Academic literature on the topic 'Medical molecular engineering of nucleic acids and proteins'
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Journal articles on the topic "Medical molecular engineering of nucleic acids and proteins"
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Kim, Jinmyeong, Seungwoo Noh, Jeong Ah Park, Sang-Chan Park, Seong Jun Park, Jin-Ho Lee, Jae-Hyuk Ahn, and Taek Lee. "Recent Advances in Aptasensor for Cytokine Detection: A Review." Sensors 21, no. 24 (December 20, 2021): 8491. http://dx.doi.org/10.3390/s21248491.
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Cytokines are proteins secreted by immune cells. They promote cell signal transduction and are involved in cell replication, death, and recovery. Cytokines are immune modulators, but their excessive secretion causes uncontrolled inflammation that attacks normal cells. Considering the properties of cytokines, monitoring the secretion of cytokines in vivo is of great value for medical and biological research. In this review, we offer a report on recent studies for cytokine detection, especially studies on aptasensors using aptamers. Aptamers are single strand nucleic acids that form a stable three-dimensional structure and have been receiving attention due to various characteristics such as simple production methods, low molecular weight, and ease of modification while performing a physiological role similar to antibodies.
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Zhou, Qun. "Site-Specific Antibody Conjugation with Payloads beyond Cytotoxins." Molecules 28, no. 3 (January 17, 2023): 917. http://dx.doi.org/10.3390/molecules28030917.
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As antibody–drug conjugates have become a very important modality for cancer therapy, many site-specific conjugation approaches have been developed for generating homogenous molecules. The selective antibody coupling is achieved through antibody engineering by introducing specific amino acid or unnatural amino acid residues, peptides, and glycans. In addition to the use of synthetic cytotoxins, these novel methods have been applied for the conjugation of other payloads, including non-cytotoxic compounds, proteins/peptides, glycans, lipids, and nucleic acids. The non-cytotoxic compounds include polyethylene glycol, antibiotics, protein degraders (PROTAC and LYTAC), immunomodulating agents, enzyme inhibitors and protein ligands. Different small proteins or peptides have been selectively conjugated through unnatural amino acid using click chemistry, engineered C-terminal formylglycine for oxime or click chemistry, or specific ligation or transpeptidation with or without enzymes. Although the antibody protamine peptide fusions have been extensively used for siRNA coupling during early studies, direct conjugations through engineered cysteine or lysine residues have been demonstrated later. These site-specific antibody conjugates containing these payloads other than cytotoxic compounds can be used in proof-of-concept studies and in developing new therapeutics for unmet medical needs.
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Nazir, Gowhar, and Josee Amin. "Molecular tools for the diagnosis of periodontitis." International Journal of Dentistry Research 6, no. 3 (December 30, 2021): 81–88. http://dx.doi.org/10.31254/dentistry.2021.6304.
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Periodontitis is a multifactorial chronic inflammatory disease associated with dysbiotic biofilms and aberrant host inflammatory response. It is characterized by destruction of the tissues that support the teeth. Periodontitis is the major cause of tooth loss in adults significantly affecting the quality of life and is associated with many chronic non communicable diseases by contributing to systemic inflammatory burden. Early and accurate diagnosis is the key to the successful management of periodontitis as the entire treatment plan, prognosis, and maintenance directly depend on the quality of periodontal diagnosis. Traditionally the diagnosis of Periodontitis is based on recording medical and dental history, periodontal examination and radiographic findings. The current periodontal diagnostic process reveals only historical tissue destruction and does not provide any information regarding current disease activity, future progression or for monitoring response to therapy. For these reasons, new molecular diagnostic aids are being developed that allow an early detection of disease, determine the presence of current disease activity, predict sites at risk for future breakdown and monitor the response to periodontal therapy. Advanced molecular diagnostic techniques are a class of diagnostic tests that are used to detect and measure nucleic acids, proteins or metabolites in clinical samples to identify risk factors, screen asymptomatic patients, provide more accurate diagnosis and guide the process of development of an ideal therapeutic intervention. This paper provides a review of the molecular diagnostic tools that have the potential to be utilized for diagnosis and management of periodontitis.
