Journal articles on the topic 'Industrial Molecular Engineering of Nucleic Acids and Proteins'
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1
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.
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Macedo, Eugénia Almeida. "Solubility of amino acids, sugars, and proteins." Pure and Applied Chemistry 77, no. 3 (January 1, 2005): 559–68. http://dx.doi.org/10.1351/pac200577030559.
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The importance of biomolecules is well recognized nowadays, owing to their application in many industrial processes, particularly in the food, pharmaceutical, and cosmetic industries.Amino acids, carbohydrates, and proteins are the three types of biomolecules considered in this review. Solubilities of several amino acids and sugars have been measured in water and, more recently, in mixed solvents, both with or without salts. Experimental data on partition of proteins in aqueous two-phase systems (ATPSs), with polymers or salts, have also been reported in the literature. The experimental techniques used are briefly discussed. Regarding modeling, the complexity of these solutions is very high. Sugars form strong hydrogen bonds with one another and with water or other solvents like alcohols. Liquid solutions with amino acids or proteins present not only short-range interaction forces, but also long-range forces, owing to the appearance of charged species. The capabilities of different molecular models and group-contribution-based methods are shown.
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Varotsis, Constantinos, Marios Papageorgiou, Charalampos Tselios, Konstantinos A. Yiannakkos, Anastasia Adamou, and Antonis Nicolaides. "Bacterial Colonization on the Surface of Copper Sulfide Minerals Probed by Fourier Transform Infrared Micro-Spectroscopy." Crystals 10, no. 11 (November 5, 2020): 1002. http://dx.doi.org/10.3390/cryst10111002.
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Biofilm formation is a molecular assembly process occurring at interfaces, such as in bioleaching processes. The real time monitoring of the marker bands of amide I/amide II by FTIR microspectroscopy during Acidithiobacillus ferrooxidans colonization on chalcopyrite surfaces revealed the central role of lipids, proteins and nucleic acids in bacterial cell attachment to copper sulfide surfaces. The Raman and FTIR spectra of the interactions of Acidithiobacillus ferrooxidans with bornite are also reported.
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Pozharov, Vitaly P., and Tamara Minko. "Nanotechnology-Based RNA Vaccines: Fundamentals, Advantages and Challenges." Pharmaceutics 15, no. 1 (January 5, 2023): 194. http://dx.doi.org/10.3390/pharmaceutics15010194.
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Over the past decades, many drugs based on the use of nanotechnology and nucleic acids have been developed. However, until recently, most of them remained at the stage of pre-clinical development and testing and did not find their way to the clinic. In our opinion, the main reason for this situation lies in the enormous complexity of the development and industrial production of such formulations leading to their high cost. The development of nanotechnology-based drugs requires the participation of scientists from many and completely different specialties including Pharmaceutical Sciences, Medicine, Engineering, Drug Delivery, Chemistry, Molecular Biology, Physiology and so on. Nevertheless, emergence of coronavirus and new vaccines based on nanotechnology has shown the high efficiency of this approach. Effective development of vaccines based on the use of nucleic acids and nanomedicine requires an understanding of a wide range of principles including mechanisms of immune responses, nucleic acid functions, nanotechnology and vaccinations. In this regard, the purpose of the current review is to recall the basic principles of the work of the immune system, vaccination, nanotechnology and drug delivery in terms of the development and production of vaccines based on both nanotechnology and the use of nucleic acids.
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Benhal, Prateek, David Quashie, Yoontae Kim, and Jamel Ali. "Insulator Based Dielectrophoresis: Micro, Nano, and Molecular Scale Biological Applications." Sensors 20, no. 18 (September 7, 2020): 5095. http://dx.doi.org/10.3390/s20185095.
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Insulator based dielectrophoresis (iDEP) is becoming increasingly important in emerging biomolecular applications, including particle purification, fractionation, and separation. Compared to conventional electrode-based dielectrophoresis (eDEP) techniques, iDEP has been demonstrated to have a higher degree of selectivity of biological samples while also being less biologically intrusive. Over the past two decades, substantial technological advances have been made, enabling iDEP to be applied from micro, to nano and molecular scales. Soft particles, including cell organelles, viruses, proteins, and nucleic acids, have been manipulated using iDEP, enabling the exploration of subnanometer biological interactions. Recent investigations using this technique have demonstrated a wide range of applications, including biomarker screening, protein folding analysis, and molecular sensing. Here, we review current state-of-art research on iDEP systems and highlight potential future work.
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Jaekel, Stegemann, and Saccà. "Manipulating Enzymes Properties with DNA Nanostructures." Molecules 24, no. 20 (October 14, 2019): 3694. http://dx.doi.org/10.3390/molecules24203694.
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Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology—and indeed its initial motivation—is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
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Kohli, Isha, Naveen C. Joshi, Swati Mohapatra, and Ajit Varma. "Extremophile – An Adaptive Strategy for Extreme Conditions and Applications." Current Genomics 21, no. 2 (May 20, 2020): 96–110. http://dx.doi.org/10.2174/1389202921666200401105908.
