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A Study Of Peptide Affinity For Carbon Nanotubes Through Phage Display Experiments
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Book Synopsis A Study of Peptide Affinity for Carbon Nanotubes Through Phage Display Experiments by : Caroline Kar Yan Lau
Download or read book A Study of Peptide Affinity for Carbon Nanotubes Through Phage Display Experiments written by Caroline Kar Yan Lau and published by . This book was released on 2004 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of biological molecules to facilitate the dispersal, separation and assembly of nanoscopic entities such as carbon nanotubes has received great attention and has been the focus of much current research activity. In this work we sought to identify peptide sequences with selective affinity for HiPco-produced SWNTs in order to gain some insight to the binding mechanisms and interactions. This was done using a phage display technique, in which a library of bacteriophages displaying greater than 109 different 12-amino acid long peptide sequences were exposed to carbon nanotubes. Non-specifically bound phages were successively washed off with increasingly stronger detergents until only tightly binding phages remained. It was observed that after six rounds of phage display tests, the percentage of sites of aromatic ring-containing amino acids increased while the percentage of sites of aliphatic amino acids decreased. Results were compared to previous phage display results on MWNTs. These results suggest that peptides are able to distinguish between different allotropes of carbon and that their highly specific binding mechanisms can be exploited in the future for use in precision placement of nanoscale components in devices such as electronic circuits and sensors.
Book Synopsis Detection of PETN Using Peptide Based Biologically Modified Carbon Nanotubes by : George D. Kubas
Download or read book Detection of PETN Using Peptide Based Biologically Modified Carbon Nanotubes written by George D. Kubas and published by . This book was released on 2017 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: Explosive detection is an area of great interest in the military, transportation, and safety sectors due to the recent terrorist attacks that have taken place in different parts of the world. Here, detection platforms with high sensitivity and selectivity features are required for the detection of explosives in these senarios. A promising candidate that can fit these specifications is a peptide functionalized carbon nanotube (CNT) due to their unique sensing properties. The present research work has studied the identification of peptides that selectively bind to PETN explosive as well as their incorporation onto CNTs for establishing a nanoscale sensor. This research work has initially concentrated on the use of a phage display technique and enzyme-linked immunosorbent assays in order to screen for those peptides with affinity toward PETNH [a surrogate of the explosive Pentaerythritol tetranitrate (PETN)]. The use of the PETN surrogate in this work allowed the immobilization of the target during the phage screening process, while retaining the chemical profile similar to PETN. The results have suggested that the library here investigated contained peptides selective to PETNH. Following the panning (screening) procedure, clones were selected and further tested for specificity toward PETNH. The ELISA results from these samples showed that each phage clone has some level of selectivity for binding to PETNH. The peptides from these clones have been sequenced and shown to contain similar amino acid segments among them. These peptides were then used to biologically functionalize single wall carbon nanotubes (SWCNTs) with the purpose of developing a liquid state PETN nanosensor. The results have shown that the peptide-SWCNT complex was able to detect the presence of PETNH. Also included in this work, is the modeling of the electrical current flow passing through a carbon nanotube field effect transistor (FET) system using density functional tight binding (DFTB) theory via a dftb+ program. The systems investigated included a plain SWCNT, a peptide functionalized SWCNT, and a peptide functionalized SWCNT interacting with PETN. The results have showed that an 8,0 SWCNT FET exhibited an ntype conduction in an oxygen less environment, and that the addition of a peptide or a peptide-PETN interaction did not affect the original n-type conduction profile of the SWCNTs. Furthermore, the results showed that the interaction of PETN with the SWCNTpeptide system displayed an increase in the electrical current of the system suggesting that the explosive sensor resulted in a donation of electrons to the SWCNT conducting channel. The results have shown that the peptide-SWCNT FET operation parameters can be modeled using DFTB theory. This modeling can reduce the experimental work required to identify the functional groups that tailor the selective features of SWCNT based sensors. It is expected that the results presented in this research program can lay out the foundations for developing solid state sensors for explosive materials.
