scholarly journals Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Sensors ◽  
2020 ◽  
Vol 20 (11) ◽  
pp. 3112
Author(s):  
Jack Freeland ◽  
Lihua Zhang ◽  
Shih-Ting Wang ◽  
Mason Ruiz ◽  
Yong Wang
Keyword(s):  
Organic Molecules ◽  
Inorganic Salts ◽  
Dna Interactions ◽  
Bent Dna ◽  
Small Organic Molecules ◽  
Cellular Processes ◽  
Economic Methods ◽  
Simple Economic ◽  
Potential Use

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

scholarly journals Bent DNA bows as amplifiers and biosensors for detecting DNA-interacting salts and molecules

2020 ◽  
Author(s):  
Jack Freeland ◽  
Lihua Zhang ◽  
Shih-Ting Wang ◽  
Mason Ruiz ◽  
Yong Wang
Keyword(s):  
Organic Molecules ◽  
Inorganic Salts ◽  
Bent Dna ◽  
Dna Damages ◽  
Small Organic Molecules ◽  
Cellular Processes ◽  
Dna Targeting ◽  
Economic Methods ◽  
Potential Use

AbstractDue to the central role of DNA, its interactions with inorganic salts and small organic molecules are important for understanding various fundamental cellular processes in living systems, deciphering the mechanism of many diseases related to DNA damages, and discovering or designing inhibitors and drugs targeting DNA. However, there is still a need for improved sensitivity to detect these interactions, especially in situations where expensive sophisticated equipment is not available. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as monitoring water quality and screening DNA-targeting molecules and drugs.

scholarly journals Drosophila SLC22 Orthologs Related to OATs, OCTs, and OCTNs Regulate Development and Responsiveness to Oxidative Stress

2020 ◽  
Vol 21 (6) ◽  
pp. 2002 ◽  
Author(s):  
Darcy C. Engelhart ◽  
Priti Azad ◽  
Suwayda Ali ◽  
Jeffry C. Granados ◽  
Gabriel G. Haddad ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Drosophila Melanogaster ◽  
Organic Molecules ◽  
Fruit Fly ◽  
Evolutionary Analysis ◽  
Oxygen Species ◽  
Small Organic Molecules ◽  
Evolutionarily Conserved

The SLC22 family of transporters is widely expressed, evolutionarily conserved, and plays a major role in regulating homeostasis by transporting small organic molecules such as metabolites, signaling molecules, and antioxidants. Analysis of transporters in fruit flies provides a simple yet orthologous platform to study the endogenous function of drug transporters in vivo. Evolutionary analysis of Drosophila melanogaster putative SLC22 orthologs reveals that, while many of the 25 SLC22 fruit fly orthologs do not fall within previously established SLC22 subclades, at least four members appear orthologous to mammalian SLC22 members (SLC22A16:CG6356, SLC22A15:CG7458, CG7442 and SLC22A18:CG3168). We functionally evaluated the role of SLC22 transporters in Drosophila melanogaster by knocking down 14 of these genes. Three putative SLC22 ortholog knockdowns—CG3168, CG6356, and CG7442/SLC22A—did not undergo eclosion and were lethal at the pupa stage, indicating the developmental importance of these genes. Additionally, knocking down four SLC22 members increased resistance to oxidative stress via paraquat testing (CG4630: p < 0.05, CG6006: p < 0.05, CG6126: p < 0.01 and CG16727: p < 0.05). Consistent with recent evidence that SLC22 is central to a Remote Sensing and Signaling Network (RSSN) involved in signaling and metabolism, these phenotypes support a key role for SLC22 in handling reactive oxygen species.

Preparation of a Novel Composite Nanofiltration Membrane

2014 ◽  
Vol 665 ◽  
pp. 272-274
Author(s):  
Wei Wang ◽  
Teng Teng Qi ◽  
Yu Feng Zhang
Keyword(s):  
Organic Molecules ◽  
Interfacial Polymerization ◽  
Ph Sensitive ◽  
Inorganic Salts ◽  
Nanofiltration Membrane ◽  
Small Organic Molecules ◽  
Ethyl Methacrylate ◽  
Separation Performances ◽  
Sensitive Behavior

PDMAEMA/PSF nanofiltration (NF) membranes were prepared through interfacial polymerization of poly [2-(N,N-dimethyl amino) ethyl methacrylate](PDMAEMA) on porous polysulfone (PSF) substrate membranes. The effects of aqueous solution’s pH and crosslinking time and on separation performances of the PDMAEMA/PSF NF membrane were investigated. The results show that the rejection and flux of the PDMAEMA/PSF NF membrane show pH-sensitive behavior in NF process. Importantly, the membrane show a different separation between inorganic salts and small organic molecules.

