scholarly journals Impact of substrate-template stability, temperature, phosphate location, and nick-site base pairs on non-enzymatic DNA ligation: Defining parameters for optimization of ligation rates and yields with carbodiimide activation

2019 ◽  
Author(s):  
Chiamaka Obianyor ◽  
Gary Newnam ◽  
Bryce Clifton ◽  
Martha A. Grover ◽  
Nicholas V. Hud
Keyword(s):  
Reaction Times ◽  
Test System ◽  
Water Soluble ◽  
Base Pairs ◽  
Chemical Ligation ◽  
Dna Structures ◽  
Dna Ligation ◽  
Wide Range ◽  
Activating Agent ◽  
Nick Site

ABSTRACTNon-enzymatic, chemical ligation is an important tool for the generation of synthetic DNA structures, which are used for a wide range of applications. Surprisingly, reported chemical ligation yields range from 30% to 95% for the same chemical activating agent and comparable DNA structures. We report a systematic study of DNA ligation using a well-defined bimolecular test system and water-soluble carbodiimide (EDC) as a phosphate-activating agent. Our results reveal interplay between template-substrate stability and the rates of the chemical steps of ligation, which can cause yields to increase or decrease with increasing temperature. Phosphate location at the nick site also exhibits a strong influence on ligation rates and yields, with a 3’ phosphate providing yields near 100% after 24 hours for particularly favourable reaction conditions, while comparable reactions with the phosphate on the 5’ position of the nick site only reach 40% ligation even after 48 hours. Ligation rates are also shown to be sensitive to the identity of base pairs flanking a nick site, with some varying by more than three-fold. Finally, DNA substrate modification by EDC can, in some cases, make long reaction times and repeated addition of EDC an ineffective strategy for increasing ligation yields.

scholarly journals Cloning of a C-phycocyanin Alpha Subunit from Thermosynechococcus sp. TUBT-T01 and Prediction of Its Properties

2017 ◽  
Vol 15 (12) ◽  
pp. 857-867
Author(s):  
Plaipol DEDVISITSAKUL ◽  
Sichon HUADRAKSASAT ◽  
Supenya CHITTAPUN ◽  
Theppanya CHAROENRAT ◽  
Chanitchote PIYAPITTAYANUN
Keyword(s):  
Hot Spring ◽  
Water Soluble ◽  
Alpha Subunit ◽  
Antioxidant Compounds ◽  
Sequencing Analysis ◽  
Base Pairs ◽  
Sequence Alignments ◽  
Gene Encoding ◽  
Wide Range ◽  
Dna Sequencing Analysis

C-Phycocyanin, a blue-colored and water soluble protein, is a class of phycobiliproteins that are the major light-harvesting pigments of a photosynthetic system in cyanobacteria. C-phycocyanins are utilized in many industries, including as natural colorants in food and cosmetics and as antioxidant compounds. However, the uses of C-phycocyanins have been limited due to their vulnerability to high temperatures. Therefore, the objective of this study was to identify and analyze the C-phycocyanin gene isolated from Thermosynechococcus sp. TUBT-T01, living in a hot spring in Surat Thani province, in the hope that this C-phycocyanin exhibited thermostable properties and that their applications could be expanded over a wide range of industries. In the present study, the polymerase chain reaction of the gene encoding alpha subunits of C-phycocyanin (cpcA) was performed, using primers designed based upon the sequence alignments of cpcA from Thermosynechococcus sp. available in the GenBank database. The putative cpcA, with an approximate size of 500 base pairs, was detected on an agarose gel. The DNA sequencing analysis indicated that the cpcA was 489 base pairs in length, and its nucleotide sequence was 94 % identical to those of thermophilic Thermosynechococcus sp. NK55, T. elongatus BP-1, and Synechococcus vulcanus. The deduced amino acid sequence was very similar to those of Thermosynechococcus sp. NK55, T. elongatus BP-1, and S. vulcanus. The data derived from the homologous model revealed that the presence of Asp28, Lys32, and Ser72 in the alpha subunit of C-phycocyanin from Thermosynechococcus sp. TUBT-T01 could provide the high thermostability property of this protein.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Microsponges: An Overview

