scholarly journals Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 480
Author(s):  
Katja Krell ◽  
Hans-Achim Wagenknecht

A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells.

Soft Matter ◽  
2021 ◽  
Author(s):  
Xinxian Ma ◽  
bo qiao ◽  
Jinlong Yue ◽  
JingJing Yu ◽  
yutao geng ◽  
...  

Based on a new designed acyl hydrazone gelator (G2), we developed an efficient energy transfer supramolecular organogel in glycol with two different hydrophobic fluorescent dyes rhodamine B (RhB) and acridine...


2000 ◽  
Vol 20 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Ekaterina I. Dementieva ◽  
Elena A. Fedorchuk ◽  
Lubov Yu. Brovko ◽  
Alexander P. Savitskii ◽  
Natalya N. Ugarova

Fluorescence of luciferases from Luciola mingrelica (single tryptophanresidue, Trp-419) and Photinus pyralis (two tryptophan residues, Trp-417,Trp-426) was studied. Analysis of quenching of tryptophan fluorescenceshowed that the tryptophan residue conserved in all luciferases is notaccessible for charged quenchers, which is explained by the presence ofpositively and negatively charged amino acid residues in the close vicinityto it. An effective energy transfer from tryptophan to luciferin wasobserved during quenching of tryptophan fluorescence of both luciferaseswith luciferin. From the data on the energy transfer, the distance betweenthe luciferin molecule and Trp-417 (419) in the luciferin–luciferasecomplex was calculated: 11–15 Å for P. pyralis and 12–17Å for L. mingrelica luciferases. The role of the conserved Trp residuein the catalysis is discussed.


2020 ◽  
Vol 21 (17) ◽  
pp. 6007
Author(s):  
Chenyu Ma ◽  
Hideyuki Takeuchi ◽  
Huilin Hao ◽  
Chizuko Yonekawa ◽  
Kazuki Nakajima ◽  
...  

Fucosylated glycans critically regulate the physiological functions of proteins and cells. Alterations in levels of fucosylated glycans are associated with various diseases. For detection and functional modulation of fucosylated glycans, chemical biology approaches using fucose (Fuc) analogs are useful. However, little is known about how efficiently each unnatural Fuc analog is utilized by enzymes in the biosynthetic pathway of fucosylated glycans. We show here that three clickable Fuc analogs with similar but distinct structures labeled cellular glycans with different efficiency and protein specificity. For instance, 6-alkynyl (Alk)-Fuc modified O-Fuc glycans much more efficiently than 7-Alk-Fuc. The level of GDP-6-Alk-Fuc produced in cells was also higher than that of GDP-7-Alk-Fuc. Comprehensive in vitro fucosyltransferase assays revealed that 7-Alk-Fuc is commonly tolerated by most fucosyltransferases. Surprisingly, both protein O-fucosyltransferases (POFUTs) could transfer all Fuc analogs in vitro, likely because POFUT structures have a larger space around their Fuc binding sites. These findings demonstrate that labeling and detection of fucosylated glycans with Fuc analogs depend on multiple cellular steps, including conversion to GDP form, transport into the ER or Golgi, and utilization by each fucosyltransferase, providing insights into design of novel sugar analogs for specific detection of target glycans or inhibition of their functions.


2020 ◽  
Vol 89 (1) ◽  
pp. 529-555 ◽  
Author(s):  
Rebecca M. Sebastian ◽  
Matthew D. Shoulders

Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology–informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.


2018 ◽  
Vol 9 ◽  
pp. 117959721878108 ◽  
Author(s):  
David Tes ◽  
Karl Kratkiewicz ◽  
Ahmed Aber ◽  
Luke Horton ◽  
Mohsin Zafar ◽  
...  

Alzheimer disease is the most common form of dementia, affecting more than 5 million people in the United States. During the progression of Alzheimer disease, a particular protein begins to accumulate in the brain and also in extensions of the brain, ie, the retina. This protein, amyloid-β (Aβ), exhibits fluorescent properties. The purpose of this research article is to explore the implications of designing a fluorescent imaging system able to detect Aβ proteins in the retina. We designed and implemented a fluorescent imaging system with a range of applications that can be reconfigured on a fluorophore to fluorophore basis and tested its feasibility and capabilities using Cy5 and CRANAD-2 imaging probes. The results indicate a promising potential for the imaging system to be used to study the Aβ biomarker. A performance evaluation involving ex vivo and in vivo experiments is planned for future study.