Labeling of Nanofiber-Forming Peptides by Site-Directed Bioconjugation: Effect of Spacer Length on Self-Assembly

2019 ◽  
Vol 16 (2) ◽  
pp. 319-325
Author(s):  
Alessandra Scelsi ◽  
Brigida Bochicchio ◽  
Antonietta Pepe
Keyword(s):  
Self Assembly ◽  
Organic Molecules ◽  
Periodate Oxidation ◽  
Photonic Devices ◽  
Serine Residue ◽  
Spacer Length ◽  
Small Organic Molecules ◽  
Self Assembling ◽  
Versatile Tool

Background: The conjugation of small organic molecules to self-assembling peptides is a versatile tool to decorate nanostructures with original functionalities. Labeling with chromophores or fluorophores, for example, creates optically active fibers with potential interest in photonic devices. Aim and Objective: In this work, we present a rapid and effective labeling procedure for a self-assembling peptide able to form nanofibers. Rapid periodate oxidation of the N-terminal serine residue of the peptide and subsequent conjugation with dansyl moiety generated fluorophore-decorated peptides. Results: Three dansyl-conjugated self-assembling peptides with variable spacer-length were synthesized and characterized and the role of the size of the linker between fluorophore and peptide in self-assembling was investigated. Our results show that a short linker can alter the self-assembly in nanofibers of the peptide. Conclusions: Herein we report on an alternative strategy for creating functionalized nanofibrils, able to expand the toolkit of chemoselective bioconjugation strategies to be used in site-specific decoration of self-assembling peptides.

scholarly journals Ferroelectric columnar assemblies from the bowl-to-bowl inversion of aromatic cores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shunsuke Furukawa ◽  
Jianyun Wu ◽  
Masaya Koyama ◽  
Keisuke Hayashi ◽  
Norihisa Hoshino ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Organic Molecule ◽  
Remanent Polarization ◽  
Organic Molecules ◽  
Materials Science ◽  
State Of The Art ◽  
Condensed Matter ◽  
Small Organic Molecules ◽  
Organic Ferroelectrics ◽  
Potential Use

AbstractOrganic ferroelectrics, in which the constituent molecules retain remanent polarization, represent an important topic in condensed-matter science, and their attractive properties, which include lightness, flexibility, and non-toxicity, are of potential use in state-of-the-art ferroelectric devices. However, the mechanisms for the generation of ferroelectricity in such organic compounds remain limited to a few representative concepts, which has hitherto severely hampered progress in this area. Here, we demonstrate that a bowl-to-bowl inversion of a relatively small organic molecule with a bowl-shaped π-aromatic core generates ferroelectric dipole relaxation. The present results thus reveal an unprecedented concept to produce ferroelectricity in small organic molecules, which can be expected to strongly impact materials science.

Small Organic Molecules for Efficient Singlet Fission: Role of Silicon Substitution

2015 ◽  
Vol 119 (46) ◽  
pp. 25696-25702 ◽  
Author(s):  
Kalishankar Bhattacharyya ◽  
Saied Md Pratik ◽  
Ayan Datta
Keyword(s):  
Organic Molecules ◽  
Singlet Fission ◽  
Small Organic Molecules

scholarly journals Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations

2017 ◽  
Author(s):  
Rafael M. Couñago ◽  
Charles K. Allerston ◽  
Pavel Savitsky ◽  
Hatylas Azevedo ◽  
Paulo H. Godoi ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Related Protein ◽  
Chemical Probes ◽  
Cellular Processes ◽  
Starting Point ◽  
Loop Conformations ◽  
Potential Use ◽  
Specific Inhibitors

ABSTRACTThe human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. However, understanding the cellular role of VRKs and establishing their potential use as targets for therapeutic intervention has been limited by the lack of tool compounds that can specifically modulate the activity of these kinases in cells. Here we identified BI-D1870, a dihydropteridine inhibitor of RSK kinases, as a promising starting point for the development of chemical probes targeting the active VRKs. We solved co-crystal structures of both VRK1 and VRK2 bound to BI-D1870 and of VRK1 bound to two broad-spectrum inhibitors. These structures revealed that both VRKs can adopt a P-loop folded conformation, which is stabilized by different mechanisms on each protein. Based on these structures, we suggest modifications to the dihydropteridine scaffold that can be explored to produce potent and specific inhibitors towards VRK1 and VRK2.

scholarly journals Brief Overview. Role of Computation Biology & Bioinformatics in Drug Design

2020 ◽  
Author(s):  
Ghafran Ali ◽  
kanza Ashfaq
Keyword(s):  
Drug Design ◽  
Organic Molecule ◽  
Organic Molecules ◽  
Clinical Sample ◽  
Research Field ◽  
Target Region ◽  
Small Organic Molecules ◽  
Bioinformatics Tools ◽  
Sample Test

Drug design is used for different applications of bioinformatics tools analyze DNA, genome, and sequence target region of a small organic molecule in order to understand the molecules of disease. Bioinformatics tools are identified a newly wide research field and minimize future risks through web servers and data mining. Clinical sample test performed with the bioinformatics tools as the biomedical detective. A particular structure and configuration of protein obliging in Drug design concluded Bioinformatics. This review bioinformatics tools and webserver will discuss functions of small organic molecules according to clinical pharmacology.

Directions and Perspectives of Political-Economic Studies

2008 ◽  
pp. 27-45
Author(s):  
A. Libman
Keyword(s):  
International Political Economy ◽  
Economic Research ◽  
Economic Power ◽  
Economic Approach ◽  
Policy Studies ◽  
Political Processes ◽  
Economic Methods ◽  
Political Economic ◽  
Economic Studies

The paper surveys the main directions of political-economic research, i.e. variants of economic and political approaches endogenizing political processes in economic models and applying economic methods to policy studies. It analyses different versions of political-economic research in different segments of scientific community: political economics, evolutionary theory of economic policy, international political economy, formal political science and theory of economic power; main methodological assumptions, content and results of positive studies are described. The author also considers the role of political-economic approach in the normative research in economics.

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