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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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Antropov, Denis N., and Grigory A. Stepanov. "Molecular Mechanisms Underlying CRISPR/Cas-Based Assays for Nucleic Acid Detection." Current Issues in Molecular Biology 45, no. 1 (January 10, 2023): 649–62. http://dx.doi.org/10.3390/cimb45010043.
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Applied to investigate specific sequences, nucleic acid detection assays can help identify novel bacterial and viral infections. Most up-to-date systems combine isothermal amplification with Cas-mediated detection. They surpass standard PCR methods in detection time and sensitivity, which is crucial for rapid diagnostics. The first part of this review covers the variety of isothermal amplification methods and describes their reaction mechanisms. Isothermal amplification enables fast multiplication of a target nucleic acid sequence without expensive laboratory equipment. However, researchers aim for more reliable results, which cannot be achieved solely by amplification because it is also a source of non-specific products. This motivated the development of Cas-based assays that use Cas9, Cas12, or Cas13 proteins to detect nucleic acids and their fragments in biological specimens with high specificity. Isothermal amplification yields a high enough concentration of target nucleic acids for the specific signal to be detected via Cas protein activity. The second part of the review discusses combinations of different Cas-mediated reactions and isothermal amplification methods and presents signal detection techniques adopted in each assay. Understanding the features of Cas-based assays could inform the choice of an optimal protocol to detect different nucleic acids.
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Palermo, Giovanna, Kandammathe Valiyaveedu Sreekanth, Nicolò Maccaferri, Giuseppe Emanuele Lio, Giuseppe Nicoletta, Francesco De Angelis, Michael Hinczewski, and Giuseppe Strangi. "Hyperbolic dispersion metasurfaces for molecular biosensing." Nanophotonics 10, no. 1 (October 7, 2020): 295–314. http://dx.doi.org/10.1515/nanoph-2020-0466.
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AbstractSensor technology has become increasingly crucial in medical research and clinical diagnostics to directly detect small numbers of low-molecular-weight biomolecules relevant for lethal diseases. In recent years, various technologies have been developed, a number of them becoming core label-free technologies for detection of cancer biomarkers and viruses. However, to radically improve early disease diagnostics, tracking of disease progression and evaluation of treatments, today’s biosensing techniques still require a radical innovation to deliver high sensitivity, specificity, diffusion-limited transport, and accuracy for both nucleic acids and proteins. In this review, we discuss both scientific and technological aspects of hyperbolic dispersion metasurfaces for molecular biosensing. Optical metasurfaces have offered the tantalizing opportunity to engineer wavefronts while its intrinsic nanoscale patterns promote tremendous molecular interactions and selective binding. Hyperbolic dispersion metasurfaces support high-k modes that proved to be extremely sensitive to minute concentrations of ultralow-molecular-weight proteins and nucleic acids.
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Mojica, Wilfrido D., Ayesha Arshad, Sanjay Sharma, and Stephen P. Brooks. "Manual Exfoliation Plus Immunomagnetic Bead Separation as an Initial Step Toward Translational Research." Archives of Pathology & Laboratory Medicine 130, no. 1 (January 1, 2006): 74–79. http://dx.doi.org/10.5858/2006-130-74-mepibs.
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Abstract Context.—The development of biotechnologic platforms capable of high throughput analysis has ushered in a promising new era of translational medicine. However, most studies to date are based on in vitro cell lines or substitute models for human disease. Although these model systems have proven insightful, it is readily becoming apparent that human clinical tissue must be studied in order to fully understand all the nuances of human disease. Studies that are based on human tissue, however, are limited by qualitative and quantitative issues, factors often precluding their use in high throughput studies. Objective.—To develop a simple and rapid tissue procurement protocol for use in obtaining a homogeneous epithelial cell population from clinical tissue and the recovery of nucleic acids and proteins of high quality and quantity. Also, to determine if the technique preserves tissue, thereby allowing morphologic correlation with molecular findings. Design.—Performance of manual exfoliation to procure cells from clinical resection specimens and use of immunomagnetic beads embedded with the antibody ber-Ep4 for the positive enrichment of a homogeneous epithelial cell population. Nucleic acids and proteins are then separated using a phenol plus guanidine thiocyante solution. Nucleic acids and proteins are quantitated and qualitatively analyzed using standard laboratory techniques. Results.—Nucleic acids and proteins of high quality and quantity were recovered following manual exfoliation and immunomagnetic bead separation. Tissue architecture was not destroyed, thus permitting histologic and molecular correlation. Conclusions.—A simple and reproducible protocol is presented that may enable the molecular profiling of clinically resected tissue. Although the technique is currently limited to certain tissue and tumor types, further research will broaden its overall application.