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The concurrence of microorganisms in niches that are hostile like extremes of temperature, pH, salt concentration and high pressure depends upon novel molecular mechanisms to enhance the stability of their proteins, nucleic acids, lipids and cell membranes. The structural, physiological and genomic features of extremophiles that make them capable of withstanding extremely selective environmental conditions are particularly fascinating. Highly stable enzymes exhibiting several industrial and biotechnological properties are being isolated and purified from these extremophiles. Successful gene cloning of the purified extremozymes in the mesophilic hosts has already been done. Various extremozymes such as amylase, lipase, xylanase, cellulase and protease from thermophiles, halothermophiles and psychrophiles are of industrial interests due to their enhanced stability at forbidding conditions. In this review, we made an attempt to point out the unique features of extremophiles, particularly thermophiles and psychrophiles, at the structural, genomic and proteomic levels, which allow for functionality at harsh conditions focusing on the temperature tolerance by them.
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Campbell, Jack, Georgia Kastania, and Dmitry Volodkin. "Encapsulation of Low-Molecular-Weight Drugs into Polymer Multilayer Capsules Templated on Vaterite CaCO3 Crystals." Micromachines 11, no. 8 (July 24, 2020): 717. http://dx.doi.org/10.3390/mi11080717.
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Polyelectrolyte multilayer capsules (PEMCs) templated onto biocompatible and easily degradable vaterite CaCO3 crystals via the layer-by-layer (LbL) polymer deposition process have served as multifunctional and tailor-made vehicles for advanced drug delivery. Since the last two decades, the PEMCs were utilized for effective encapsulation and controlled release of bioactive macromolecules (proteins, nucleic acids, etc.). However, their capacity to host low-molecular-weight (LMW) drugs (<1–2 kDa) has been demonstrated rather recently due to a limited retention ability of multilayers to small molecules. The safe and controlled delivery of LMW drugs plays a vital role for the treatment of cancers and other diseases, and, due to their tunable and inherent properties, PEMCs have shown to be good candidates for smart drug delivery. Herein, we summarize recent progress on the encapsulation of LMW drugs into PEMCs templated onto vaterite CaCO3 crystals. The drug loading and release mechanisms, advantages and limitations of the PEMCs as LMW drug carriers, as well as bio-applications of drug-laden capsules are discussed based upon the recent literature findings.
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Marwicka, Justyna, and Anna Zięba. "Antioxidants as a defence against reactive oxygen species." Aesthetic Cosmetology and Medicine 10, no. 6 (December 2021): 271–76. http://dx.doi.org/10.52336/acm.2021.10.6.02.
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Reactive oxygen species are formed as a natural product of metabolic processes occurring in the organism or under the influence of external factors. Under homeostasis, they play an important role as a cellular signaling device. During oxidative stress, when they are produced in excess, they can cause damages to proteins, lipids, carbohydrates or nucleic acids. Exposure of cells and extracellular structures to free radicals activate natural mechanisms to eliminate free radicals and their derivatives. The aim of the article was to present what antioxidants are, and how they protect cells against the free radicals. The protective system against the free radicals consists of antioxidant enzymes: superoxide dismutase, catalase, glutathione peroxidases, and reductase. Low-molecular antioxidants such as vitamin C, E, carotenoids, coenzyme Q10, flavonoids, glutathione and melatonin also play an important role.
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Poghossian, Arshak, and Michael J. Schöning. "Capacitive Field-Effect EIS Chemical Sensors and Biosensors: A Status Report." Sensors 20, no. 19 (October 2, 2020): 5639. http://dx.doi.org/10.3390/s20195639.
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Electrolyte-insulator-semiconductor (EIS) field-effect sensors belong to a new generation of electronic chips for biochemical sensing, enabling a direct electronic readout. The review gives an overview on recent advances and current trends in the research and development of chemical sensors and biosensors based on the capacitive field-effect EIS structure—the simplest field-effect device, which represents a biochemically sensitive capacitor. Fundamental concepts, physicochemical phenomena underlying the transduction mechanism and application of capacitive EIS sensors for the detection of pH, ion concentrations, and enzymatic reactions, as well as the label-free detection of charged molecules (nucleic acids, proteins, and polyelectrolytes) and nanoparticles, are presented and discussed.
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Park, Goeun, Hanbin Park, Sang-Chan Park, Moonbong Jang, Jinho Yoon, Jae-Hyuk Ahn, and Taek Lee. "Recent Developments in DNA-Nanotechnology-Powered Biosensors for Zika/Dengue Virus Molecular Diagnostics." Nanomaterials 13, no. 2 (January 16, 2023): 361. http://dx.doi.org/10.3390/nano13020361.
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Zika virus (ZIKV) and dengue virus (DENV) are highly contagious and lethal mosquito-borne viruses. Global warming is steadily increasing the probability of ZIKV and DENV infection, and accurate diagnosis is required to control viral infections worldwide. Recently, research on biosensors for the accurate diagnosis of ZIKV and DENV has been actively conducted. Moreover, biosensor research using DNA nanotechnology is also increasing, and has many advantages compared to the existing diagnostic methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA). As a bioreceptor, DNA can easily introduce a functional group at the 5′ or 3′ end, and can also be used as a folded structure, such as a DNA aptamer and DNAzyme. Instead of using ZIKV and DENV antibodies, a bioreceptor that specifically binds to viral proteins or nucleic acids has been fabricated and introduced using DNA nanotechnology. Technologies for detecting ZIKV and DENV can be broadly divided into electrochemical, electrical, and optical. In this review, advances in DNA-nanotechnology-based ZIKV and DENV detection biosensors are discussed.
