Academic literature on the topic 'Industrial Molecular Engineering of Nucleic Acids and Proteins'
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Journal articles on the topic "Industrial Molecular Engineering of Nucleic Acids and Proteins"
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Gupta, Ms Veenu. "Microbial Production of Biopolymers and Polymer Precursors." International Journal for Research in Applied Science and Engineering Technology 10, no. 7 (July 31, 2022): 47–54. http://dx.doi.org/10.22214/ijraset.2022.45052.
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Abstract: Living organisms, namely, prokaryotes and eukaryotes, are able to synthesize a variety of polymers, such as nucleic acids, proteins, and other polyamides, polysaccharides, polyesters, polythioesters, polyanhydrides, polyisoprenoids, and lignin. Microorganisms provide a source of biopolymers and biopolysaccharides from renewable sources. Bacteria are capable of yielding biopolymers with properties comparable to plastics derived from petrochemicals, though more expensive. They have the additional advantage of being biodegradable. A wide range of microbial polysaccharides have been studied, and structure/function relationships for a number of these macromolecules have been determined. These biopolymers accomplish different essential and beneficial functions for the organisms. Among the biopolymers produced, many are used for various industrial applications. Currently, the biotechnological production of polymers has been mostly achieved by fermentation of microorganisms in stirred bioreactors. The biopolymers can be obtained as extracellular or intracellular compounds. Alternatively, biopolymers can also be produced by in vitro enzymatic processes. However, the largest amounts of biopolymers are still extracted from plant and animal sources. Biopolymers exhibit fascinating properties and play a major role in the food processing industry, e.g., modifying texture and other properties. Among the various biopolymers, polysaccharides and bioplastics are the most important in the food industry. This chapter will discuss the sources of polymers, their biosynthesis by different organisms, and their application in different fields. A huge variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are naturally produced by microorganisms. These range from viscous solutions to plastics and their physical properties are dependent on the composition and molecular weight of the polymer. The genetic manipulation of microorganisms opens up an enormous potential for the biotechnological production of biopolymers with tailored properties suitable for highvalue medical application such as tissue engineering and drug delivery.
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Nishimura, Tomoki, and Kazunari Akiyoshi. "Artificial Molecular Chaperone Systems for Proteins, Nucleic Acids, and Synthetic Molecules." Bioconjugate Chemistry 31, no. 5 (April 26, 2020): 1259–67. http://dx.doi.org/10.1021/acs.bioconjchem.0c00133.
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Feng, Wei, Ashley M. Newbigging, Jeffrey Tao, Yiren Cao, Hanyong Peng, Connie Le, Jinjun Wu, et al. "CRISPR technology incorporating amplification strategies: molecular assays for nucleic acids, proteins, and small molecules." Chemical Science 12, no. 13 (2021): 4683–98. http://dx.doi.org/10.1039/d0sc06973f.
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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) protein systems revolutionize genome engineering and advance analytical chemistry and diagnostic technology.
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Banerjee, Ashis Gopal, Sagar Chowdhury, Wolfgang Losert, and Satyandra K. Gupta. "Survey on indirect optical manipulation of cells, nucleic acids, and motor proteins." Journal of Biomedical Optics 16, no. 5 (2011): 051302. http://dx.doi.org/10.1117/1.3579200.
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Li, Hanying, Thomas H. LaBean, and Kam W. Leong. "Nucleic acid-based nanoengineering: novel structures for biomedical applications." Interface Focus 1, no. 5 (June 28, 2011): 702–24. http://dx.doi.org/10.1098/rsfs.2011.0040.
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Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.
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Digel, I., P. Kayser, and G. M. Artmann. "Molecular Processes in Biological Thermosensation." Journal of Biophysics 2008 (May 12, 2008): 1–9. http://dx.doi.org/10.1155/2008/602870.
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Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins) can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”.
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Bogomolova, E. G., P. M. Kopeykin, and A. A. Tagaev. "Genetic engineering approaches to the development of modern therapeutics." Medical academic journal 20, no. 3 (September 15, 2020): 49–60. http://dx.doi.org/10.17816/maj34092.
