skip to main content

Title: Bio-orthogonal chemistry-based method for fluorescent labelling of ribosomal RNA in live mammalian cells
A bio-orthogonal chemistry-based approach for fluorescent labelling of ribosomal RNA is described. It involves an adenosine analogue modified with trans -cyclooctene and masked 5′-phosphate group using aryl phosphoramidate. The incorporation into rRNA has been confirmed using agarose gel electrophoresis, as well as a highly sensitive UHPLC-MS/MS method. Fluorescent labelling of rRNA has been achieved in live HeLa cells via an inverse electron demand Diels–Alder reaction with a tetrazine conjugated to an Oregon Green fluorophore. This communication describes the stepwise approach that led to the development and characterization of the probe. The results demonstrate a new strategy towards development of future fluorescent probes to investigate the biochemistry of nucleic acids.  more » « less
Award ID(s):
1726724 1664577
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Chemical Communications
Page Range / eLocation ID:
10456 to 10459
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and microbes in the “Plastisphere”—the thin layer of life on the surface of PMD—has been technology‐limited. Research into microbe–microbe and microbe–substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling and spectral imaging – fluorescencein situhybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria,Alpha‐, andGammaproteobacteria) and four newly designed probes (targetingBacteroidetes,Vibrionaceae,RhodobacteraceaeandAlteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell‐count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro‐metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales.

    more » « less
  2. Chemically functional hydrogel microspheres hold significant potential in a range of applications including biosensing, drug delivery, and tissue engineering due to their high degree of flexibility in imparting a range of functions. In this work, we present a simple, efficient, and high-throughput capillary microfluidic approach for controlled fabrication of monodisperse and chemically functional hydrogel microspheres via formation of double emulsion drops with an ultra-thin oil shell as a sacrificial template. This method utilizes spontaneous dewetting of the oil phase upon polymerization and transfer into aqueous solution, resulting in poly(ethylene glycol) (PEG)-based microspheres containing primary amines (chitosan, CS) or carboxylates (acrylic acid, AA) for chemical functionality. Simple fluorescent labelling of the as-prepared microspheres shows the presence of abundant, uniformly distributed and readily tunable functional groups throughout the microspheres. Furthermore, we show the utility of chitosan's primary amine as an efficient conjugation handle at physiological pH due to its low pKa by direct comparison with other primary amines. We also report the utility of these microspheres in biomolecular conjugation using model fluorescent proteins, R-phycoerythrin (R-PE) and green fluorescent protein (GFPuv), via tetrazine– trans -cyclooctene (Tz–TCO) ligation for CS-PEG microspheres and carbodiimide chemistry for AA-PEG microspheres, respectively. The results show rapid coupling of R-PE with the microspheres' functional groups with minimal non-specific adsorption. In-depth protein conjugation kinetics studies with our microspheres highlight the differences in reaction and diffusion of R-PE with CS-PEG and AA-PEG microspheres. Finally, we demonstrate orthogonal one-pot protein conjugation of R-PE and GFPuv with CS-PEG and AA-PEG microspheres via simple size-based encoding. Combined, these results represent a significant advancement in the rapid and reliable fabrication of monodisperse and chemically functional hydrogel microspheres with tunable properties. 
    more » « less
  3. null (Ed.)