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Scognamiglio, Viviana, and Amina Antonacci. "Structural Changes as a Tool for Affinity Recognition: Conformational Switch Biosensing." Crystals 12, no. 9 (August 27, 2022): 1209. http://dx.doi.org/10.3390/cryst12091209.
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Biosensors draw inspiration from natural chemosensing based on molecular switches between different bond-induced conformational states. Proteins and nucleic acids can be adapted into switch-based biosensors with a wide plethora of different configurations, taking advantage of the variety of transduction systems, from optical to electrochemical or electrochemiluminescence, as well as from nanomaterials for signal augmentation. This review reports the latest trends in conformational switch biosensors reported in the literature in the last 10 years, focusing on the main representative and recent examples of protein-based switching biosensors, DNA nanomachines, and structure-switched aptamers being applied for the detection of a wide range of target analytes with interest in biomedical and agro-environmental sectors.
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Zhu, Mengxi, Shan Li, Sanqiang Li, Haojie Wang, Juanjuan Xu, Yili Wang, and Gaofeng Liang. "Strategies for Engineering Exosomes and Their Applications in Drug Delivery." Journal of Biomedical Nanotechnology 17, no. 12 (December 1, 2021): 2271–97. http://dx.doi.org/10.1166/jbn.2021.3196.
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Exosomes are representative of a promising vehicle for delivery of biomolecules. Despite their discovery nearly 40 years, knowledge of exosomes and extracellular vesicles (EVs) and the role they play in etiology of disease and normal cellular physiology remains in its infancy. EVs are produced in almost all cells, containing nucleic acids, lipids, and proteins delivered from donor cells to recipient cells. Consequently, they act as mediators of intercellular communication and molecular transfer. Recent studies have shown that, exosomes are associated with numerous physiological and pathological processes as a small subset of EVs, and they play a significant role in disease progression and treatment. In this review, we discuss several key questions: what are exosomes, why do they matter, and how do we repurpose them in their strategies and applications in drug delivery systems. In addition, opportunities and challenges of exosome-based theranostics are also described and directions for future research are presented.
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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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Carpenter, Alexander, Ian Paulsen, and Thomas Williams. "Blueprints for Biosensors: Design, Limitations, and Applications." Genes 9, no. 8 (July 26, 2018): 375. http://dx.doi.org/10.3390/genes9080375.
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Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range of industrial, medical, ecological, and scientific applications. Approaches to biosensor design are as diverse as their applications, with major biosensor classes including nucleic acids, proteins, and transcription factors. Each of these biosensor types has advantages and limitations based on the intended application, and the parameters that are required for optimal performance. Specifically, the choice of biosensor design must consider factors such as the ligand specificity, sensitivity, dynamic range, functional range, mode of output, time of activation, ease of use, and ease of engineering. This review discusses the rationale for designing the major classes of biosensor in the context of their limitations and assesses their suitability to different areas of biotechnological application.
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Han, Guoliang, Ziqi Qiao, Yuxia Li, Chengfeng Wang, and Baoshan Wang. "The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance." International Journal of Molecular Sciences 22, no. 15 (August 3, 2021): 8327. http://dx.doi.org/10.3390/ijms22158327.
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Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.
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Liebana-Jordan, Marc, Bruno Brotons, Juan Manuel Falcon-Perez, and Esperanza Gonzalez. "Extracellular Vesicles in the Fungi Kingdom." International Journal of Molecular Sciences 22, no. 13 (July 5, 2021): 7221. http://dx.doi.org/10.3390/ijms22137221.
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Extracellular vesicles (EVs) are membranous, rounded vesicles released by prokaryotic and eukaryotic cells in their normal and pathophysiological states. These vesicles form a network of intercellular communication as they can transfer cell- and function-specific information (lipids, proteins and nucleic acids) to different cells and thus alter their function. Fungi are not an exception; they also release EVs to the extracellular space. The vesicles can also be retained in the periplasm as periplasmic vesicles (PVs) and the cell wall. Such fungal vesicles play various specific roles in the lives of these organisms. They are involved in creating wall architecture and maintaining its integrity, supporting cell isolation and defence against the environment. In the case of pathogenic strains, they might take part in the interactions with the host and affect the infection outcomes. The economic importance of fungi in manufacturing high-quality nutritional and pharmaceutical products and in remediation is considerable. The analysis of fungal EVs opens new horizons for diagnosing fungal infections and developing vaccines against mycoses and novel applications of nanotherapy and sensors in industrial processes.
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Kim, Seohyun, Sangmin Ji, and Hye Ran Koh. "CRISPR as a Diagnostic Tool." Biomolecules 11, no. 8 (August 6, 2021): 1162. http://dx.doi.org/10.3390/biom11081162.
