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https://www.readbyqxmd.com/read/28432850/a-detailed-experimental-study-of-a-dna-computer-with-two-endonucleases
#1
Sebastian Sakowski, Tadeusz Krasiński, Joanna Sarnik, Janusz Blasiak, Jacek Waldmajer, Tomasz Poplawski
Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e...
April 22, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28432684/characterization-of-interactions-of-metal-containing-nanoparticles-with-biomolecules-by-ce-an-update-2012-2016
#2
REVIEW
Svetlana S Aleksenko, Magdalena Matczuk, Andrei R Timerbaev
The methodological developments and applications of CE related to studying biotransformations of metal-based nanoscale particles of impending medicinal use are overviewed. This is an update to a previous review article (Aleksenko, S. S., Shmykov, A. Y., Oszwałdowski, S., Timerbaev, A. R., Metallomics 2012, 4, 1141-1148) and it covers the research papers published within the last five years. As was anticipated in that review, CE can now be seen as a customary technique in the analysis of biomolecular interactions that exert an impact on the mechanism of action of nanoparticles, comprising metabolism, delivery, cell processing, and targeting...
April 22, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#3
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#4
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta Energy Function, REF15...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28430221/numerical-simulation-on-the-performance-analysis-of-a-graphene-coated-optical-fiber-plasmonic-sensor-at-anti-crossing
#5
Jeeban Kumar Nayak, Rajan Jha
A graphene-based surface plasmon resonance sensor using D-shaped fiber in anti-crossing has been designed. Silver as a plasmon active metal is followed by graphene, which helps in preventing oxidation and shows better adsorption efficiency to biomolecules. A wavelength interrogation technique based on the finite element method has been used to evaluate performance parameters. Design parameters such as thickness of silver, residual cladding, and GeO<sub>2</sub> dopant concentration have been optimized...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28430199/control-over-differentiation-of-a-metastable-supramolecular-assembly-in-one-and-two-dimensions
#6
Tomoya Fukui, Shinnosuke Kawai, Satoko Fujinuma, Yoshitaka Matsushita, Takeshi Yasuda, Tsuneaki Sakurai, Shu Seki, Masayuki Takeuchi, Kazunori Sugiyasu
Molecular self-assembly under kinetic control is expected to yield nanostructures that are inaccessible through the spontaneous thermodynamic process. Moreover, time-dependent evolution, which is reminiscent of biomolecular systems, may occur under such out-of-equilibrium conditions, allowing the synthesis of supramolecular assemblies with enhanced complexities. Here we report on the capacity of a metastable porphyrin supramolecular assembly to differentiate into nanofibre and nanosheet structures. Mechanistic studies of the relationship between the molecular design and pathway complexity in the self-assembly unveiled the energy landscape that governs the unique kinetic behaviour...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28426228/ultrafast-dynamics-of-a-triazene-excited-state-pathways-and-the-impact-of-binding-to-the-minor-groove-of-dna-and-further-biomolecular-systems
#7
Lena Grimmelsmann, Alireza Marefat Khah, Christian Spies, Christof Hättig, Patrick Nuernberger
Many synthetic DNA minor groove binders exhibit a strong increase in fluorescence when bound to DNA. The pharmaceutical-relevant berenil (diminazene aceturate) is an exception with an extremely low fluorescence quantum yield (on the order of 10(-4)). We investigate the ultrafast excited-state dynamics of this triazene by femtosecond time-resolved fluorescence experiments in water, ethylene glycol, and buffer and bound to the enzyme β-trypsin, the minor groove of AT-rich DNA, and G-quadruplex DNA. Ab initio calculations provide additional mechanistic insight...