    Element-calcium ratios in the skeleton of cold-water coral Desmophyllum dianthus represent potential archives for paleo-reconstruction of several ocean properties including temperature and nutrient concentrations. However, relatively large uncertainties in these proxy calibrations and heterogeneity in the skeletal composition have limited its application to date. We address these issues by analyzing corals cultured under systematically varied seawater conditions (phosphate, barium, temperature, pH, feeding frequency) over a two-year period, and refine the calibration of P/Ca, Ba/Ca, U/Ca, and Li/Mg proxies for seawater phosphate, barium, carbonate ion concentration, and temperature, respectively. Composition of the corals is determined using laser-ablation ICPMS, with robust plasma conditions established using the Normalized Argon Index [1], and proxy element incorporation is evaluated for influences of temperature, pH, and feeding frequency. The aragonite precipitated during the stages of the culturing experiment is identified using fluorescent and geochemical labelling of the skeleton through calcein and lead isotopes, respectively. This approach allows us to resolve monthly and annual increments in these slow growing (1-2mm/year) organisms, and also to evaluate the influence of calcification rate on the composition. We address the issue of heterogeneity by adapting methods for LA-ICPMS imaging to create macroscale images to reveal the full pattern of skeletogenesis and related compositional variability of D. dianthus. Preliminary images suggest that heterogeneity stems from the asymmetric precipitation of aragonite, and from centers of calcification (also known as early mineralization zones) that complicate the interpretation of elemental signals throughout the skeleton, but also help to identify new skeletal regions suitable for proxy measurement. Finally, we also discuss the role of endolithic organisms in some of these specimens. [1] Fietzke, J. & Frische, M. (2016), J. Anal. At. Spectrom. 31, 234–244. 
    more » « less
  4. We report the development of in vitro propagation protocols through an adventitious shoot induction pathway for a rare and medicinal Scutellaria havanensis. In vitro propagation studies using nodal explants showed MS medium supplemented with 10 µM 6-Benzylaminopurine induced the highest number of adventitious shoots in a time-dependent manner. A ten-day incubation was optimum for shoot bud induction as longer exposures resulted in hyperhydricity of the explants and shoots induced. We also report preliminary evidence of Agrobacterium tumefaciens EHA105-mediated gene transfer transiently expressing the green fluorescent protein in this species. Transformation studies exhibited amenability of various explant tissues, internode being the most receptive. As the plant has medicinal value, research was carried out to evaluate its potential antioxidant capacity and the efficacy of methanolic leaf extracts in curbing the viability of human colorectal cancer cell line HCT116. Comparative total polyphenol and flavonoid content measurement of fresh and air-dried leaf extract revealed that the fresh leaf extracts contain higher total polyphenol and flavonoid content. The HCT 116 cell viability was assessed by colorimetric assay using a 3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide, showed a steady growth inhibition after 24 h of incubation. Scanning electron microscopy of leaf surface revealed a high density of glandular and non-glandular trichomes. This research provides a basis for the conservation of this rare plant and future phytochemical screening and clinical research. 
    more » « less
  5. Plastics have long been an environmental contaminant of concern as both large-scale plastic debris and as micro- and nano-plastics with demonstrated wide-scale ubiquity. Research in the past decade has focused on the potential toxicological risks posed by microplastics, as well as their unique fate and transport brought on by their colloidal nature. These efforts have been slowed by the lack of analytical techniques with sufficient sensitivity and selectivity to adequately detect and characterize these contaminants in environmental and biological matrices. To improve analytical analyses, microplastic tracers are developed with recognizable isotopic, metallic, or fluorescent signatures capable of being identified amidst a complex background. Here we describe the synthesis, characterization, and application of a novel synthetic copolymer nanoplastic based on polystyrene (PS) and poly(2-vinylpyridine) (P2VP) intercalated with gold, platinum or palladium nanoparticles that can be capped with different polymeric shells meant to mimic the intended microplastic. In this work, particles with PS and polymethylmethacrylate (PMMA) shells are used to examine the behavior of microplastic particles in estuarine sediment and coastal waters. The micro- and nanoplastic tracers, with sizes between 300 and 500 nm in diameter, were characterized using multiple physical, chemical, and colloidal analysis techniques. The metallic signatures of the tracers allow for quantification by both bulk and single-particle inductively-coupled plasma mass spectrometry (ICP-MS and spICP-MS, respectively). As a demonstration of environmental applicability, the tracers were equilibrated with sediment collected from Bellingham Bay, WA, United States to determine the degree to which microplastics bind and sink in an estuary based of grain size and organic carbon parameters. In these experiments, between 80 and 95% of particles were found to associate with the sediment, demonstrative of estuaries being a major anticipated sink for these contaminants. These materials show considerable promise in their versatility, potential for multiplexing, and utility in studying micro- and nano-plastic transport in real-world environments. 
    more » « less