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Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
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Hwang, Hee Sook, Hyosuk Kim, Geonhee Han, Jong Won Lee, Kwangmeyung Kim, Ick Chan Kwon, Yoosoo Yang, and Sun Hwa Kim. "Extracellular Vesicles as Potential Therapeutics for Inflammatory Diseases." International Journal of Molecular Sciences 22, no. 11 (May 22, 2021): 5487. http://dx.doi.org/10.3390/ijms22115487.
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Extracellular vesicles (EV) deliver cargoes such as nucleic acids, proteins, and lipids between cells and serve as an intercellular communicator. As it is revealed that most of the functions associated to EVs are closely related to the immune response, the important role of EVs in inflammatory diseases is emerging. EVs can be functionalized through EV surface engineering and endow targeting moiety that allows for the target specificity for therapeutic applications in inflammatory diseases. Moreover, engineered EVs are considered as promising nanoparticles to develop personalized therapeutic carriers. In this review, we highlight the role of EVs in various inflammatory diseases, the application of EV as anti-inflammatory therapeutics, and the current state of the art in EV engineering techniques.
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Mehta, Piyush. "Dry Powder Inhalers: A Focus on Advancements in Novel Drug Delivery Systems." Journal of Drug Delivery 2016 (October 27, 2016): 1–17. http://dx.doi.org/10.1155/2016/8290963.
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Administration of drug molecules by inhalation route for treatment of respiratory diseases has the ability to deliver drugs, hormones, nucleic acids, steroids, proteins, and peptides, particularly to the site of action, improving the efficacy of the treatment and consequently lessening adverse effects of the treatment. Numerous inhalation delivery systems have been developed and studied to treat respiratory diseases such as asthma, COPD, and other pulmonary infections. The progress of disciplines such as biomaterials science, nanotechnology, particle engineering, molecular biology, and cell biology permits further improvement of the treatment capability. The present review analyzes modern therapeutic approaches of inhaled drugs with special emphasis on novel drug delivery system for treatment of various respiratory diseases.
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Bardhan, Jaydeep P. "Gradient models in molecular biophysics: progress, challenges, opportunities." Journal of the Mechanical Behavior of Materials 22, no. 5-6 (December 1, 2013): 169–84. http://dx.doi.org/10.1515/jmbm-2013-0024.
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AbstractIn the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.
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Ahmed, Zahoor, Hasan Zulfiqar, Lixia Tang, and Hao Lin. "A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins." International Journal of Molecular Sciences 23, no. 17 (September 4, 2022): 10116. http://dx.doi.org/10.3390/ijms231710116.
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Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor–Hydrogen–Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.
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Keysberg, Christoph, Oliver Hertel, Louise Schelletter, Tobias Busche, Chiara Sochart, Jörn Kalinowski, Raimund Hoffrogge, Kerstin Otte, and Thomas Noll. "Exploring the molecular content of CHO exosomes during bioprocessing." Applied Microbiology and Biotechnology 105, no. 9 (May 2021): 3673–89. http://dx.doi.org/10.1007/s00253-021-11309-8.
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Abstract In biopharmaceutical production, Chinese hamster ovary (CHO) cells derived from Cricetulus griseus remain the most commonly used host cell for recombinant protein production, especially antibodies. Over the last decade, in-depth multi-omics characterization of these CHO cells provided data for extensive cell line engineering and corresponding increases in productivity. However, exosomes, extracellular vesicles containing proteins and nucleic acids, are barely researched at all in CHO cells. Exosomes have been proven to be a ubiquitous mediator of intercellular communication and are proposed as new biopharmaceutical format for drug delivery, indicator reflecting host cell condition and anti-apoptotic factor in spent media. Here we provide a brief overview of different separation techniques and subsequently perform a proteome and regulatory, non-coding RNA analysis of exosomes, derived from lab-scale bioreactor cultivations of a CHO-K1 cell line, to lay out reference data for further research in the field. Applying bottom-up orbitrap shotgun proteomics and next-generation small RNA sequencing, we detected 1395 proteins, 144 micro RNA (miRNA), and 914 PIWI-interacting RNA (piRNA) species differentially across the phases of a batch cultivation process. The exosomal proteome and RNA data are compared with other extracellular fractions and cell lysate, yielding several significantly exosome-enriched species. Key points • First-time comprehensive protein and miRNA characterization of CHO exosomes. • Isolation protocol and time point of bioprocess strongly affect quality of extracellular vesicles. • CHO-derived exosomes also contain numerous piRNA species of yet unknown function.
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Tariq, Muhammad, Muhammad Waseem, Muhammad Hidayat Rasool, Muhammad Asif Zahoor, and Irshad Hussain. "Isolation and molecular characterization of the indigenous Staphylococcus aureus strain K1 with the ability to reduce hexavalent chromium for its application in bioremediation of metal-contaminated sites." PeerJ 7 (October 11, 2019): e7726. http://dx.doi.org/10.7717/peerj.7726.
