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https://www.readbyqxmd.com/read/29342091/dna-based-single-molecule-electronics-from-concept-to-function
#1
REVIEW
Kun Wang
Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics...
January 17, 2018: Journal of Functional Biomaterials
https://www.readbyqxmd.com/read/29341686/nonequilibrium-chromosome-looping-via-molecular-slip-links
#2
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook, D Marenduzzo
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341675/many-molecule-reaction-triggered-by-a-single-photon-in-polaritonic-chemistry
#3
Javier Galego, Francisco J Garcia-Vidal, Johannes Feist
The second law of photochemistry states that, in most cases, no more than one molecule is activated for an excited-state reaction for each photon absorbed by a collection of molecules. In this Letter, we demonstrate that it is possible to trigger a many-molecule reaction using only one photon by strongly coupling the molecular ensemble to a confined light mode. The collective nature of the resulting hybrid states of the system (the so-called polaritons) leads to the formation of a polaritonic "supermolecule" involving the degrees of freedom of all molecules, opening a reaction path on which all involved molecules undergo a chemical transformation...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341672/helicase-stepping-investigated-with-one-nucleotide-resolution-fluorescence-resonance-energy-transfer
#4
Wenxia Lin, Jianbing Ma, Daguan Nong, Chunhua Xu, Bo Zhang, Jinghua Li, Qi Jia, Shuoxing Dou, Fangfu Ye, Xuguang Xi, Ying Lu, Ming Li
Single-molecule Förster resonance energy transfer is widely applied to study helicases by detecting distance changes between a pair of dyes anchored to overhangs of a forked DNA. However, it has been lacking single-base pair (1-bp) resolution required for revealing stepping kinetics of helicases. We designed a nanotensioner in which a short DNA is bent to exert force on the overhangs, just as in optical or magnetic tweezers. The strategy improved the resolution of Förster resonance energy transfer to 0.5 bp, high enough to uncover differences in DNA unwinding by yeast Pif1 and E...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341644/scale-dependent-stiffness-and-internal-tension-of-a-model-brush-polymer
#5
John P Berezney, Amanda B Marciel, Charles M Schroeder, Omar A Saleh
Bottle-brush polymers exhibit closely grafted side chains that interact by steric repulsion, thereby causing stiffening of the main polymer chain. We use single-molecule elasticity measurements of model brush polymers to quantify this effect. We find that stiffening is only significant on long length scales, with the main chain retaining flexibility on short scales. From the elasticity data, we extract an estimate of the internal tension generated by side-chain repulsion; this estimate is consistent with the predictions of blob-based scaling theories...
September 22, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341365/how-and-why-helium-permeates-non-porous-arsenolite-under-high-pressure
#6
Piotr Aleksander Guńka, Michał Hapka, Michael Hanfland, Maciej Dranka, Grzegorz Chałasiński, Janusz Zachara
Investigations into the helium permeation of arsenolite, the cubic, molecular arsenic(III) oxide polymorph As₄O₆, were carried out in order to understand how and why arsenolite helium clathrate As₄O₆∙2He is formed. High-pressure synchrotron X-ray diffraction experiments on arsenolite single crystals revealed that the permeation of helium into non-porous arsenolite depends on the time during which the crystal is subjected to high pressure and on the crystal history. The single crystal was totally transformed into As₄O₆·2He within 45 h under 5 GPa...
January 17, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/29341353/fluorescence-redox-blinking-adaptable-to-structural-analysis-of-nucleic-acids
#7
Takafumi Miyata, Naohiko Shimada, Atsushi Maruyama, Kiyohiko Kawai
The phenomenon of "blinking" is unique to single-molecule fluorescence measurements. By designing a fluorophore with an appropriate dark state lifetime (τoff), we have devised a kinetic analysis based on the control of fluorescence blinking (KACB) to investigate the dynamics of biomolecules. By controlling the redox reaction based blinking (rKACB), we have previously investigated conformational dynamics of RNA at the single-molecule level. However, there have been little knowledge about suitable fluorescent molecules for rKACB, and the application of rKACB has been limited to the analysis of hairpins and duplex structures of nucleic acids...