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The classic approach to production of protein-based therapeutics is their isolation from natural sources. This approach was associated with a number of difficulties, such as collecting the primary material from natural sources, isolating and purifying the protein, and its standardizing. With the development of recombinant DNA technology, itbecame possible to obtain large quantities of protein preparations lacking any contaminations. Human insulin produced using recombinant DNA technology is the first commercial therapeutic obtained by this way. Due to the rapid development of genetic engineering technologies, a large number of proteins have been obtained inEscherichia colicells. In recent years, the approach for the development of drugs based on DNA molecules containing genes encoding therapeutic proteins has been developing more actively. Today, many scientists believe in the prospects of application of DNA vaccines. The ease of production, stability, the ability to mimic natural infections and elicit appropriate immune responses make this vaccine platform extremely attractive. Delivery and targeting of immunologically relevant cells are major tasks for maximizing the immunogenicity of DNA vaccines. Several different approaches that are currently being used to achieve this goal are discussed in this review. Pharmaceuticals based on nucleic acids have a number of undeniable advantages. The main options for prophylactic RNA vaccines, the methods used to deliver RNA to the cell, and methods for increasing the effectiveness of RNA vaccines are discussed. Usage of therapeutic drugs based on protein molecules and low molecular weight compounds is complicated by the fact that they cannot be targeted at a specific gene or its protein product, responsible for the occurrence of the disease. Action of nucleic acids can be directly directed to a particular DNA region in order to edit its nucleotide sequence. This method allows to correct a genetic defect, eliminating the cause of the disease. The principles of gene therapy and the successes achieved in this area are discussed. This review summarizes current achievements in the development of drugs based on recombinant proteins and nucleic acids.
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Privalov, Peter L. "Thermodynamic problems in structural molecular biology." Pure and Applied Chemistry 79, no. 8 (January 1, 2007): 1445–62. http://dx.doi.org/10.1351/pac200779081445.
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The most essential feature of living biological systems is their high degree of structural organization. The key role is played by two linear heteropolymers, the proteins and nucleic acids. Under environmental conditions close to physiological, these biopolymers are folded into unique native conformations, genetically determined by the arrangement of their standard building blocks. In their native conformation, biological macromolecules recognize their partners and associate with them, forming specific, higher-order complexes, the "molecular machines". Folding of biopolymers into their native conformation and their association with partners is in principle a reversible, thermodynamically driven process. Investigation of the thermodynamics of these basic biological processes has prime importance for understanding the mechanisms of forming these supra-macromolecular constructions and their functioning.
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Crnković, Ana, Marija Srnko, and Gregor Anderluh. "Biological Nanopores: Engineering on Demand." Life 11, no. 1 (January 5, 2021): 27. http://dx.doi.org/10.3390/life11010027.
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Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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Zhang, Zhenjiang, Jenna A. Dombroski, and Michael R. King. "Engineering of Exosomes to Target Cancer Metastasis." Cellular and Molecular Bioengineering 13, no. 1 (December 23, 2019): 1–16. http://dx.doi.org/10.1007/s12195-019-00607-x.
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AbstractAs a nanoscale subset of extracellular vehicles, exosomes represent a new pathway of intercellular communication by delivering cargos such as proteins and nucleic acids to recipient cells. Importantly, it has been well documented that exosome-mediated delivery of such cargo is involved in many pathological processes such as tumor progression, cancer metastasis, and development of drug resistance. Innately biocompatible and possessing ideal structural properties, exosomes offer distinct advantages for drug delivery over artificial nanoscale drug carriers. In this review, we summarize recent progress in methods for engineering exosomes including isolation techniques and exogenous cargo encapsulation, with a focus on applications of engineered exosomes to target cancer metastasis.
Dissertations / Theses on the topic "Industrial Molecular Engineering of Nucleic Acids and Proteins"
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Becerril-Garcia, Hector Alejandro. "DNA-Templated Nanomaterials." Diss., CLICK HERE for online access, 2007. http://contentdm.lib.byu.edu/ETD/image/etd1823.pdf.
Full textBooks on the topic "Industrial Molecular Engineering of Nucleic Acids and Proteins"
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Ducruix, Arnaud, and Richard Giegé, eds. Crystallization of Nucleic Acids and Proteins. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199636792.001.0001.