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Background Urbanization and industrialization are the main anthropogenic activities that are adding toxic heavy metals to the environment. Among these, chromium (in hexavalent: Cr+6 and/or trivalent Cr+3) is being released abundantly in wastewater due to its uses in different industrial processes. It becomes highly mutagenic and carcinogenic once it enters the cell through sulfate uptake pathways after interacting with cellular proteins and nucleic acids. However, Cr+6 can be bio-converted into more stable, less toxic and insoluble trivalent chromium using microbes. Hence in this study, we have made efforts to utilize chromium tolerant bacteria for bio-reduction of Cr+6 to Cr+3. Methods Bacterial isolate, K1, from metal contaminated industrial effluent from Kala Shah Kaku-Lahore Pakistan, which tolerated up to 22 mM of Cr6+ was evaluated for chromate reduction. It was further characterized biochemically and molecularly by VITEK®2 system and 16S rRNA gene sequencing respectively. Other factors affecting the reduction of chromium such as initial chromate ion concentration, pH, temperature, contact-time were also investigated. The role of cellular surface in sorption of Cr6+ ion was analyzed by FTIR spectroscopy. Results Both biochemical and phylogenetic analyses confirmed that strain K1 was Staphylococcusaureus that could reduce 99% of Cr6+ in 24 hours at 35 °C (pH = 8.0; initial Cr6+ concentration = 100 mg/L). FTIR results assumed that carboxyl, amino and phosphate groups of cell wall were involved in complexation with chromium. Our results suggested that Staphylococcusaureus K1 could be a promising gram-positive bacterium that might be utilized to remove chromium from metal polluted environments.
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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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Box, Allison M., Matthew J. McGuffie, Brendan J. O'Hara, and Kimberley D. Seed. "Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering." Journal of Bacteriology 198, no. 3 (November 23, 2015): 578–90. http://dx.doi.org/10.1128/jb.00747-15.
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ABSTRACTThe classical and El Tor biotypes ofVibrio choleraeserogroup O1, the etiological agent of cholera, are responsible for the sixth and seventh (current) pandemics, respectively. A genomic island (GI), GI-24, previously identified in a classical biotype strain ofV. cholerae, is predicted to encode clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins); however, experimental evidence in support of CRISPR activity inV. choleraehas not been documented. Here, we show that CRISPR-Cas is ubiquitous in strains of the classical biotype but excluded from strains of the El Tor biotype. We also providein silicoevidence to suggest that CRISPR-Cas actively contributes to phage resistance in classical strains. We demonstrate that transfer of GI-24 toV. choleraeEl Tor via natural transformation enables CRISPR-Cas-mediated resistance to bacteriophage CP-T1 under laboratory conditions. To elucidate the sequence requirements of this type I-E CRISPR-Cas system, we engineered a plasmid-based system allowing the directed targeting of a region of interest. Through screening for phage mutants that escape CRISPR-Cas-mediated resistance, we show that CRISPR targets must be accompanied by a 3′ TT protospacer-adjacent motif (PAM) for efficient interference. Finally, we demonstrate that efficient editing ofV. choleraelytic phage genomes can be performed by simultaneously introducing an editing template that allows homologous recombination and escape from CRISPR-Cas targeting.IMPORTANCECholera, caused by the facultative pathogenVibrio cholerae, remains a serious public health threat. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) provide prokaryotes with sequence-specific protection from invading nucleic acids, including bacteriophages. In this work, we show that one genomic feature differentiating sixth pandemic (classical biotype) strains from seventh pandemic (El Tor biotype) strains is the presence of a CRISPR-Cas system in the classical biotype. We demonstrate that the CRISPR-Cas system from a classical biotype strain can be transferred to aV. choleraeEl Tor biotype strain and that it is functional in providing resistance to phage infection. Finally, we show that this CRISPR-Cas system can be used as an efficient tool for the editing ofV. choleraelytic phage genomes.
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Matsuzaka, Yasunari, and Ryu Yashiro. "Extracellular Vesicles as Novel Drug-Delivery Systems through Intracellular Communications." Membranes 12, no. 6 (May 25, 2022): 550. http://dx.doi.org/10.3390/membranes12060550.
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Since it has been reported that extracellular vesicles (EVs) carry cargo using cell-to-cell comminication according to various in vivo situations, they are exprected to be applied as new drug-delivery systems (DDSs). In addition, non-coding RNAs, such as microRNAs (miRNAs), have attracted much attention as potential biomarkers in the encapsulated extracellular-vesicle (EV) form. EVs are bilayer-based lipids with heterogeneous populations of varying sizes and compositions. The EV-mediated transport of contents, which includes proteins, lipids, and nucleic acids, has attracted attention as a DDS through intracellular communication. Many reports have been made on the development of methods for introducing molecules into EVs and efficient methods for introducing them into target vesicles. In this review, we outline the possible molecular mechanisms by which miRNAs in exosomes participate in the post-transcriptional regulation of signaling pathways via cell–cell communication as novel DDSs, especially small EVs.
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Rowe, Rhianon K., and P. Shing Ho. "Relationships between hydrogen bonds and halogen bonds in biological systems." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 2 (March 29, 2017): 255–64. http://dx.doi.org/10.1107/s2052520617003109.
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The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.
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Butreddy, Arun, Nagavendra Kommineni, and Narendar Dudhipala. "Exosomes as Naturally Occurring Vehicles for Delivery of Biopharmaceuticals: Insights from Drug Delivery to Clinical Perspectives." Nanomaterials 11, no. 6 (June 3, 2021): 1481. http://dx.doi.org/10.3390/nano11061481.