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Wiebe, Leonard I. "Applications of nucleoside-based molecular probes for the in vivo assessment of tumour biochemistry using positron emission tomography (PET)." Brazilian Archives of Biology and Technology 50, no. 3 (May 2007): 445–59. http://dx.doi.org/10.1590/s1516-89132007000300011.
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Positron emission tomography (PET) is a non-invasive nuclear imaging technique. In PET, radiolabelled molecules decay by positron emission. The gamma rays resulting from positron annihilation are detected in coincidence and mapped to produce three dimensional images of radiotracer distribution in the body. Molecular imaging with PET refers to the use of positron-emitting biomolecules that are highly specific substrates for target enzymes, transport proteins or receptor proteins. Molecular imaging with PET produces spatial and temporal maps of the target-related processes. Molecular imaging is an important analytical tool in diagnostic medical imaging, therapy monitoring and the development of new drugs. Molecular imaging has its roots in molecular biology. Originally, molecular biology meant the biology of gene expression, but now molecular biology broadly encompasses the macromolecular biology and biochemistry of proteins, complex carbohydrates and nucleic acids. To date, molecular imaging has focused primarily on proteins, with emphasis on monoclonal antibodies and their derivative forms, small-molecule enzyme substrates and components of cell membranes, including transporters and transmembrane signalling elements. This overview provides an introduction to nucleosides, nucleotides and nucleic acids in the context of molecular imaging.
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Ye, Dekai, Xiaolei Zuo, and Chunhai Fan. "DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development." Annual Review of Analytical Chemistry 11, no. 1 (June 12, 2018): 171–95. http://dx.doi.org/10.1146/annurev-anchem-061417-010007.
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Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.
Dissertations / Theses on the topic "Medical molecular engineering of nucleic acids and proteins"
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Goel, Vritti R. "A Proposal to Test the Effects of Factor ECAT1 on Pluripotency, from Reprogramming to Differentiation of Human Somatic Cells." Scholarship @ Claremont, 2012. http://scholarship.claremont.edu/cmc_theses/470.
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The field of stem cell research has been growing more because of the interest in using stem cells to cure diseases and heal injuries. Human embryonic stem cells, because of the controversy surrounding them—and subsequently the difficulties in acquiring samples of the existing aging cell lines—can only be used in limited capacities. While the development of induced pluripotent stem cells in the last decade has allowed the field to progress closer to medical treatments, the low efficiency of reprogramming a somatic cell to a pluripotent state, and the vast molecular and genomic differences between human embryonic stem cells and human induced pluripotent stem cells is still an issue. Therefore, the goal is to discover methods, chemicals, and factors that can reduce these differences and increase the efficiency of inducing pluripotency.
This proposal aims to look at the effects of the protein ECAT1 in inducing pluripotency in human somatic cells. Little is known about ECAT1, otherwise known as Embryonic Stem Cell-Associated Transcript 1, beyond its presence in human embryonic stem cells and oocytes and its absence in differentiated cells. While originally considered by scientists during the development of the reprogramming technique, ECAT1's effects have not been tested in humans. Therefore, a series of experiments will be performed in which ECAT1 will be used in conjunction with OSKM to induce pluripotency in adult human dermal fibroblasts, which will then be differentiated into spinal motor neurons. The three stages of this proposal--inducing pluripotency, comparing pluripotencies in the reprogrammed cells and embryonic stem cells, and differentiating the stem cells--should answer questions about ECAT1 and the reprogramming process. It is predicted that ECAT1 should reduce the genomic and molecular differences between embryonic stem cells and induced pluripotent stem cells. ECAT1's presence should also increase the efficiency of reprogramming as well as successful differentiation to other cell types.