January 17, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29341024/advanced-contrast-agents-for-multimodal-biomedical-imaging-based-on-nanotechnology
#8
Daniel Calle, Paloma Ballesteros, Sebastián Cerdán
Clinical imaging modalities have reached a prominent role in medical diagnosis and patient management in the last decades. Different image methodologies as Positron Emission Tomography, Single Photon Emission Tomography, X-Rays, or Magnetic Resonance Imaging are in continuous evolution to satisfy the increasing demands of current medical diagnosis. Progress in these methodologies has been favored by the parallel development of increasingly more powerful contrast agents. These are molecules that enhance the intrinsic contrast of the images in the tissues where they accumulate, revealing noninvasively the presence of characteristic molecular targets or differential physiopathological microenvironments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340900/xenin-the-oldest-after-insulin
#9
Alexander T Maryanovich, Dmitry Yu Kormilets, Andrey D Polyanovsky
Xenin is a regulatory peptide first isolated from the human gastric mucosa. Using an open-access protein database MEDLINE (33 million molecules; 11 billion amino acid residues) and our original computer program, we conducted a search for the xenin motifs in the primary structure of proteins across almost the entire taxonomic range of evolution. Motifs with 40% homology to human xenin are already present in prokaryotes. Homology reaches 84-96% in single-cell algae and plants, becoming complete since bony fishes...
January 16, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29340415/alkaline-earth-metal-phenylphosphonates-and-their-intercalation-chemistry
#10
Klára Melánová, Ludvík Beneš, Jan Svoboda, Vítězslav Zima, Miroslav Pospíšil, Petr Kovář
The intercalation chemistry of layered alkaline-earth metal phenylphosphonates with the general formula MeC6H5PO3·2H2O (Ca, Sr, Ba) is reviewed. The preparation of the host materials is described and their behavior in dependence on the relative humidity and pH of the reaction medium is discussed. Mutual relationships between MeC6H5PO3·2H2O and Me(C6H5PO3H)2 were investigated using a method of computer-controlled addition of reagents. The MeC6H5PO3·2H2O compounds are able to intercalate species having a free electron pair through the so-called coordination intercalation...
January 17, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29340378/chemical-dynamics-simulations-of-cid-of-peptide-ions-comparisons-between-tik-h-2-and-tlk-h-2-fragmentation-dynamics-and-with-thermal-simulations
#11
Zahra Homayoon, Veronica Macaluso, Ana Martin-Somer, Maria Carolina Nicola Barbosa Muniz, Itamar Borges, William L Hase, Riccardo Spezia
Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N2, and previous thermal activation simulation results; Z...
January 17, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29340316/npt-iib-inhibition-does-not-improve-hyperphosphatemia-in-ckd
#12
Tobias E Larsson, Chisato Kameoka, Ikumi Nakajo, Yuta Taniuchi, Satoshi Yoshida, Tadao Akizawa, Ronald A Smulders
Introduction: Serum phosphate levels are insufficiently controlled in many patients with end-stage renal disease (ESRD), and novel therapeutic strategies are needed. Blocking intestinal phosphate absorption mediated by sodium-dependent phosphate co-transporter type 2b (NPT-IIb) holds promise; thus, we evaluated the efficacy, safety, tolerability, and pharmacokinetics of the novel and specific small molecule NPT-IIb inhibitor ASP3325 for the first time in humans. Methods: We conducted a randomized, double-blind, placebo-controlled, phase 1a single (n = 88) and multiple (n = 36) ascending dose study in healthy subjects, and a randomized, open-label, uncontrolled, phase 1b study in hyperphosphatemic ESRD patients on hemodialysis (single oral dose, n = 5; multiple oral doses, n = 17)...
January 2018: KI Reports
https://www.readbyqxmd.com/read/29339755/a-prebiotic-template-directed-peptide-synthesis-based-on-amyloids
#13
Saroj K Rout, Michael P Friedmann, Roland Riek, Jason Greenwald
The prebiotic replication of information-coding molecules is a central problem concerning life's origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29339721/single-molecule-fret-reveals-multiscale-chromatin-dynamics-modulated-by-hp1%C3%AE
#14
Sinan Kilic, Suren Felekyan, Olga Doroshenko, Iuliia Boichenko, Mykola Dimura, Hayk Vardanyan, Louise C Bryan, Gaurav Arya, Claus A M Seidel, Beat Fierz
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29339581/strain-induced-bi-thermoelectricity-in-tapered-carbon-nanotubes
#15
Laith A Algharagholy, Tom Pope, Colin J Lambert
We show that carbon-based nanostructured materials are a novel testbed for controlling thermoelectricity and have the potential to underpin the development of new cost-effective environmentally-friendly thermoelectric materials. In single-molecule junctions, it is known that transport resonances associated with the discrete molecular levels play a key role in the thermoelectric performance, but such resonances have not been exploited in carbon nanotubes (CNTs). Here we study junctions formed from tapered CNTs and demonstrate that such structures possess transport resonances near the Fermi level, whose energetic location can be varied by applying strain, resulting in an ability to tune the sign of their Seebeck coefficient...