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Exosomes as nanosized vesicles are emerging as drug delivery systems for therapeutics owing to their natural origin, their ability to mediate intercellular communication, and their potential to encapsulate various biological molecules such as proteins and nucleic acids within the lipid bilayer membrane or in the lumen. Exosomes contain endogenous components (proteins, lipids, RNA) that could be used to deliver cargoes to target cells, offering an opportunity to diagnose and treat various diseases. Owing to their ability to travel safely in extracellular fluid and to transport cargoes to target cells with high efficacy, exosomes offer enhanced delivery of cargoes in vivo. However, several challenges related to the stabilization of the exosomes, the production of sufficient amounts of exosomes with safety and efficacy, the efficient loading of drugs into exosomes, the clearance of exosomes from circulation, and the transition from the bench scale to clinical production may limit their development and clinical use. For the clinical use of exosomes, it is important to understand the molecular mechanisms behind the transport and function of exosome vesicles. This review exploits techniques related to the isolation and characterization of exosomes and their drug delivery potential to enhance the therapeutic outcome and stabilization methods. Further, routes of administration, clinical trials, and regulatory aspects of exosomes will be discussed in this review.
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Huang, Jiahao, Jueqi Wu, and Zhigang Li. "Biosensing using hairpin DNA probes." Reviews in Analytical Chemistry 34, no. 1-2 (January 1, 2015): 1–27. http://dx.doi.org/10.1515/revac-2015-0010.
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AbstractHairpin DNA probes (HDPs) are specially designed single-stranded DNA and have excellent sensing specificity. The past decade has witnessed the fast development of HDP-based biosensors due to the tremendous applications in biology, medicine, environmental science, and engineering. Their detectable targets include nucleic acids, proteins, small molecules, and metal ions. In this review, we summarize the recent progress in HDP-based biosensors by categorizing them into molecular beacon (MB)-based sensing in homogeneous systems and other HDP-based solid-state sensors. The basic design of MBs with diverse signaling pairs is introduced first. Then, various detectable targets and the detection principles of all HDP-based biosensors are extensively discussed. Furthermore, the methods for amplifying the response signal and improving the detection performance are covered. Finally, the limitations and possible solutions about the sensors are discussed.
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Yang, Fan, Xiaolei Zuo, Chunhai Fan, and Xian-En Zhang. "Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing." National Science Review 5, no. 5 (February 10, 2018): 740–55. http://dx.doi.org/10.1093/nsr/nwx134.
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Abstract Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Chen, Feng, Yingxia Liu, Nai-Kei Wong, Jia Xiao, and Kwok-Fai So. "Oxidative Stress in Stem Cell Aging." Cell Transplantation 26, no. 9 (September 2017): 1483–95. http://dx.doi.org/10.1177/0963689717735407.
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Stem cell aging is a process in which stem cells progressively lose their ability to self-renew or differentiate, succumb to senescence or apoptosis, and eventually become functionally depleted. Unresolved oxidative stress and concomitant oxidative damages of cellular macromolecules including nucleic acids, proteins, lipids, and carbohydrates have been recognized to contribute to stem cell aging. Excessive production of reactive oxygen species and insufficient cellular antioxidant reserves compromise cell repair and metabolic homeostasis, which serves as a mechanistic switch for a variety of aging-related pathways. Understanding the molecular trigger, regulation, and outcomes of those signaling networks is critical for developing novel therapies for aging-related diseases by targeting stem cell aging. Here we explore the key features of stem cell aging biology, with an emphasis on the roles of oxidative stress in the aging process at the molecular level. As a concept of cytoprotection of stem cells in transplantation, we also discuss how systematic enhancement of endogenous antioxidant capacity before or during graft into tissues can potentially raise the efficacy of clinical therapy. Finally, future directions for elucidating the control of oxidative stress and developing preventive/curative strategies against stem cell aging are discussed.
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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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Kim, Seung-Woo, Sunbum Kwon, and Young-Kwan Kim. "Graphene Oxide Derivatives and Their Nanohybrid Structures for Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Analysis of Small Molecules." Nanomaterials 11, no. 2 (January 22, 2021): 288. http://dx.doi.org/10.3390/nano11020288.
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Matrix-assisted laser desorption/ionization (MALDI) has been considered as one of the most powerful analytical tools for mass spectrometry (MS) analysis of large molecular weight compounds such as proteins, nucleic acids, and synthetic polymers thanks to its high sensitivity, high resolution, and compatibility with high-throughput analysis. Despite these advantages, MALDI cannot be applied to MS analysis of small molecular weight compounds (<500 Da) because of the matrix interference in low mass region. Therefore, numerous efforts have been devoted to solving this issue by using metal, semiconductor, and carbon nanomaterials for MALDI time-of-flight MS (MALDI-TOF-MS) analysis instead of organic matrices. Among those nanomaterials, graphene oxide (GO) is of particular interest considering its unique and highly tunable chemical structures composed of the segregated sp2 carbon domains surrounded by sp3 carbon matrix. Chemical modification of GO can precisely tune its physicochemical properties, and it can be readily incorporated with other functional nanomaterials. In this review, the advances of GO derivatives and their nanohybrid structures as alternatives to organic matrices are summarized to demonstrate their potential and practical aspect for MALDI-TOF-MS analysis of small molecules.