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Throm, Quinlan Angela M. "Mechanical Activation of Valvular Interstitial Cell Phenotype: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/640.
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During heart valve remodeling, and in many disease states, valvular interstitial cells (VICs) shift to an activated myofibroblast phenotype which is characterized by enhanced synthetic and contractile activity. Pronounced alpha smooth muscle actin (αSMA)-containing stress fibers, the hallmark of activated myofibroblasts, are also observed when VICs are placed under tension due to altered mechanical loading in vivo or during in vitro culture on stiff substrates or under high mechanical loads and in the presence of transforming growth factor-beta1 (TGF-β1). The work presented herein describes three distinct model systems for application of controlled mechanical environment to VICs cultured in vitro. The first system uses polyacrylamide (PA) gels of defined stiffness to evaluate the response of VICs over a large range of stiffness levels and TGF-β1 concentration. The second system controls the boundary stiffness of cell-populated gels using springs of defined stiffness. The third system cyclically stretches soft or stiff two-dimensional (2D) gels while cells are cultured on the gel surface as it is deformed. Through the use of these model systems, we have found that the level of 2D stiffness required to maintain the quiescent VIC phenotype is potentially too low for a material to both act as matrix to support cell growth in the non-activated state and also to withstand the mechanical loading that occurs during the cardiac cycle. Further, we found that increasing the boundary stiffness on a three-dimensional (3D) cell populated collagen gel resulted in increased cellular contractile forces, αSMA expression, and collagen gel (material) stiffness. Finally, VIC morphology is significantly altered in response to stiffness and stretch. On soft 2D substrates, VICs cultured statically exhibit a small rounded morphology, significantly smaller than on stiff substrates. Following equibiaxial cyclic stretch, VICs spread to the extent of cells cultured on stiff substrates, but did not reorient in response to uniaxial stretch to the extent of cells stretched on stiff substrates. These studies provide critical information for characterizing how VICs respond to mechanical stimuli. Characterization of these responses is important for the development of tissue engineered heart valves and contributes to the understanding of the role of mechanical cues on valve pathology and disease onset and progression. While this work is focused on valvular interstitial cells, the culture conditions and methods for applying mechanical stimulation could be applied to numerous other adherent cell types providing information on the response to mechanical stimuli relevant for optimizing cell culture, engineered tissues or fundamental research of disease states.
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Haraszti, Reka A. "Engineered Exosomes for Delivery of Therapeutic siRNAs to Neurons." eScholarship@UMMS, 2018. https://escholarship.umassmed.edu/gsbs_diss/971.
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Extracellular vesicles (EVs), exosomes and microvesicles, transfer endogenous RNAs between neurons over short and long distances. We have explored EVs for siRNA delivery to brain. (1) We optimized siRNA chemical modifications and siRNA conjugation to lipids for EV-mediated delivery. (2) We developed a GMP-compatible, scalable method to manufacture active EVs in bulk. (3) We characterized lipid and protein content of EVs in detail. (4) We established how protein and lipid composition relates to siRNA delivering activity of EVs, and we reverse engineered natural exosomes (small EVs) into artificial exosomes based on these data.
We established that cholesterol-conjugated siRNAs passively associate to EV membrane and can be productively delivered to target neurons. We extensively characterized this loading process and optimized exosome-to-siRNA ratios for loading. We found that chemical stabilization of 5'-phosphate with 5'-E-vinylphosphonate and chemical stabilization of all nucleotides with 2'-O-methyl and 2'-fluoro increases the accumulation of siRNA and the level of mRNA silencing in target cells. Therefore, we recommend using fully modified siRNAs for lipid-mediated loading to EVs. Later, we identified that α-tocopherol-succinate (vitamin E) conjugation to siRNA increases productive loading to exosomes compared to originally described cholesterol.