January 17, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29339484/probabilistic-switching-circuits-in-dna
#16
Daniel Wilhelm, Jehoshua Bruck, Lulu Qian
A natural feature of molecular systems is their inherent stochastic behavior. A fundamental challenge related to the programming of molecular information processing systems is to develop a circuit architecture that controls the stochastic states of individual molecular events. Here we present a systematic implementation of probabilistic switching circuits, using DNA strand displacement reactions. Exploiting the intrinsic stochasticity of molecular interactions, we developed a simple, unbiased DNA switch: An input signal strand binds to the switch and releases an output signal strand with probability one-half...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339440/repurposing-tin-mesoporphyrin-as-an-immune-checkpoint-inhibitor-shows-therapeutic-efficacy-in-preclinical-models-of-cancer
#17
Tamara Muliaditan, James W Opzoomer, Jonathan Caron, Mary Okesola, Paris Kosti, Sharanpreet Lall, Mieke Van Hemelrijck, Francesco Dazzi, Andrew Tutt, Anita Grigoriadis, Cheryl Gillett, Stephen F Madden, Joy M Burchell, Shahram Kordasti, Sandra S Diebold, James Spicer, James N Arnold
PURPOSE: Unprecedented clinical outcomes have been achieved in a variety of cancers by targeting immune checkpoint molecules. This preclinical study investigates heme oxygenase-1 (HO-1), an immune suppressive enzyme that is expressed in a wide variety of cancers, as a potential immune checkpoint target in the context of a chemotherapy-elicited anti-tumor immune response. We evaluate repurposing tin mesoporphyrin (SnMP), which has demonstrated safety and efficacy targeting hepatic HO in the clinic for the treatment of hyperbilirubinaemia, as an immune checkpoint blockade therapy for the treatment of cancer...
January 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29339430/simultaneous-binding-of-multiple-ef-tu-copies-to-translating-ribosomes-in-live-escherichia-coli
#18
Mainak Mustafi, James C Weisshaar
In bacteria, elongation factor Tu is a translational cofactor that forms ternary complexes with aminoacyl-tRNA (aa-tRNA) and GTP. Binding of a ternary complex to one of four flexible L7/L12 units on the ribosome tethers a charged tRNA in close proximity to the ribosomal A site. Two sequential tests for a match between the aa-tRNA anticodon and the current mRNA codon then follow. Because one elongation cycle can occur in as little as 50 ms and the vast majority of aa-tRNA copies are not cognate with the current mRNA codon, this testing must occur rapidly...
January 16, 2018: MBio
https://www.readbyqxmd.com/read/29339216/in-vivo-biotinylated-calpastatin-improves-the-affinity-purification-of-human-m-calpain
#19
Hung Huy Nguyen, Alexander N Volkov, Guy Vandenbussche, Peter Tompa, Kris Pauwels
Recently we established a novel affinity purification method for calpain by exploiting the specific and reversible binding properties of its intrinsically disordered protein inhibitor, calpastatin. The immobilization strategy relied on the strength and specificity of the biotin - streptavidin interaction. Here, we report an improved and optimized method that even enables the general applicability of in vivo biotinylated (intrinsically disordered) proteins in any affinity capture strategy. Since in vitro chemical biotinylation is only accomplished with reagents that lack exact site specificity, it can not only cause sample heterogeneity but it can also hamper the functionality of the biotinylated molecules...
January 12, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29339162/a-method-to-improve-prediction-of-secondary-structure-for-large-single-rna-sequences
#20
Ali El-Lakkani, Eman M Ibrahim
The function of a particular RNA molecule within an organic system is principally determined by its structure. The current physical methods available for structure determination are time consuming and expensive. Hence, computational methods for structure prediction are often used. The prediction of the structure of a large single sequence of RNA needs a lot of research work. In the present work, a method is introduced to improve the prediction of large single sequence RNA secondary structure obtained by Mfold program using the concept of minimum free energy...
January 12, 2018: Biochemical and Biophysical Research Communications
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