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Bae, Sang-Wook, Jiyun Kim, and Sunghoon Kwon. "Recent Advances in Polymer Additive Engineering for Diagnostic and Therapeutic Hydrogels." International Journal of Molecular Sciences 23, no. 6 (March 9, 2022): 2955. http://dx.doi.org/10.3390/ijms23062955.
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Hydrogels are hydrophilic polymer materials that provide a wide range of physicochemical properties as well as are highly biocompatible. Biomedical researchers are adapting these materials for the ever-increasing range of design options and potential applications in diagnostics and therapeutics. Along with innovative hydrogel polymer backbone developments, designing polymer additives for these backbones has been a major contributor to the field, especially for expanding the functionality spectrum of hydrogels. For the past decade, researchers invented numerous hydrogel functionalities that emerge from the rational incorporation of additives such as nucleic acids, proteins, cells, and inorganic nanomaterials. Cases of successful commercialization of such functional hydrogels are being reported, thus driving more translational research with hydrogels. Among the many hydrogels, here we reviewed recently reported functional hydrogels incorporated with polymer additives. We focused on those that have potential in translational medicine applications which range from diagnostic sensors as well as assay and drug screening to therapeutic actuators as well as drug delivery and implant. We discussed the growing trend of facile point-of-care diagnostics and integrated smart platforms. Additionally, special emphasis was given to emerging bioinformatics functionalities stemming from the information technology field, such as DNA data storage and anti-counterfeiting strategies. We anticipate that these translational purpose-driven polymer additive research studies will continue to advance the field of functional hydrogel engineering.
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Rahman, Saeed, Malvika Nagrath, Sasikumar Ponnusamy, and Praveen Arany. "Nanoscale and Macroscale Scaffolds with Controlled-Release Polymeric Systems for Dental Craniomaxillofacial Tissue Engineering." Materials 11, no. 8 (August 20, 2018): 1478. http://dx.doi.org/10.3390/ma11081478.
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Tremendous progress in stem cell biology has resulted in a major current focus on effective modalities to promote directed cellular behavior for clinical therapy. The fundamental principles of tissue engineering are aimed at providing soluble and insoluble biological cues to promote these directed biological responses. Better understanding of extracellular matrix functions is ensuring optimal adhesive substrates to promote cell mobility and a suitable physical niche to direct stem cell responses. Further, appreciation of the roles of matrix constituents as morphogen cues, termed matrikines or matricryptins, are also now being directly exploited in biomaterial design. These insoluble topological cues can be presented at both micro- and nanoscales with specific fabrication techniques. Progress in development and molecular biology has described key roles for a range of biological molecules, such as proteins, lipids, and nucleic acids, to serve as morphogens promoting directed behavior in stem cells. Controlled-release systems involving encapsulation of bioactive agents within polymeric carriers are enabling utilization of soluble cues. Using our efforts at dental craniofacial tissue engineering, this narrative review focuses on outlining specific biomaterial fabrication techniques, such as electrospinning, gas foaming, and 3D printing used in combination with polymeric nano- or microspheres. These avenues are providing unprecedented therapeutic opportunities for precision bioengineering for regenerative applications.
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Mauriz, Elba. "Clinical Applications of Visual Plasmonic Colorimetric Sensing." Sensors 20, no. 21 (October 30, 2020): 6214. http://dx.doi.org/10.3390/s20216214.
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Colorimetric analysis has become of great importance in recent years to improve the operationalization of plasmonic-based biosensors. The unique properties of nanomaterials have enabled the development of a variety of plasmonics applications on the basis of the colorimetric sensing provided by metal nanoparticles. In particular, the extinction of localized surface plasmon resonance (LSPR) in the visible range has permitted the exploitation of LSPR colorimetric-based biosensors as powerful tools for clinical diagnostics and drug monitoring. This review summarizes recent progress in the biochemical monitoring of clinical biomarkers by ultrasensitive plasmonic colorimetric strategies according to the distance- or the morphology/size-dependent sensing modes. The potential of colorimetric nanosensors as point of care devices from the perspective of naked-eye detection is comprehensively discussed for a broad range of analytes including pharmaceuticals, proteins, carbohydrates, nucleic acids, bacteria, and viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The practical suitability of plasmonic-based colorimetric assays for the rapid visual readout in biological samples, considering current challenges and future perspectives, is also reviewed.
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Rastegari, Elham, Yu-Jer Hsiao, Wei-Yi Lai, Yun-Hsien Lai, Tien-Chun Yang, Shih-Jen Chen, Pin-I. Huang, Shih-Hwa Chiou, Chung-Yuan Mou, and Yueh Chien. "An Update on Mesoporous Silica Nanoparticle Applications in Nanomedicine." Pharmaceutics 13, no. 7 (July 12, 2021): 1067. http://dx.doi.org/10.3390/pharmaceutics13071067.