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Crystallography is the major method of determining structures of biological macromolecules yet crystallization techniques are still regarded as difficult to perform. This new edition of Crystallization of Nucleic Acids and Proteins: A Practical Approach continues in the vein of the first edition by providing a detailed and rational guide to producing crystals of proteins and nucleic acids of sufficient quantity and quality for diffraction studies. It has been thoroughly updated to include all the major new techniques such as the uses of molecular biology in structural biology (maximizing expression systems, sequence modifications to enable crystallization, and the introduction of anomalous scatterers); diagnostic analysis of prenucleation and nucleation by spectroscopic methods; and the two- dimensional electron crystallography of soluble proteins on planar lipid films. As well as an introduction to crystallogenesis, the other topics covered are: Handling macromolecular solutions, experimental design, seeding, proceeding from solutions to crystals Crystallization in gels Crystallization of nucleic acid complexes and membrane proteins Soaking techniques Preliminary characterization of crystals in order to tell whether they are suitable for diffraction studies. As with all Practical Approach books the protocols have been written by experienced researchers and are tried an tested methods. The underlying theory is brought together with the laboratory protocols to provide researchers with the conceptual and methodological tools necessary to exploit these powerful techniques. Crystallization of Nucleic Acids and Proteins: A Practical Approach 2e will be an invaluable manual of practical crystallization methods to researchers in molecular biology, crystallography, protein engineering, and biological chemistry.
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PCR Cloning Protocols: From Molecular Cloning to Genetic Engineering (Methods in Molecular Biology). Humana Press, 1997.
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White, Bruce A. Pcr Cloning Protocols: From Molecular Cloning to Genetic Engineering (Methods in Molecular Biology). Humana Press, 1997.
Find full textBook chapters on the topic "Industrial Molecular Engineering of Nucleic Acids and Proteins"
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Berne, P. F., and S. Doublié. "Molecular Biology for Structural Biology." In Crystallization of Nucleic Acids and Proteins. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199636792.003.0007.
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The number of published 3D structures has increased exponentially in the last decade and the resulting mass of structural data has contributed significantly to the understanding of mechanisms underlying the biology of living cells. However, these mechanisms are so complex that structural biologists face still greater challenges, such as the study of higher-order functional complexes. As an example, we can mention the protein complexes that assemble around activated growth factor receptors to allow the transduction of extracellular signals through the membrane and inside the cell (1). Because of their diverse intrinsic properties, proteins exhibit variable difficulty for structural biology studies. Before the rise of recombinant expression methods, only a minority of protein structures were determined, representing mainly favourable cases: proteins of high abundance in their natural source which could be purified and crystallized, in contrast to rare proteins that were often refractory to crystallization. The advent of methods for recombinant protein overexpression was a breakthrough in this area. It was followed by an increasing number of publications describing the crystallization of proteins, not under their native form, but in modified versions after sequence engineering. First we will consider the classical use of molecular biology applied to optimize the expression system for a recombinant protein for structural biology, without modification of its sequence. In the second part, we will deal with molecular biology procedures aimed at engineering the properties of a protein through sequence modifications in order to make its crystallization possible. In the last part we will give an example where molecular biology can help solve a crystallographic problem, namely that of phase determination by introducing anomalous scatterers (e.g. selenium atoms) into the protein of interest. Whenever extraction of a protein from its natural source appears unsuitable for structural studies, molecular biology resources can be brought in, initially aiming at choosing and setting up an appropriate expression system. This initial approach could involve comparing various expression hosts and vectors and deciding if the protein is to be produced as a fusion to facilitate its purification.
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Misra, Gauri. "Microscopic Perspectives on Macromolecular Interactions: Proteins and Nucleic Acids." In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. Elsevier, 2018. http://dx.doi.org/10.1016/b978-0-12-409547-2.14318-5.
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Stura, E. A. "Seeding Techniques." In Crystallization of Nucleic Acids and Proteins. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199636792.003.0011.