April 20, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28426223/over-destabilization-of-protein-protein-interaction-in-generalized-born-model-and-utility-of-energy-density-integration-cutoff
#8
Yukinobu Mizuhara, Dan Parkin, Koji Umezawa, Jun Ohnuki, Mitsunori Takano
The generalize Born (GB) model is frequently used in MD simulations of biomolecular systems in aqueous solution. The GB model is usually based on the so-called Coulomb field approximation (CFA) for the energy density integration. In this study, we report that the GB model with CFA overdestabilizes the long-range electrostatic attraction between oppositely-charged molecules (ionic bond forming two-helix system and kinesin-tubulin system) when the energy density integration cutoff, rmax, which is used to calculate the Born energy, is set to a large value...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28426045/enzyme-coated-janus-nanoparticles-that-selectively-bind-cell-receptors-as-a-function-of-the-concentration-of-glucose
#9
Gabriele Rucinskaite, Sebastian A Thompson, Sureyya Paterson, Roberto de la Rica
A method is proposed for controlling the number of nanoparticles bound to cell membranes via RGDS peptide-integrin interactions. It consists of propelling nanoparticles bearing the peptides with enzymes (glucose oxidase), which disrupts biomolecular interactions as a function of the concentration of enzyme substrate (glucose).
April 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28425189/the-global-ethics-corner-foundations-beliefs-and-the-teaching-of-biomedical-and-scientific-ethics-around-the-world
#10
Henry Jakubowski, Jianping Xie, Arup Kumar Mitra, Ravindra Ghooi, Saman Hosseinkhani, Mohsen Alipour, Behnam Hajipour, George Obiero
The profound advances in the biomolecular sciences over the last decades have enabled similar advances in biomedicine. These advances have increasingly challenged our abilities to deploy them in an equitable and ethically acceptable manner. As such, it has become necessary and important to teach biomedical and scientific ethics to our students who will become the researchers, medical professionals, and global citizens of the future. As advances in the biosciences and medicine are made, developed, and used across the globe, our survival on an endangered planet requires global dialog and consensual action...
April 19, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28424990/proteomic-analysis-of-the-hippocampus-in-mouse-models-of-trigeminal-neuralgia-and-inescapable-shock-induced-depression
#11
Qing-Huan Guo, Qing-He Tong, Ning Lu, Hong Cao, Liu Yang, Yu-Qiu Zhang
To investigate the behavioral and biomolecular similarity between neuralgia and depression, a trigeminal neuralgia (TN) mouse model was established by constriction of the infraorbital nerve (CION) to mimic clinical trigeminal neuropathic pain. A mouse learned helplessness (LH) model was developed to investigate inescapable foot-shock-induced psychiatric disorders like depression in humans. Mass spectrometry was used to assess changes in the biomolecules and signaling pathways in the hippocampus from TN or LH mice...
April 19, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/28417509/a-biomolecular-recognition-approach-for-the-functionalization-of-cellulose-with-gold-nanoparticles
#12
A Almeida, A M M Rosa, A M Azevedo, D M F Prazeres
Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody...
April 17, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28417365/quantifying-cbm-carbohydrate-interactions-using-microscale-thermophoresis
#13
Haiyang Wu, Cédric Y Montanier, Claire Dumon
MicroScale Thermophoresis (MST) is an emerging technology for studying a broad range of biomolecular interactions with high sensitivity. The affinity constant can be obtained for a wide range of molecules within minutes based on reactions in microliters. Here, we describe the application of MST in quantifying two CBM-carbohydrate interactions, a CBM3a toward cellulose nanocrystals and a CBM4 against xylohexaose.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28415863/thermophysical-properties-and-phase-behavior-of-fluids-for-application-in-carbon-capture-and-storage-processes
#14
J P Martin Trusler
Phase behavior and thermophysical properties of mixtures of carbon dioxide with various other substances are very important for the design and operation of carbon capture and storage (CCS) processes. The available empirical data are reviewed, together with some models for the calculation of these properties. The systems considered in detail are, first, mixtures of carbon dioxide, water, and salts; second, carbon dioxide-rich nonelectrolyte mixtures; and third, mixtures of carbon dioxide with water and amines...