Book Synopsis Identifying Unique Material Binding Peptides Using a High Throughput Method by : Rachel M. Krabacher
Download or read book Identifying Unique Material Binding Peptides Using a High Throughput Method written by Rachel M. Krabacher and published by . This book was released on 2016 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: Through biotic-abiotic interactions, it has been shown that peptides can recognize and selectively bind to a wide variety of materials dependent on both their surface properties and the environment. Better understanding of these peptides and the materials to which they bind can be beneficial in the development of biofunctionalization approaches for creating hybrid materials and sensors. Several research groups have identified material binding peptides using biopanning with phage or cell peptide display libraries. However, limitations with sequence diversity of traditional bacteriophage (phage) display libraries and loss of unique phage clones during the amplification cycles results in a smaller pool of peptide sequences identified. In order to overcome some of the limitations of traditional biopanning methodology, a modified method using phage display along with high-throughput next generation sequencing to select for unique peptides specific for different classes of single wall carbon nanotubes has been devised. The process, analysis and characterization of peptide sequences identified using the modified method is described and compared to peptides identified using the traditional methods. Selected sequences from this study were immobilized on surfaces and used in site-specific capture of metallic and/or semiconducting carbon nanotubes. A dispersion experiment was carried out to identify chiral specific peptides. From this research, successful methods have been identified to select and confirm binding peptides specific to various materials. Knowledge of chiral specific recognizing peptides can allow for the potential purification and separation of specific chirality carbon nanotubes, thus opening the door for a number of carbon nanotube applications which had been previously hindered by mixed carbon nanotube samples.
Book Synopsis Investigation of Peptides that Exhibit Affinity Towards Advanced Materials by : Hyun Seok Kim
Download or read book Investigation of Peptides that Exhibit Affinity Towards Advanced Materials written by Hyun Seok Kim and published by . This book was released on 2017 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of commercially employed polymers are refractory to surface modification and may require harsh conditions ranging from corona discharge to halogenation to assemble a functional surface. We are exploring combinatorial peptide screening using phage display to identify peptides capable of non-covalent binding to advanced polymeric materials to discover mild yet useful surface modification agents. Through the application of phage display techniques, identification of polymer-binding peptides ("adhesons") are the focus of this research. Our studies in this area, including the ability to fabricate phage fibers and membranes, will be presented. Results in this area should contribute to our basic understanding of the interactions between polymeric surfaces and biomolecules, but also lead to potential applications in the area of advanced functional materials.
Download or read book Beyond Helper Phage written by and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The "helper cell" packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Here, based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.
Book Synopsis Modeling of Nanotoxicity by : Ruhong Zhou
Download or read book Modeling of Nanotoxicity written by Ruhong Zhou and published by Springer. This book was released on 2015-09-04 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the fundamentals of nanotoxicity modeling and its implications for the development of novel nanomedicines. It lays out the fundamentals of nanotoxicity modeling for an array of nanomaterial systems, ranging from carbon-based nanoparticles to noble metals, metal oxides, and quantum dots. The author illustrates how molecular (classical mechanics) and atomic (quantum mechanics) modeling approaches can be applied to bolster our understanding of many important aspects of this critical nanotoxicity issue. Each chapter is organized by types of nanomaterials for practicality, making this an ideal book for senior undergraduate students, graduate students, and researchers in nanotechnology, chemistry, physics, molecular biology, and computer science. It is also of interest to academic and industry professionals who work on nanodrug delivery and related biomedical applications, and aids readers in their biocompatibility assessment efforts in the coming age of nanotechnology. This book also provides a critical assessment of advanced molecular modeling and other computational techniques to nanosafety, and highlights current and future biomedical applications of nanoparticles in relation to nanosafety.