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A seed provides a template for the assembly of molecules to form a crystal with the same characteristics as the crystal from which it originated. Seeding has often been used as a method of last resort, rather than a standard practice. Recently, these techniques have gained popularity, in particular, macroseeding, used to enlarge the size of crystals. Seeding has many more applications, and the use of seeding in crystallization can simplify the task of the crystallographer even when crystals can be obtained without it. We will explore the various seeding techniques, and their applications, in the growth of large single crystals and the methods by which we may attempt to obtain crystals that diffract to higher resolution. Crystallogenesis can be divided into two separate phases. The first being the screening of crystallization conditions to obtain the first crystals, the second consisting of the optimization of these conditions to improve crystal size and quality. Seeding can be used advantageously in both these situations. The first stage in crystallogenesis consists of the discovery of initial crystals, crystalline aggregates, or microcrystalline precipitate. This may result from a standardized screening method (1, 2), a systematic method (3), an incomplete factorial search (see Chapter 4 and refs 4 and 5), or by extensive screening of many conditions. This may be bypassed by starting with seeds from crystals of a related molecule that has been previously crystallized. Molecules that have been obtained by genetic or molecular engineering of a previously crystallized macromolecule fall in this category. This method is termed cross-seeding. It has been used to obtain crystals of pig aspartate aminotransferase starting with crystal from the chicken enzyme (6) and between native and complexed Fab molecules (7). Whatever the method used to obtain the initial crystals, seeding may provide a fast and effective way to facilitate the optimization of growth conditions without the uncertainty which is intrinsic in the process of spontaneous nucleation. The streak seeding technique can be used to carry out a search quickly and efficiently over a wide range of growth conditions.
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Rachamalla, Harikrishnareddy, Anubhab Mukherjee, and Manash K. Paul. "Nanotechnology Application and Intellectual Property Right Prospects of Mammalian Cell Culture." In Cell Culture [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99146.
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The significant challenges faced by modern-day medicine include designing a target-specific drug delivery system with a controlled release mechanism, having the potential to avoid opsonization and reduce bio-toxicity. Nanoparticles are materials with nanoscale dimensions and maybe natural and synthetic in origin. Engineered nano-sized materials are playing an indispensable role in the field of nanomedicine and nanobiotechnology. Besides, engineered nano-sized particles impart therapeutic applications with enhanced specificity because of their unique bespoke properties. Moreover, such application-customized nanoparticles offer an enormous possibility for their compatibility with different biological molecules like proteins, genetic materials, cell membranes, and organelles at the nano-bio frame. Besides, surface functionalization with targeting moieties such as small molecule ligands, monoclonal antibodies, aptamers, cell-penetrating peptides, and proteins facilitate nanoparticle-based specific tissue targeting. This review summarizes some of the advances in nanoparticle-based therapeutics and theranostics. A better understanding of idealistic preparation methods, physicochemical attributes, surface functionalization, biocompatibility can empower the potential translation of nanomaterials from the ‘bench-to-bedside’. In modern-day medicine, engineered nanoparticles have a wide range of demands ranging from bio-imaging, theranostics, tissue engineering, sensors, drug and nucleic acid delivery, and other pharmaceuticals applications. 2D and 3D mammalian cell-based assays are widely used to model diseases, screening of drugs, drug discovery, and toxicity analyses. Recent advances in cell culture technology and associated progress in nanotechnology have enabled researchers to study a wide variety of physiologically relevant questions. This chapter explores the properties of nanoparticles, different targeted delivery methods, biological analysis, and theranostics. Moreover, this chapter also emphasizes biosafety and bioethics associated with mammalian cell culture and discusses the significance of intellectual property rights from an industrial and academic perspective.
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"Molecular Biology Techniques." In Advances in Environmental Engineering and Green Technologies, 401–85. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-4312-2.ch012.
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The development of vast array of laboratory methods and their applications provided great leaps in the ability of the researchers to discover new features and functions of macro-molecules. Most of them represent procedures for measuring or visualizing ever-smaller quantities or tinier features of molecules, or part of molecules. Especially when applied in combination, these methods have led to enormous advances in understanding the structural features of proteins and nucleic acids. New techniques have been regularly introduced and the sensitivity of older techniques greatly improved upon. The originators of several of those breakthrough methods were awarded Nobel Prizes. Basic principles of some of most important techniques invented and applied in molecular biology research are described in this chapter.