April 17, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28415862/multivariate-analysis-and-statistics-in-pharmaceutical-process-research-and-development
#15
José E Tabora, Nathan Domagalski
The application of statistics in pharmaceutical process research and development has evolved significantly over the past decades, motivated in part by the introduction of the Quality by Design paradigm, a landmark change in regulatory expectations for the level of scientific understanding associated with the manufacturing process. Today, statistical methods are increasingly applied to accelerate the characterization and optimization of new drugs created via numerous unit operations well known to the chemical engineering discipline...
April 17, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28415861/atmospheric-aerosols-clouds-chemistry-and-climate
#16
V Faye McNeill
Although too small to be seen with the human eye, atmospheric particulate matter has major impacts on the world around us, from our health to global climate. Understanding the sources, properties, and transformations of these particles in the atmosphere is among the major challenges in air quality and climate research today. Significant progress has been made over the past two decades in understanding atmospheric aerosol chemistry and its connections to climate. Advances in technology for characterizing aerosol chemical composition and physical properties have enabled rapid discovery in this area...
April 17, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28412902/nanosafety-towards-safer-nanoparticles-by-design
#17
Neus G Bastús, Víctor Puntes
The continuous development of Nanotechnology is progressively introducing nanoparticles into society. However, little is known about the safety of nanoparticles and functions of engineered nanomaterials, in particular how the physicochemical properties of the materials relate to mechanisms of injury at the nano-bio interface. While comprehensive knowledge on the potential toxicity of NPs is still lacking, as time goes by and research in the field continues, different aspects, such as interactions with the immune system, perturbation of cellular membranes, transportation of toxic moieties and others are emerging as potentially hazardous aspects of NPs...
April 13, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28411641/nanoarmoring-of-proteins-by-conjugation-to-block-copolymer-micelles
#18
Nisaraporn Suthiwangcharoen, Ramanathan Nagarajan
The creation of polymer nanoparticles with protein functionality is of great interest to many applications such as targeted drug or gene delivery, diagnostic imaging, cancer theranostics, delivery of protein therapeutics, sensing chemical and biomolecular analytes in complex environments, and design of protective clothing resembling a second skin. Many approaches to achieving this goal are being explored in the current literature. In this chapter, we describe a relatively simple and flexible approach of conjugating the protein to an amphiphilic block copolymer and creating polymer nanoparticles with protein functionality by taking advantage of the intrinsic self-assembly behavior of the amphiphilic block copolymer...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28407563/recent-advances-in-fret-for-the-study-of-protein-interactions-and-dynamics
#19
REVIEW
Kenji Okamoto, Yasushi Sako
Förster/fluorescence resonance energy transfer (FRET) has been extensively used to detect the binding state or conformation of biomolecules. In the past few decades, various in vitro and in vivo applications of FRET measurement have been developed, including FRET probes, in-cell measurements, single-molecule measurements, and combination with computer simulation. In this review, we describe recent advances in FRET methods for examining biomolecular interactions and dynamics: (i) phasor plot analysis for quantitative analysis of protein interactions, (ii) single-molecule FRET measurement for detecting conformational dynamics in live cells, and (iii) data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein...
April 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28402043/near-infrared-circularly-polarized-light-triggered-enantioselective-photo-polymerization-using-upconversion-nanophosphors
#20
Guang Yang, Liangfu Zhu, Jingang Hu, Hongyan Xia, Dong Qiu, Qijin Zhang, Douguo Zhang, Gang Zou
Circularly polarized light (CPL), is considered to be a true chiral entity and has been suggested as an explanation for the introduction of initial chiral biases into key biomolecular building blocks. CPL used in recently asymmetric photochemical reactions are mainly in UV and visible region, while natural CPL observed in star-forming regions of the Orion constellation are in the infrared (IR) band. Whether CPL in the IR or near IR (NIR) region could be utilized to trigger asymmetric photochemical reactions remains a question to be answered...
April 12, 2017: Chemistry: a European Journal
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