantum information processing. Moreover, although alternating current magnetic fields are the most natural choice to drive spin transitions and implement quantum gates, they are difficult to confine spatially to the level of a single donor, thus requiring alternative approaches...
August 14, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28805817/room-temperature-current-blockade-in-atomically-defined-single-cluster-junctions
#6
Giacomo Lovat, Bonnie Choi, Daniel W Paley, Michael L Steigerwald, Latha Venkataraman, Xavier Roy
Fabricating nanoscopic devices capable of manipulating and processing single units of charge is an essential step towards creating functional devices where quantum effects dominate transport characteristics. The archetypal single-electron transistor comprises a small conducting or semiconducting island separated from two metallic reservoirs by insulating barriers. By enabling the transfer of a well-defined number of charge carriers between the island and the reservoirs, such a device may enable discrete single-electron operations...
August 14, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28805744/aptamer-cell-based-selection-overview-and-advances
#7
REVIEW
Silvia Catuogno, Carla Lucia Esposito
Aptamers are high affinity single-stranded DNA/RNA molecules, produced by a combinatorial procedure named SELEX (Systematic Evolution of Ligands by Exponential enrichment), that are emerging as promising diagnostic and therapeutic tools. Among selection strategies, procedures using living cells as complex targets (referred as "cell-SELEX") have been developed as an effective mean to generate aptamers for heavily modified cell surface proteins, assuring the binding of the target in its native conformation. Here we give an up-to-date overview on cell-SELEX technology, discussing the most recent advances with a particular focus on cancer cell targeting...
August 14, 2017: Biomedicines
https://www.readbyqxmd.com/read/28805544/rna-silencing-in-plant-symbiotic-bacteria-insights-from-a-protein-centric-view
#8
José I Jiménez-Zurdo, Marta Robledo
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28805383/cu-ii-catalyzed-ortho-selective-aminomethylation-of-phenols
#9
Jin-Ling Dai, Nan-Qi Shao, Jin Zhang, Run-Ping Jia, Dong-Hui Wang
A Cu(II)-catalyzed ortho-selective functionalization of free phenols with trifluoroborates to afford Csp2-Csp3 coupling products under mild conditions has been developed. A variety of functional groups on the phenol and the potassium ami-nomethyltrifluoroborate substrates were found compatible, fur-nishing the corresponding products in moderate to excellent yields. A single-electron transfer radical coupling mechanism involving a six-membered transition state is proposed to rationalize the high levels of ortho-selectivity in the reaction...
August 14, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28805376/discovery-and-biosensing-applications-of-diverse-rna-cleaving-dnazymes
#10
Meng Liu, Dingran Chang, Yingfu Li
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors...
August 14, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28805223/the-effect-of-defects-on-the-catalytic-activity-of-single-au-atom-supported-carbon-nanotubes-and-reaction-mechanism-for-co-oxidation
#11
Sajjad Ali, Tian Fu Liu, Zan Lian, Bo Li, Dang Sheng Su
The mechanism of CO oxidation by O2 on a single Au atom supported on pristine, mono atom vacancy (m), di atom vacancy (di) and the Stone Wales defect (SW) on single walled carbon nanotube (SWCNT) surface is systematically investigated theoretically using density functional theory. We determine that single Au atoms can be trapped effectively by the defects on SWCNTs. The defects on SWCNTs can enhance both the binding strength and catalytic activity of the supported single Au atom. Fundamental aspects such as adsorption energy and charge transfer are elucidated to analyze the adsorption properties of CO and O2 and co-adsorption of CO and O2 molecules...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28805060/substrate-induced-facilitated-dissociation-of-competitive-inhibitor-from-the-active-site-of-o-acetyl-serine-sulfhydrylase-reveal-a-competitive-allostery-mechanism
#12
Appu Kumar Singh, Mary Krishna Ekka, Abhishek Kaushik, Vaibhav Kumar Pandya, Ravi Pratap Singh, Srijita Banerjee, Monica Mittal, Vijay Singh, Sangaralingam Kumaran
By classical competitive-antagonism, substrate and competitive-inhibitor must bind mutually exclusively to the active site. The competitive inhibition of O-acetyl serine sulfhydrylase (OASS) by C-terminal of serine acetyltransferase (SAT) presents a paradox, because the C-terminal of SAT binds to the active site of OASS with 4-6 log fold (104 -106) more affinity than that of the substrate. Therefore, we employed multiple approaches to understand how substrate gains access to OASS active site under physiological conditions...
August 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28805059/probing-membrane-receptor-ligand-specificity-with-surface-and-tip-enhanced-raman-scattering
#13
Lifu Xiao, Karen A Bailey, Hao Wang, Zachary D Schultz
The specific interaction between a ligand and a protein is a key component in minimizing off-target effects in drug discovery. Investigating these interactions with membrane protein receptors can be quite challenging. In this report, we show how spectral variance observed in surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) can be correlated with ligand specificity in affinity-based assays. Variations in the enhanced Raman spectra of three peptide ligands (i.e. cyclic-RGDFC, cyclic-isoDGRFC, and CisoDGRC), which have different binding affinity to αvβ3 integrin, are reported from isolated proteins and from receptors in intact cancer cell membranes...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28804000/the-mechanics-of-dna-loops-bridged-by-proteins-unveiled-by-single-molecule-experiments
#14
REVIEW
Catherine Tardin
Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process...