Low EV yield has been a rate-limiting factor in preclinical development of the EV technology. We developed a scalable EV manufacturing process based on three-dimensional, xenofree culture of mesenchymal stem cells and concentration of EVs from conditioned media using tangential flow filtration. This process yields exosomes more efficient at siRNA delivery than exosomes isolated via differential ultracentrifugation from two-dimensional cultures of the same cells.
In-depth characterization of EV content is required for quality control of EV preparations as well as understanding composition–activity relationship of EVs. We have generated mass-spectrometry data on more than 3000 proteins and more than 2000 lipid species detected in exosomes (small EVs) and microvesicles (large EVs) isolated from five different producer cells: two cell lines (U87 and Huh7) and three mesenchymal stem cell types (derived from bone marrow, adipose tissue and umbilical cord Wharton’s jelly). These data represent an indispensable resource for the community. Furthermore, relating composition change to activity change of EVs isolated from cells upon serum deprivation allowed us to identify essential components of siRNA-delivering exosomes. Based on these data we reverse engineered natural exosomes into artificial exosomes consisting of dioleoyl-phosphatidylcholine, cholesterol, dilysocardiolipin, Rab7, AHSG and Desmoplakin. These artificial exosomes reproduced efficient siRNA delivery of natural exosomes both in vitro and in vivo. Artificial exosomes may facilitate manufacturing, quality control and cargo loading challenge that currently impede the therapeutic EV field.
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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 "Medical 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.
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Chaiken, Irwin. Macromolecular Biorecognition: Principles And Methods. Humana, 2011.
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Macromolecular Biorecognition: Principles and Methods. Humana Press, 2011.
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Macromolecular biorecognition: Principles and methods. Clifton, N.J: Humana Press, 1987.
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Chaiken, Irwin, Emilia Chiancone, and Angelo Fontana. Macromolecular Biorecognition: Principles and Methods (Experimental Biology and Medicine). Humana Press, 1988.
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Chaiken, Irwin, Emilia Chiancone, Angelo Fontana, and Paolo Neri. Macromolecular Biorecognition: Principles and Methods. Humana Press, 2012.
Find full textBook chapters on the topic "Medical 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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"Biological Products: Molecular Structure and Function." In The Law and Regulation of Medicines and Medical Devices, edited by Tony Fox, 130–57. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780192847546.003.0005.
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This chapter analyses biological products that are defined by the method of manufacture and distinguished by a production process that separates biological drug products from orthodox, ‘small molecule’ drugs. It explains how biological products are synthesised by a variety of living cells, such as bacteria, fungi, or mammalian cells. It also refers to the types of modern biological therapies that range among proteins, nucleic acids, and whole cells. The chapter discusses monoclonal antibodies, which is considered the largest class of biological products in clinical use and are designed to attach to diseased cells, like cancer cells, that are expressing abnormal proteins on their surface. It describes proteins as chains of amino acids linked to each other chemically by peptide bonds, hence the alternative term ‘polypeptides’.
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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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"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.
Conference papers on the topic "Medical 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.
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Daly, John, and Mark Davies. "A Quantitative Free Convection DNA Amplifier." In ASME/JSME 2007 Thermal Engineering Heat Transfer Summer Conference collocated with the ASME 2007 InterPACK Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/ht2007-32381.
Full textAbstract:
The Polymerase Chain Reaction (PCR) has been used extensively to amplify targeted nucleic acids for many applications in molecular biology and, increasingly, in medical diagnostics. Outlined in this paper is a PCR device which takes account of the advantages offered by free convection. The design is, in it fundamental format a time-wise isothermal well-based thermocycler. A temperature gradient induced across the well causes convection forces to circulate the sample through the required temperatures necessary for amplification. Quantitative amplification is demonstrated with real time measurements of SYBR Green I fluorescence within the free convective DNA amplifier. Amplification of an 86-bp fragment of the pGEM®-T vector (Promega) is performed in a 25μl volume in eight minutes. A 10-fold dilution series and methods for calculating effective cycle times are presented. Also detailed within this paper are PIV and thermal imaging results of the free convection cavity. This device presents an opportunity for the development of a practical and inexpensive gene-expression measurement system.