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The efficient and safe delivery of therapeutic drugs, proteins, and nucleic acids are essential for meaningful therapeutic benefits. The field of nanomedicine shows promising implications in the development of therapeutics by delivering diagnostic and therapeutic compounds. Nanomedicine development has led to significant advances in the design and engineering of nanocarrier systems with supra-molecular structures. Smart mesoporous silica nanoparticles (MSNs), with excellent biocompatibility, tunable physicochemical properties, and site-specific functionalization, offer efficient and high loading capacity as well as robust and targeted delivery of a variety of payloads in a controlled fashion. Such unique nanocarriers should have great potential for challenging biomedical applications, such as tissue engineering, bioimaging techniques, stem cell research, and cancer therapies. However, in vivo applications of these nanocarriers should be further validated before clinical translation. To this end, this review begins with a brief introduction of MSNs properties, targeted drug delivery, and controlled release with a particular emphasis on their most recent diagnostic and therapeutic applications.
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Wu, Yingfen, Diane C. Darland, and Julia Xiaojun Zhao. "Nanozymes—Hitting the Biosensing “Target”." Sensors 21, no. 15 (July 31, 2021): 5201. http://dx.doi.org/10.3390/s21155201.
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Nanozymes are a class of artificial enzymes that have dimensions in the nanometer range and can be composed of simple metal and metal oxide nanoparticles, metal nanoclusters, dots (both quantum and carbon), nanotubes, nanowires, or multiple metal-organic frameworks (MOFs). They exhibit excellent catalytic activities with low cost, high operational robustness, and a stable shelf-life. More importantly, they are amenable to modifications that can change their surface structures and increase the range of their applications. There are three main classes of nanozymes including the peroxidase-like, the oxidase-like, and the antioxidant nanozymes. Each of these classes catalyzes a specific group of reactions. With the development of nanoscience and nanotechnology, the variety of applications for nanozymes in diverse fields has expanded dramatically, with the most popular applications in biosensing. Nanozyme-based novel biosensors have been designed to detect ions, small molecules, nucleic acids, proteins, and cancer cells. The current review focuses on the catalytic mechanism of nanozymes, their application in biosensing, and the identification of future directions for the field.
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Schudoma, Christian. "It's a loop world – single strands in RNA as structural and functional elements." BioMolecular Concepts 2, no. 3 (June 1, 2011): 171–81. http://dx.doi.org/10.1515/bmc.2011.016.
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AbstractUnpaired regions in RNA molecules – loops – are centrally involved in defining the characteristic three-dimensional (3D) architecture of RNAs and are of high interest in RNA engineering and design. Loops adopt diverse, but specific conformations stabilised by complex tertiary structural interactions that provide structural flexibility to RNA structures that would otherwise not be possible if they only consisted of the rigid A-helical shapes usually formed by canonical base pairing. By participating in sequence-non-local contacts, they furthermore contribute to stabilising the overall fold of RNA molecules. Interactions between RNAs and other nucleic acids, proteins, or small molecules are also generally mediated by RNA loop structures. Therefore, the function of an RNA molecule is generally dependent on its loops. Examples include intermolecular interactions between RNAs as part of the microRNA processing pathways, ribozymatic activity, or riboswitch-ligand interactions. Bioinformatics approaches have been successfully applied to the identification of novel RNA structural motifs including loops, local and global RNA 3D structure prediction, and structural and conformational analysis of RNAs and have contributed to a better understanding of the sequence-structure-function relationships in RNA loops.
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Smith, Andrew M. "(Keynote) Quantum Dot Coatings for Aqueous Stabilization and Applications in Biomolecular Analysis." ECS Meeting Abstracts MA2022-02, no. 20 (October 9, 2022): 909. http://dx.doi.org/10.1149/ma2022-0220909mtgabs.
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Semiconductor quantum dots have been commercially available as molecular probes for applications in the life sciences and clinical diagnostics for two decades, however they have only been adopted in niche applications. Part of the reason for limited adoption is attributable to challenges in colloidal stabilization, as these solid nanocrystals tend to aggregate and nonspecifically adsorb to surfaces and cellular structures. This can largely be alleviated by use of nanocrystal coatings that resist nonspecific binding and promote aqueous dispersion, however the vast majority of such coatings are based on neutral and zwitterionic polymers that add considerable hydrodynamic size to the product. This size increase is due to the bulk of the coating itself as well as adsorption of water molecules and ions in solution. The size increase causes steric hindrance and inaccurate molecular labeling when these probes are used to analyze targets that have considerable size or ones that are located in crowded regions of cells or tissues. Furthermore, the bioaffinity label that attaches the quantum dot to its intended molecular target often contributes substantially to the final size and stability of the probe. This is especially challenging for protein labeling using antibodies, which themselves are fairly large proteins that attach heterogeneously to quantum dots, typically yielding large, polydisperse products. This talk will focus on developments in quantum dot engineering, monolayer polymeric coatings, and bioconjugation strategies to optimize offsetting characteristics of size, homogeneity, bioaffinity, and specificity. In particular, multidentate polymer coatings in recent years have enabled the production of quantum dots with long-term shelf life, small hydrodynamic diameters, and efficient click chemistry conjugations. By tuning the conjugation methods to antibody fragments and single-stranded DNA, we can now prepare bioaffinity labels for proteins and nucleic acids in the ~10 nm range, with further size reductions possible through nanocrystal heterostructure engineering. This talk will also cover how in situ protein and nucleic acid labeling applications can benefit from these advances in addition to current challenges in processing, scale-up, and user adoption.