Visualization of DNA and RNA Molecules, and Protein-DNA Complexes for Electron Microscopy

2000 ◽  
Vol 15 (2) ◽  
pp. 167-184 ◽  
Author(s):  
M.A. Nasser Hajibagheri
Author(s):  
Ruchama Baum ◽  
J.T. Seto

The ribonucleic acid (RNA) of paramyxoviruses has been characterized by biochemical and physiochemical methods. However, paramyxovirus RNA molecules have not been studied by electron microscopy. The molecular weights of these single-stranded viral RNA molecules are not known as yet. Since electron microscopy has been found to be useful for the characterization of single-stranded RNA, this investigation was initiated to examine the morphology and length measurements of paramyxovirus RNA's.Sendai virus Z strain and Newcastle disease virus (NDV), Milano strain, were used. For these studies it was necessary to develop a method of extracting RNA molecules from purified virus particles. Highly purified Sendai virus was treated with pronase (300 μg/ml) at 37°C for 30 minutes and the RNA extracted by the sodium dodecyl sulfate (SDS)-phenol procedure.


Parasitology ◽  
1990 ◽  
Vol 101 (2) ◽  
pp. 163-169 ◽  
Author(s):  
J. Ellis ◽  
H. Revets

There is increasing support for the presence of viruses and virus-like particles inside protozoan cells. This study describes viral-like RNA molecules that have been detected in two species of Eimeria that infect the chicken. The RNA molecule identified in E. maxima has been characterized: subcellular fractionation studies have shown that the RNA is present in the cytoplasm, probably as an abundant ribonucleoprotein that is insensitive to RNAse A treatment. Electron microscopy has demonstrated that this RNA molecule is double stranded. In addition, all E. maxima strains examined so far contain this RNA molecule.


1992 ◽  
Vol 5 (2) ◽  
pp. 193-207 ◽  
Author(s):  
Yuri Y. Vengerov ◽  
Timur E. Semenov

2021 ◽  
Vol 22 (22) ◽  
pp. 12215
Author(s):  
Francisco Javier Manzano-Moreno ◽  
Victor J. Costela-Ruiz ◽  
Enrique García-Recio ◽  
Maria Victoria Olmedo-Gaya ◽  
Concepción Ruiz ◽  
...  

Oral squamous cell carcinoma (OSCC) is the most prevalent oral malignant tumor worldwide. An early diagnosis can have a major positive impact on its prognosis. Human saliva contains cytokines, DNA and RNA molecules, circulating cells, and derivatives of tissues and extracellular vesicles, among other factors that can serve as biomarkers. Hence, the analysis of saliva may provide useful information for the early diagnosis of OSCC for its prognosis. The objective of this review was to determine the potential usefulness of salivary biomarkers (cytokines and microRNA) to diagnose OSCC and improve its prognosis. A combination of salivary miRNA and proteomic data could allow a definitive and early diagnosis to be obtained. However, there remains a need to optimize and standardize the protocols used to quantify miRNAs.


2012 ◽  
Vol 66 (3-4) ◽  
pp. 273-283
Author(s):  
Jelka Stevanovic ◽  
Suncica Borozan ◽  
Tatjana Bozic ◽  
Slavoljub Jovic ◽  
Tatjana Djekic ◽  
...  

The unceasing need for oxygen is in contradiction to the fact that it is in fact toxic to mammals. Namely, its monovalent reduction can have as a consequence the production of short-living, chemically very active free radicals and certain non-radical agents (nitrogen-oxide, superoxide-anion-radicals, hydroxyl radicals, peroxyl radicals, singlet oxygen, peroxynitrite, hydrogen peroxide, hypochlorous acid, and others). There is no doubt that they have numerous positive roles, but when their production is stepped up to such an extent that the organism cannot eliminate them with its antioxidants (superoxide-dismutase, glutathione-peroxidase, catalase, transferrin, ceruloplasmin, reduced glutathion, and others), a series of disorders is developed that are jointly called ?oxidative stress.? The reactive oxygen species which characterize oxidative stress are capable of attacking all main classes of biological macromolecules, actually proteins, DNA and RNA molecules, and in particular lipids. The free radicals influence lipid peroxidation in cellular membranes, oxidative damage to DNA and RNA molecules, the development of genetic mutations, fragmentation, and the altered function of various protein molecules. All of this results in the following consequences: disrupted permeability of cellular membranes, disrupted cellular signalization and ion homeostasis, reduced or loss of function of damaged proteins, and similar. That is why the free radicals that are released during oxidative stress are considered pathogenic agents of numerous diseases and ageing. The type of damage that will occur, and when it will take place, depends on the nature of the free radicals, their site of action and their source.


2020 ◽  
Vol 21 (1) ◽  
pp. 81-100 ◽  
Author(s):  
Grzegorz Kudla ◽  
Yue Wan ◽  
Aleksandra Helwak

RNA proximity ligation is a set of molecular biology techniques used to analyze the conformations and spatial proximity of RNA molecules within cells. A typical experiment starts with cross-linking of a biological sample using UV light or psoralen, followed by partial fragmentation of RNA, RNA–RNA ligation, library preparation, and high-throughput sequencing. In the past decade, proximity ligation has been used to study structures of individual RNAs, networks of interactions between small RNAs and their targets, and whole RNA–RNA interactomes, in models ranging from bacteria to animal tissues and whole animals. Here, we provide an overview of the field, highlight the main findings, review the recent experimental and computational developments, and provide troubleshooting advice for new users. In the final section, we draw parallels between DNA and RNA proximity ligation and speculate on possible future research directions.


Author(s):  
P. Serwer

To package the DNA of bacteriophage T7, a preformed, DNA-free capsid (capsid I) with an envelope thicker than the envelope of bacteriophage T7:(a) binds DNA, (b) converts to a capsid (capsid II) with a bacteriophage-like envelope prior to packaging DNA and (c) draws in DNA (1). During attempts to understand T7 DNA packaging, complexes of capsids with mature T7 DNA and complexes of capsids with longer than mature, linear T7 DNA have been isolated (2). Objects with capsid-like dimensions were observed on a fast sedimenting, replicating complex of T7 DNA (100S+ DNA) prepared for electron microscopy using a protein monolayer-shadowing technique (3). This procedure for preparation of specimens does not, however, reveal sufficient detail to rigorously identify an object as a capsid. To better visualize objects bound to 100S+ T7 DNA, this DNA has been prepared for electron microscopy using the aqueous technique for the negative staining of capsid-DNA complexes more recently described (4) (the DNA is coated with cytochrome c and is revealed in an extended configuration).


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