2017 ◽  
Vol 4 (4) ◽  
Author(s):  
Hamid Hussain ◽  
Divya Juyal ◽  
Archana Dhyani
Keyword(s):  
Controlled Release ◽  
Delivery System ◽  
Oral Delivery ◽  
Active Agent ◽  
Topical Delivery ◽  
Water Soluble ◽  
Wide Range ◽  
Porous Beads

Microsponge and Nanosponge delivery System was originally developed for topical delivery of drugs can also be used for controlled oral delivery of drugs using water soluble and bioerodible polymers. Microsponge delivery system (MDS) can entrap wide range of drugs and then release them onto the skin over a time by difussion mechanism to the skin. It is a unique technology for the controlled release of topical agents and consists of nano or micro porous beads loaded with active agent and also use for oral delivery of drugs using bioerodible polymers.

The content of decenoic acids in drone brood preparations and combined preparations based on it

Biomics ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 389-393
Author(s):  
D.V. Mitrofanov ◽  
N.V. Budnikova
Keyword(s):  
Royal Jelly ◽  
Storage Conditions ◽  
Water Soluble ◽  
Biologically Active Substances ◽  
Biologically Active ◽  
Strict Adherence ◽  
Drone Brood ◽  
Wide Range ◽  
Active Substances ◽  
Melanin Complex

The drone brood contains a large number of substances with antioxidant activity. These substances require stabilization and strict adherence to storage conditions. Among these substances are unique decenoic acids, the content of which is an indicator of the quality of drone brood and products based on it. The ability of drone brood to reduce the manifestations of oxidative stress is shown. There are dietary supplements for food and drugs based on drone brood, which are used for a wide range of diseases. Together with drone brood, chitosan-containing products, propolis, royal jelly can be used. They enrich the composition with their own biologically active substances and affect the preservation of the biologically active substances of the drone brood. Promising are the products containing, in addition to the drone brood, a chitin-chitosan-melanin complex from bees, propolis, royal jelly. The chitin-chitosan-melanin complex in the amount of 5% in the composition of the adsorbent practically does not affect the preservation of decenic acids, while in the amount of 2% and 10% it somewhat worsens. The acid-soluble and water-soluble chitosan of marine crustaceans significantly worsens the preservation of decenoic acids in the product. Drone brood with royal jelly demonstrates a rather high content of decenoic acids. When propolis is introduced into the composition of the product, the content of decenoic acids increases according to the content of propolis.

Advances in Triazole Synthesis from Copper-catalyzed Azide-alkyne Cycloadditions (CuAAC) Based on Eco-friendly Procedures

2019 ◽  
Vol 16 (2) ◽  
pp. 244-257 ◽  
Author(s):  
Marcus Vinicius Nora de Souza ◽  
Cristiane França da Costa ◽  
Victor Facchinetti ◽  
Claudia Regina Brandão Gomes ◽  
Paula Mázala Pacheco
Keyword(s):  
Biological Activities ◽  
Reaction Times ◽  
Water Extract ◽  
Fish Bone ◽  
New Drugs ◽  
Bone Powder ◽  
Wide Range ◽  
Recoverable Catalysts ◽  
Egg Shell ◽  
Work Up

Background: 1,2,3-triazoles are an important class of organic compounds and because of their aromatic stability, they are not easily reduced, oxidized or hydrolyzed in acidic and basic environments. Moreover, 1,2,3-triazole derivatives are known by their important biological activities and have drawn considerable attention due to their variety of properties. The synthesis of this nucleus, based on the click chemistry concept, through the 1,3-dipolar addition reaction between azides and alkynes is a well-known procedure. This reaction has a wide range of applications, especially on the development of new drugs. Methods: The most prominent eco-friendly methods for the synthesis of triazoles under microwave irradiation published in articles from 2012-2018 were reviewed. Results: In this review, we cover some of the recent eco-friendly CuAAC procedures for the click synthesis of 1,2,3-triazoles with remarks to new and easily recoverable catalysts, such as rhizobial cyclic β-1,2 glucan; WEB (water extract of banana); biosourced cyclosophoraose (CyS); egg shell powder (ESP); cyclodextrin (β- CD); fish bone powder; nanoparticle-based catalyst, among others. Conclusion: These eco-friendly procedures are a useful tool for the synthesis of 1,2,3-triazoles, providing many advantages on the synthesis of this class, such as shorter reaction times, easier work-up and higher yields when compared to classical procedures. Moreover, these methodologies can be applied to the industrial synthesis of drugs and to other areas.