Polymers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1353
Author(s):  
Natalia Lopez-Barbosa ◽  
Ana Lucía Campaña ◽  
Juan C. Cruz ◽  
Nancy Ornelas-Soto ◽  
Johann F. Osma

Polymeric microcapsules with the fungal laccase from Pycnoporus sanguineus CS43 may represent an attractive avenue for the removal or degradation of dyes from wastewaters. Microcapsules of alginate/chitosan (9.23 ± 0.12 µm) and poly(styrenesulfonate) (PSS) (9.25 ± 0.35 µm) were synthesized and subsequently tested for catalytic activity in the decolorization of the diazo dye Congo Red. Successful encapsulation into the materials was verified via confocal microscopy of labeled enzyme molecules. Laccase activity was measured as a function of time and the initial reaction rates were recovered for each preparation, showing up to sevenfold increase with respect to free laccase. The ability of substrates to diffuse through the pores of the microcapsules was evaluated with the aid of fluorescent dyes and confocal microscopy. pH and thermal stability were also measured for encapsulates, showing catalytic activity for pH values as low as 4 and temperatures of about 80 °C. Scanning electron microscope (SEM) analyses demonstrated the ability of PSS capsules to avoid accumulation of byproducts and, therefore, superior catalytic performance. This was corroborated by the direct observation of substrates diffusing in and out of the materials. Compared with our PSS preparation, alginate/chitosan microcapsules studied by others degrade 2.6 times more dye, albeit with a 135-fold increase in units of enzyme per mg of dye. Similarly, poly(vinyl) alcohol microcapsules from degrade 1.7 times more dye, despite an eightfold increase in units of enzyme per mg of dye. This could be potentially beneficial from the economic viewpoint as a significantly lower amount of enzyme might be needed for the same decolorization level achieved with similar encapsulated systems.


2007 ◽  
Vol 13 (3) ◽  
pp. 349-355 ◽  
Author(s):  
Belén Fernández ◽  
Natividad Gálvez ◽  
Purificación Sánchez ◽  
Rafael Cuesta ◽  
Ruperto Bermejo ◽  
...  

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3905-3905
Author(s):  
Bin Li ◽  
Matthew Pagni ◽  
Justin Cates ◽  
D. Brent Polk ◽  
Pampee P. Young

Abstract Whereas in many contexts myeloid cells are cytotoxic, it is well-established that as yet unknown microenvironment cues instruct the infiltrating tumor associated myeloid cells (TAMs) to drive malignant progression and dissemination. Recently, we and others have characterized a significant subpopulation of tumor associated myeloid cells that co-express endothelial and myeloid markers designated “vascular leukocytes”. Studies suggest that vascular leukocytes play an important role in tumor progression and also demonstrate modest contribution to functional vessels, i.e. vasculogenesis, suggesting that they represent a critical tumor-promoting TAM subpopulation. We have identified TNFα as a key regulator of the vascular transdifferentiation of myeloid progenitors in vitro and within the tumor milieu. TNFα at 40ng/ml significantly increased the numbers of flk-1/VE-cadherin dual positive, early outgrowth EPCs from human CD14+ cells by day 7 (about five fold of the control), starting with increased spindle-shaped population appeared as early as day 3. Consistent with this, we observed increased flk-1 expression by ∼9-fold (p<0.05) in cells treated with 40ng/ml TNFα by real time RT-PCR. Transcripts for VE-cadherin and tie2, both endothelial-enriched, were detected by day 3 in cells exposed to 40ng/ml TNFa but not in its absence (control). TNFα-directed upregulation of endothelial markers in mouse monocytes in vitro was dependent on TNFα receptors as monocytes isolated from mice lacking both TNF receptors displayed significantly delayed endothelial marker upregulation. These data suggested that TNF was a component of the molecular pathway that accelerated, but was not required for, endothelial transdifferentiation of murine and human myeloid cells. Enhanced TNFα expression in both B16 murine melanoma and PyV-mT tumor showed local TNFα significantly promoted tumor growth versus control (>5-fold increase for B16 tumor, p=0.04; >8-fold increase for PyV-mT tumor, p<0.01). Both tumor models indicated that overexpressing TNFα caused higher vascular density over control, while tumor necrosis was significantly reduced. Additionally, we observed increased bone marrow-derived vessels (vasculogenesis) in mouse TNFα-overexpressing tumors, which can be specifically inhibited by an anti-TNFα blocking antibody. A significant increase in association of vascular leukoctyes was detected in tumors overexpressing TNFα by FACs, which was abrogated in the mice lacking TNF receptors. Interestingly, TNF-overexpressing tumors did not recruit greater overall numbers of tumor-associated (myeloid or lymphoid) leukocytes, suggesting a specific role in myeloid to endothelial transdifferentiation in vivo. Our studies suggest that TNFα constitutes part of the microenvironment repertoire that biases recruited myeloid cells towards a proangiogenic/provasculogenic phenotype.


Sign in / Sign up

Export Citation Format

Share Document