Book Synopsis Structural Studies and Phage Display of the Alpha-bungarotoxin Binding Peptide by : Lena Zagyanskiy
Download or read book Structural Studies and Phage Display of the Alpha-bungarotoxin Binding Peptide written by Lena Zagyanskiy and published by . This book was released on 2004 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Conformational Study of Nano-1 Peptide at the Water/carbon Nanotube Interface Using Molecular Dynamics Simulations by : Chi-cheng Chiu
Download or read book Conformational Study of Nano-1 Peptide at the Water/carbon Nanotube Interface Using Molecular Dynamics Simulations written by Chi-cheng Chiu and published by . This book was released on 2007 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Interaction of Peptides with Functionalized Carbon Nanotubes by : Poulami Barman
Download or read book The Interaction of Peptides with Functionalized Carbon Nanotubes written by Poulami Barman and published by . This book was released on 2009 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: "A literature study was conducted to review peptide adhesion to carbon nanotubes and they were found to be important in the drug designing industries. To attain target specificity CNTs (functionalized with DNA, peptides etc.) have been used as potential vector system. Prior studies show that single walled nanotubes (SWNTs) when functionalized with peptides have been proven to be better delivery systems than the previous vector delivery systems. Functionalized SWNTs can deliver the peptides to the specific target organs in the right concentration without having prominent toxic effect. Toxicity studies show that since the SWNTs have shorter half life periods most of them get washed away after they deliver the ligands to the target organs. It has been shown that SWNTs that are toxic to the body are so solely due to manufacturing defects. Pure SWNTs are not toxic to the body. Recently functionalized CNTs are also used for cancer therapy. A docking study was carried out on interaction of hydrogen and nitrogen functionalized SWNTs with peptides where vasopressin is the model peptide. In order to study the effect of dimensions of SWNTs and functionalized group attached to the SWNTs on the strength of a bond, binding free energies were calculated from the docking models. Hydrogen functionalized, nitrogen functionalized and non-functionalized SWNTs binding energies were compared with each other. Results show that functionalized SWNTs tend to bind with more peptide molecules than nonfunctionalized SWNTs. The interactions on the inner walls of SWNTs are more unstable than the outer wall interactions."--Abstract.
Book Synopsis The Use of Phage Display to Identify Specific Peptide Ligands by : Sheila J. Sang
Download or read book The Use of Phage Display to Identify Specific Peptide Ligands written by Sheila J. Sang and published by . This book was released on 2014 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phage display allows the expression of peptides on filamentous phage when the peptide of interest is fused to the gene for a virus coat protein. The goal of this project was to use phage display to produce peptide molecules that bind specifically to human serum albumin. An M13 library displaying random linear heptapeptides linked to coat protein pIII (Ph.D.-7[trademark], New England BioLabs) was amplified by infecting E. coli host strain ER2738 to produce phage library stocks Amp LA (2.1x1012 pfu/ml) and Amp LS (1.0x109 pfu/ml). The amplified phage were titered on LB plates containing X-gal, IPTG, and tetracycline to ensure expression of the F pilus. Three rounds of biopanning on HSA-coated polyvinyl chloride plates and amplification of the virus was performed (Amp P3A and Amp P3S). Individual plaques were picked and amplified to produce clones (HSA1- HSA8). We developed a phage concentration ELISA to test for the quantity of phage needed to detect binding in an ELISA using peroxidase-conjugated antibodies against M13. Phage were diluted in sodium carbonate to bind the protein to the plate, followed by block and anti-M13-PO. It was found that a concentration greater than 106 pfu/ml was needed to give a positive M13 ELISA. We then tested the conditions needed to produce an ELISA that measures phage binding to a specific ligand (M13 ELISA). Three different plates were tested. Although MaxiSorp® plates are thought to give a good signal and more consistent data, we found that specific binding of Amp LA was best when using polyvinyl chloride plates. The influence of blocking buffer (ovalbumin and casein) was also tested. Casein block and sample buffer gave a good signal in the presence of HSA with the least non-specific binding. These studies demonstrate that phage display is an effective method for producing HSA-binding peptides.