August 10, 2017: Biochimie
https://www.readbyqxmd.com/read/28803930/identification-of-neuroglobin-as-a-novel-player-in-anti-bacterial-responses-in-amphioxus
#15
Yu Bai, Shousheng Liu, Xia Wang, Xiaoyuan Du, Guangdong Ji, Shicui Zhang
Theoretical considerations support various functions of neuroglobin (Ngb), but further studies are required for full characterization of these functions. In this study, we identified the presence of a single Ngb gene, BjNgb, in the amphioxus Branchiostoma japonicum. BjNgb was expressed in various tissues including the notochord, gonads (ovary and testis) and gill, and up-regulated significantly in response to the challenge with LPS and LTA, suggesting involvement in immune response of amphioxus against bacterial infection...
August 10, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28803843/high-throughput-screening-of-hybridoma-supernatants-using-multiplexed-fluorescent-cell-barcoding-on-live-cells
#16
Mei Lu, Brian M Chan, Peter W Schow, Wesley S Chang, Chadwick T King
With current available assay formats using either immobilized protein (ELISA, enzyme-linked immunosorbent assay) or immunostaining of fixed cells for primary monoclonal antibody (mAb) screening, researchers often fail to identify and characterize antibodies that recognize the native conformation of cell-surface antigens. Therefore, screening using live cells has become an integral and important step contributing to the successful identification of therapeutic antibody candidates. Thus the need for developing high-throughput screening (HTS) technologies using live cells has become a major priority for therapeutic mAb discovery and development...
August 10, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28803781/myc-regulates-chromatin-decompaction-and-nuclear-architecture-during-b-cell-activation
#17
Kyong-Rim Kieffer-Kwon, Keisuke Nimura, Suhas S P Rao, Jianliang Xu, Seolkyoung Jung, Aleksandra Pekowska, Marei Dose, Evan Stevens, Ewy Mathe, Peng Dong, Su-Chen Huang, Maria Aurelia Ricci, Laura Baranello, Ying Zheng, Francesco Tomassoni Ardori, Wolfgang Resch, Diana Stavreva, Steevenson Nelson, Michael McAndrew, Adriel Casellas, Elizabeth Finn, Charles Gregory, Brian Glenn St Hilaire, Steven M Johnson, Wendy Dubois, Maria Pia Cosma, Eric Batchelor, David Levens, Robert D Phair, Tom Misteli, Lino Tessarollo, Gordon Hager, Melike Lakadamyali, Zhe Liu, Monique Floer, Hari Shroff, Erez Lieberman Aiden, Rafael Casellas
50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input...
July 28, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28803466/deciphering-the-fluorine-code-the-many-hats-fluorine-wears-in-a-protein-environment
#18
Allison Ann Berger, Jan-Stefan Völler, Nediljko Budisa, Beate Koksch
Deciphering the fluorine code is how we describe not only the focus of this Account, but also the systematic approach to studying the impact of fluorine's incorporation on the properties of peptides and proteins used by our groups and others. The introduction of fluorine has been shown to impart favorable, but seldom predictable, properties to peptides and proteins, but up until about two decades ago the outcomes of fluorine modification of peptides and proteins were largely left to chance. Driven by the motivation to extend the application of the unique properties of the element fluorine from medicinal and agro chemistry to peptide and protein engineering we have established extensive research programs that enable the systematic investigation of effects that accompany the introduction of fluorine into this class of biopolymers...
August 12, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28802547/good-ol-fat-links-between-lipid-signaling-and-longevity
#19
REVIEW
Victor Bustos, Linda Partridge
Aging is the single greatest risk factor for the development of disease. Understanding the biological molecules and mechanisms that modulate aging is therefore critical for the development of health-maximizing interventions for older people. The effect of fats on longevity has traditionally been disregarded as purely detrimental. However, new studies are starting to uncover the possible beneficial effects of lipids working as signaling molecules on health and longevity. These studies highlight the complex links between aging and lipid signaling...
August 9, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28802212/pharmacophore-based-design-of-some-multi-targeted-compounds-targeted-against-pathways-of-diabetic-complications
#20
Navriti Chadha, Om Silakari
Diabetic complications is a complex metabolic disorder developed primarily due to prolonged hyperglycemia in the body. The complexity of the disease state as well as the unifying pathophysiology discussed in the literature reports exhibited that the use of multi-targeted agents with multiple complementary biological activities may offer promising therapy for the intervention of the disease over the single-target drugs. In the present study, novel thiazolidine-2,4-dione analogues were designed as multi-targeted agents implicated against the molecular pathways involved in diabetic complications using knowledge based as well as in-silico approaches such as pharmacophore mapping, molecular docking etc...
July 21, 2017: Journal of Molecular Graphics & Modelling
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