scholarly journals ChCl: Gly (DESs) Promote Environmentally Benign Synthesis of Xanthene Derivatives and Their Antitubercular Activity

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3667
Author(s):  
Mashooq A. Bhat ◽  
Ahmed M. Naglah ◽  
Siddique Akber Ansari ◽  
Hanaa M. Al-Tuwajiria ◽  
Abdullah Al-Dhfyan
Keyword(s):  
Reaction Times ◽  
Antitubercular Activity ◽  
Antimycobacterial Activity ◽  
Environmentally Benign ◽  
Reaction Yield ◽  
Benign Synthesis ◽  
Xanthene Derivatives ◽  
Wide Range ◽  
Major Application

A ChCl: Gly (DESs) promoted environmentally benign method was developed for the first time using the reaction of aryl aldehydes and dimedone to give excellent yields of xanthene analogues. The major application of this present protocol is the use of green solvent, a wide range of substrate, short reaction times, ease of recovery, the recyclability of the catalyst, high reaction yield, and ChCl: Gly as an alternative catalyst and solvent. In addition to this, all the synthesized compounds were evaluated for their in vitro antimycobacterial activity against M. tuberculosis H37Ra (MTB) and M. bovis BCG strains. The compounds 3d, 3e, 3f, and 3j showed significant antitubercular activity against MTB and M. bovis strains with minimum inhibitory concentration (MIC) values of 2.5−15.10 µg/mL and 0.26–14.92 µg/mL, respectively. The compounds 3e, 3f, and 3j were found to be nontoxic against MCF-7, A549, HCT 116, and THP-1 cell lines. All the prepared compounds were confirmed by 1H NMR and 13C NMR analysis.

scholarly journals Hybrid Nanoassemblies from Viruses and DNA Nanostructures

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1413
Author(s):  
Sofia Ojasalo ◽  
Petteri Piskunen ◽  
Boxuan Shen ◽  
Mauri A. Kostiainen ◽  
Veikko Linko
Keyword(s):  
Cell Activation ◽  
Immune Cell ◽  
Dna Nanotechnology ◽  
Biological Properties ◽  
Dna Nanostructures ◽  
Dna Structures ◽  
Nanoscale Structures ◽  
Immune Cell Activation ◽  
Wide Range ◽  
Structural Dna Nanotechnology

Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as “structured” genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.

scholarly journals Ureido Functionalization through Amine-Urea Transamidation under Mild Reaction Conditions

Polymers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1583
Author(s):  
Natalia Guerrero-Alburquerque ◽  
Shanyu Zhao ◽  
Daniel Rentsch ◽  
Matthias M. Koebel ◽  
Marco Lattuada ◽  
...  
Keyword(s):  
Aqueous Media ◽  
Reaction Times ◽  
Reaction Rates ◽  
Secondary Amines ◽  
Isocyanic Acid ◽  
Advantages And Disadvantages ◽  
Major Disadvantage ◽  
Wide Range ◽  
Potential Alternative ◽  
Full Conversion