Book Synopsis From Phage Display and Venoms to Protease-resistant Peptides: Design of BBB-shuttles and Peptides Targeting EGF by : Cristina Díaz Perlas
Download or read book From Phage Display and Venoms to Protease-resistant Peptides: Design of BBB-shuttles and Peptides Targeting EGF written by Cristina Díaz Perlas and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Peptides play a critical role in human physiology and harbour a huge potential as therapeutic agents. In this thesis, new peptides have been discovered as ligands for the epidermal growth factor (EGF) and as new BBB-shuttles, using phage display and chemical synthesis of peptides and proteins. EGF is overexpressed in several cancers, inducing the proliferation and survival of these cells. By inhibiting EGF, we will prevent the activation of the receptor and, consequently, its negative effects. Moreover, phage display is a powerful tool to identify peptide ligands. However, only L-peptides can be displayed, which are protease unstable. Hence, mirror image phage display was developed to identify D-peptides, more stable in front of proteases. In this methodology, the selection is carried out against the mirror image of the original target and, after the panning selection and the synthesis of the enantiomer of the ligand, D-peptides are obtained. In this regard, the enantiomer of EGF was synthesised using a combination of solid-phase peptide synthesis and native chemical ligation. After the panning of two phage display peptide libraries against the immobilised protein, nine sequences were selected and synthesised with D-amino acids. Three of these peptides have high affinities for EGF and are stable in serum proteases for more than 24h. Most potential drugs for the treatment of central nervous system disorders (such as brain cancer and Alzheimer's disease) do not cross the blood-brain barrier (BBB). Much effort has been devoted to the discovery of BBB-shuttle peptides – entities that have the capacity to carry cargoes across the BBB. The sources of BBB-shuttle peptides are diverse, ranging from the mimicry of endogenous proteins to the use of phage display. Phage display has been applied against a human BBB cellular model which consists in the co-culture of human brain capillary endothelial cells and bovine pericytes. From the screening of a phage display library containing random 12-amino acid sequences, SGVYKVAYDWQH (SGV) was selected. Validation studies were performed confirming that SGV is able to increase the uptake of a model protein in endothelial cells. When a BBB-shuttle is conjugated to a cargo, the ratio BBB-shuttle:cargo can range from 1:1 to 400:1, depending on the cargo. However, there are cases where the modification of the cargo with one copy of the BBB-shuttle is not sufficient to promote its passage through the BBB. More copies can be introduced, but a mixture of ratios of BBB-shuttle:cargo conjugates may be obtained. In those cases, it may be interesting to use multivalent BBB-shuttles, where more than one copy of the shuttle is attached to a core, which is linked to the cargo at one position. In this regard, branched dimerisation of a known BBB-shuttle was explored to enhance BBB permeability of model proteins. The results obtained with THRre peptide as the BBB-shuttle suggest that the mild improvement in permeability may not compensate the increased synthetic effort that these constructs represent. Moreover, chlorotoxin (CTX), a disulphide-rich peptide found in the venom of a scorpion, is reported to be able to enter the brain and bind specifically to tumour tissue. However, CTX is a relatively large peptide (36 amino acids) to be used as a BBB-shuttle, where we may need to scale it up or modify it. In this regard, we designed minimised versions of CTX (MiniCTXs) and evaluated their BBB properties, as well as their toxicity and stability. The results from these experiments produced two peptides as good BBB-shuttles, with similar stability, cellular uptake and BBB permeability than the best BBB-shuttles.
Book Synopsis Biological Nanostructures and Applications of Nanostructures in Biology by : Michael A. Stroscio
Download or read book Biological Nanostructures and Applications of Nanostructures in Biology written by Michael A. Stroscio and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological Nanostructures and Applications of Nanostructures in Biology: Electrical, Mechanical, and Optical Properties contains reviews and discussions of contemporary and relevant topics dealing with the interface between the science and technology of nanostructures and the science of biology. Moreover, this book supplements these past groundbreaking discoveries with discussions of promising new avenues of research that reveal the enormous potential of emerging approaches in nanobiotechnology. The topics include: - Biomedical applications of semiconductor quantum dots, - Integrating and tagging biological structures with nanoscale quantum dots, - Applications of carbon nanotubes in bioengineering, - Nanophysical properties of living cells, - Bridging natural nanotubes with fabricated nanotubes, - Bioinspired approaches to building nanoscale devices and systems, - Hairpin formation in polynucleotides. This state-of-the-art survey of key developments in nanotechnology - as they apply to bioengineering and biology - is essential reading for all academics, biomedical engineers, medical physicists, and industry professionals wishing to take advantage of the latest developments and highly-promising discoveries in nanoscience underlying applications in bioengineering and biology.
Book Synopsis Physical Properties Of Carbon Nanotubes by : G Dresselhaus
Download or read book Physical Properties Of Carbon Nanotubes written by G Dresselhaus and published by World Scientific. This book was released on 1998-07-22 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is an introductory textbook for graduate students and researchers from various fields of science who wish to learn about carbon nanotubes. The field is still at an early stage, and progress continues at a rapid rate. This book focuses on the basic principles behind the physical properties and gives the background necessary to understand the recent developments. Some useful computational source codes which generate coordinates for carbon nanotubes are also included in the appendix.