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Sefika Feyza, Maden, Sezer Selin, and Acuner Saliha Ece. "Fundamentals of Molecular Docking and Comparative Analysis of Protein–Small-Molecule Docking Approaches." In Biomedical Engineering. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.105815.
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Proteins (e.g., enzymes, receptors, hormones, antibodies, transporter proteins, etc.) seldom act alone in the cell, and their functions rely on their interactions with various partners such as small molecules, other proteins, and/or nucleic acids. Molecular docking is a computational method developed to model these interactions at the molecular level by predicting the 3D structures of complexes. Predicting the binding site and pose of a protein with its partner through docking can help us to unveil protein structure-function relationship and aid drug design in numerous ways. In this chapter, we focus on the fundamentals of protein docking by describing docking methods including search algorithm, scoring, and assessment steps as well as illustrating recent successful applications in drug discovery. We especially address protein–small-molecule (drug) docking by comparatively analyzing available tools implementing different approaches such as ab initio, structure-based, ligand-based (pharmacophore-/shape-based), information-driven, and machine learning approaches.
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M. Skowron, Piotr, and Agnieszka Zylicz-Stachula. "DNA-FACE™ - An Escherichia coli-based DNA Amplification-Expression Technology for Automatic Assembly of Concatemeric ORFs and Proteins." In Escherichia coli [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.101640.
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DNA-FACE™ (DNA Fragment Amplification & Concatemeric Expressed Nucleic Acids and Proteins) is a universal biotechnological platform, developed as Escherichia coli (E. coli) system. It is based on the ordered, head-to-tail directional ligation of the amplified DNA fragments. The technology enables the construction of targeted biomolecules - genetically programmed, concatemeric DNA, RNA, and proteins, designed to fit a particular task. The constructed, “artificial” (never seen in Nature) tandem repeat macromolecules, with specialized functions, may contain up to 500 copies of monomeric units. The technology greatly exceeds the current capabilities of chemical gene synthesis. The vector-enzymatic DNA fragment amplification assembles the DNA segments, forming continuous Open Reading Frames (ORFs). The obtained ORFs are ready for high-level expression in E. coli without a need for subcloning. The presented method has potential applications in pharmaceutical industry and tissue engineering, including vaccines, biological drugs, drug delivery systems, mass-production of peptide-derived biomaterials, industrial and environmental processes. The technology has been patented worldwide and used successfully in the construction of anti-HBV vaccines, pro-regenerative biological drugs and, recently, the anti-SARS-CoV-2 vaccine. The anti-SARS-CoV-2 vaccine, developed using the DNA-FACE™ technology, is nontoxic and induces strong immunological response to recombinant human spike and nucleocapsid proteins, as shown in animal studies.
Conference papers on the topic "Industrial Molecular Engineering of Nucleic Acids and Proteins"
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Chirikjian, Gregory S. "Kinematics Meets Crystallography: The Concept of a Motion Space." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-34243.
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In this paper, it is shown how rigid-body kinematics can be used to assist in determining the atomic structure of proteins and nucleic acids when using x-ray crystallography, which is a powerful method for structure determination. The importance of determining molecular structures for understanding biological processes and for the design of new drugs is well known. Phasing is a necessary step in determining the three-dimensional structure of molecules from x-ray diffraction patterns. A computational approach called molecular replacement (MR) is a well-established method for phasing of x-ray diffraction patterns for crystals composed of biological macromolecules. In MR, a search is performed over positions and orientations of a known biomolecular structure within a model of the crystallographic asymmetric unit, or, equivalently, multiple symmetry-related molecules in the crystallographic unit cell. Unlike the discrete space groups known to crystallographers and the continuous rigid-body motions known to kinematicians, the set of motions over which molecular replacement searches are performed does not form a group. Rather, it is a coset space of the group of continuous rigid-body motions, SE(3), with respect to the crystallographic space group of the crystal, which is a discrete sub-group of SE(3). Properties of these ‘motion spaces’ (which are compact manifolds) are investigated here.