Ureido-functionalized compounds play an indispensable role in important biochemical processes, as well as chemical synthesis and production. Isocyanates, and KOCN in particular, are the preferred reagents for the ureido functionalization of amine-bearing compounds. In this study, we evaluate the potential of urea as a reagent to graft ureido groups onto amines at relatively low temperatures (<100 °C) in aqueous media. Urea is an inexpensive, non-toxic and biocompatible potential alternative to KOCN for ureido functionalization. From as early as 1864, urea was the go-to reagent for polyurea polycondensation, before falling into disuse after the advent of isocyanate chemistry. We systematically re-investigate the advantages and disadvantages of urea for amine transamidation. High ureido-functionalization conversion was obtained for a wide range of substrates, including primary and secondary amines and amino acids. Reaction times are nearly independent of substrate and pH, but excess urea is required for practically feasible reaction rates. Near full conversion of amines into ureido can be achieved within 10 h at 90 °C and within 24 h at 80 °C, and much slower reaction rates were determined at lower temperatures. The importance of the urea/amine ratio and the temperature dependence of the reaction rates indicate that urea decomposition into an isocyanic acid or a carbamate intermediate is the rate-limiting step. The presence of water leads to a modest increase in reaction rates, but the full conversion of amino groups into ureido groups is also possible in the absence of water in neat alcohol, consistent with a reaction mechanism mediated by an isocyanic acid intermediate (where the water assists in the proton transfer). Hence, the reaction with urea avoids the use of toxic isocyanate reagents by in situ generation of the reactive isocyanate intermediate, but the requirement to separate the excess urea from the reaction product remains a major disadvantage.

scholarly journals Two-photon polymerization nanolithography technology for fabrication of stimulus-responsive micro/nano-structures for biomedical applications

2020 ◽  
Vol 9 (1) ◽  
pp. 1118-1136
Author(s):  
Zhenjia Huang ◽  
Gary Chi-Pong Tsui ◽  
Yu Deng ◽  
Chak-Yin Tang
Keyword(s):  
Biomedical Applications ◽  
Three Dimensional ◽  
Water Soluble ◽  
Fabrication Technology ◽  
Nano Fabrication ◽  
Two Photon ◽  
Nano Structures ◽  
Wide Range ◽  
Stimulus Responsive ◽  
Two Photon Polymerization

AbstractMicro/nano-fabrication technology via two-photon polymerization (TPP) nanolithography is a powerful and useful manufacturing tool that is capable of generating two dimensional (2D) to three dimensional (3D) arbitrary micro/nano-structures of various materials with a high spatial resolution. This technology has received tremendous interest in cell and tissue engineering and medical microdevices because of its remarkable fabrication capability for sophisticated structures from macro- to nano-scale, which are difficult to be achieved by traditional methods with limited microarchitecture controllability. To fabricate precisely designed 3D micro/nano-structures for biomedical applications via TPP nanolithography, the use of photoinitiators (PIs) and photoresists needs to be considered comprehensively and systematically. In this review, widely used commercially available PIs are first discussed, followed by elucidating synthesis strategies of water-soluble initiators for biomedical applications. In addition to the conventional photoresists, the distinctive properties of customized stimulus-responsive photoresists are discussed. Finally, current limitations and challenges in the material and fabrication aspects and an outlook for future prospects of TPP for biomedical applications based on different biocompatible photosensitive composites are discussed comprehensively. In all, this review provides a basic understanding of TPP technology and important roles of PIs and photoresists for fabricating high-precision stimulus-responsive micro/nano-structures for a wide range of biomedical applications.

scholarly journals Severe violations of independence in response inhibition tasks

2021 ◽  
Vol 7 (12) ◽  
pp. eabf4355
Author(s):  
Patrick G. Bissett ◽  
Henry M. Jones ◽  
Russell A. Poldrack ◽  
Gordon D. Logan
Keyword(s):  
Response Inhibition ◽  
Theoretical Foundation ◽  
Reaction Times ◽  
Stop Signal ◽  
Experimental Paradigm ◽  
Signal Delay ◽  
Independence Assumption ◽  
Analysis Techniques ◽  
Wide Range ◽  
Saccadic Responses

The stop-signal paradigm, a primary experimental paradigm for understanding cognitive control and response inhibition, rests upon the theoretical foundation of race models, which assume that a go process races independently against a stop process that occurs after a stop-signal delay (SSD). We show that severe violations of this independence assumption at short SSDs occur systematically across a wide range of conditions, including fast and slow reaction times, auditory and visual stop signals, manual and saccadic responses, and especially in selective stopping. We also reanalyze existing data and show that conclusions can change when short SSDs are excluded. Last, we suggest experimental and analysis techniques to address this violation, and propose adjustments to extant models to accommodate this finding.

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