Book Synopsis Bacteriophages by : Martha R. J. Clokie
Download or read book Bacteriophages written by Martha R. J. Clokie and published by Humana. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ranging from the evolution of pathogenicity to oceanic carbon cycling, the many and varied roles that bacteriophages play in microbial ecology and evolution have inspired increased interest within the scientific community. Bacteriophages: Methods and Protocols pulls together the vast body of knowledge and expertise from top international bacteriophage researchers to provide both classical and state-of-the-art molecular techniques. With its well-organized modular design, Volume 2: Molecular and Applied Aspects examines a multitude of topics, including the bacteriophage genomics, metagenomics, transcriptomics, and proteomics, along with applied bacteriophage biology. Written in the highly successful Methods in Molecular BiologyTM series format, chapters consist of brief introductions to the subject, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and a Notes section which details tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Bacteriophages: Methods and Protocols is a valuable reference for experienced bacteriophage researchers as well as an easily accessible introduction for newcomers to the subject.
Download or read book Phage Display written by Carlos F. Barbas and published by CSHL Press. This book was released on 2001 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phage-display technology has begun to make critical contributions to the study of molecular recognition. DNA sequences are cloned into phage, which then present on their surface the proteins encoded by the DNA. Individual phage are rescued through interaction of the displayed protein with a ligand, and the specific phage is amplified by infection of bacteria. Phage-display technology is powerful but challenging and the aim of this manual is to provide comprehensive instruction in its theoretical and applied so that any scientist with even modest molecular biology experience can effectively employ it. The manual reflects nearly a decade of experience with students of greatly varying technical expertise andexperience who attended a course on the technology at Cold Spring Harbor Laboratory. Phage-display technology is growing in importance and power. This manual is an unrivalled source of expertise in its execution and application.
Book Synopsis The Combinatorial Index by : Barry A. Bunin
Download or read book The Combinatorial Index written by Barry A. Bunin and published by Elsevier. This book was released on 1998-04-15 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the explosion of combinatorial solid-phase methods, access to information has become one of the main barriers facing a synthetic chemist who is contemplating a combinatorial approach to a medicinal chemistry problem. The Combinatorial Index is an answer to that problem. This compendium of methods from the primary literature provides quick and convenient access to reliable synthetic transformations as well as information on linkers and analytical methods. Each synthetic procedure is preceded by a section entitled"Points of Interest,"which highlights the strengths and weaknesses of the various studies. The index also covers the use of solution-based synthesis for the generation of molecular diversity. Organized for rapid retrieval of published information on classes of synthetic transformations, linkers, and analytical methods Serves as a laboratory manual for bench chemists Includes a chapter on linkers to assist in choice of linking strategy Discusses strengths and limitations of the various methods Contains a structural index showing functional group transformations in solid-phase synthesis
Book Synopsis The Supramolecular Chemistry of Organic-Inorganic Hybrid Materials by : Knut Rurack
Download or read book The Supramolecular Chemistry of Organic-Inorganic Hybrid Materials written by Knut Rurack and published by John Wiley & Sons. This book was released on 2010-04-07 with total page 800 pages. Available in PDF, EPUB and Kindle. Book excerpt: The combination of supramolecular chemistry, inorganic solids, and nanotechnology has already led to significant advances in many areas such as sensing, controlled motion, and delivery. By making possible an unprecedented tunability of the properties of nanomaterials, these techniques open up whole new areas of application for future supramolecular concepts. The Supramolecular Chemistry of Organic–Inorganic Hybrid Materials gathers current knowledge on the subject and provides an overview of the present state and upcoming challenges in this rapidly growing, highly cross- or interdisciplinary research field. The book details how these designed materials can improve existing materials or generate novel functional features such as chemical amplification, cooperative binding and signal enhancement that are difficult or not at all achievable by classical organic supramolecular chemistry. It also discusses issues related to nanofabrication or nanotechnology such as the directed and controlled assembly or disassembly, biomimetic functions and strategies, and the gating and switching of surface functions or morphology.
