Properties of the single protein and two nucleic acids of tomato ring-spot virus

1977 ◽  
Vol 55 (8) ◽  
pp. 1028-1037 ◽  
Author(s):  
Wayne R. Allen ◽  
H. F. Dias
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Gel Electrophoresis ◽  
Average Molecular Weight ◽  
Virus Genome ◽  
Protein Subunit ◽  
Spot Virus ◽  
Single Protein ◽  
Middle Component ◽  
Ring Spot

Purified preparations of several isolates of tomato ring-spot virus were shown by rate-zonal centrifugation in sucrose and equilibrium centrifugation in CsCl to be composed of two individual nucleoprotein components. Acrylamide-gel electrophoresis showed that the lighter (middle) component contained a nucleic acid (RNA 2) that was distinct from the species (RNA 1) contained in the heavier (bottom) component. The bottom was more infectious than the middle component and infectivity was enhanced by mixing the components, indicating that the virus genome is divided between component types. Similar results were obtained from infectivity tests on the two nucleic acids. The nucleic acid contents of the middle and bottom components were about 40 and 41%, respectively. The average molecular weights of RNA 2 and RNA 1 from three virus isolates, as determined by acrylamide-gel electrophoresis, were 2.5 and 2.6 × 106, respectively. Molecular complexing between the RNA species during electrophoresis was prevented with the use of formamide. The single protein subunit from the same three isolates had an average molecular weight of about 58 000. Serological comparisons of five tomato ring-spot isolates associated with diseases of fruit trees and grapevines indicated that only the grape yellow vein strain was antigenically distinct. These and other properties indicate that this virus is similar to other members of the nepovirus group.

Characterization of the single protein and two nucleic acids of peach rosette mosaic virus

1980 ◽  
Vol 58 (16) ◽  
pp. 1747-1754 ◽  
Author(s):  
H. F. Dias ◽  
W. R. Allen
Keyword(s):  
Mosaic Virus ◽  
Nucleotide Composition ◽  
Temperature Transition ◽  
Protein Subunit ◽  
Spot Virus ◽  
Molecular Weights ◽  
Single Protein ◽  
Ring Spot ◽  
Equilibrium Centrifugation

Purified preparations of peach rosette mosaic virus (PRMV), were shown by rate-zonal centrifugation in sucrose and equilibrium centrifugation in CsCl to be composed of two nucleoprotein components with buoyant densities of 1.47 (middle) and 1.51 (bottom) g/cm3. The virus contains two RNA species with molecular weights of 2.5 × 106 (RNA 1) and 2.2 × I06 (RNA 2), and a single protein subunit with a molecular weight of 57 000. RNA 1 and RNA 2 reside separately in components B and M, respectively. Both RNAs are required for infection thus indicating that the virus has a divided genome. The nucleotide composition of both RNAs is similar except for cytidilic acid. The hyperchromic profile for the M component is broader than that of B and the Tm value is higher (for M Tm = 55 °C; for B Tm = 48 °C). Particle disruption and release of RNA progresses slowly over the absorbance–temperature transition. Only half of the particles were dissociated at the Tm value. Freezing dissociates most of M component into RNA 2 and protein but had no effect on the B component. Sodium chloride protected the M particles from low temperature disruption. The data support the conclusion that PRMV is a nepovirus with particular properties of the tomato ring-spot virus (TomRSV) subgroup.

Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis

2005 ◽  
Vol 43 (8) ◽  
Author(s):  
Qing Huang ◽  
Wei-Ling Fu
Keyword(s):  
Comparative Analysis ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Ethidium Bromide ◽  
Gel Electrophoresis ◽  
Fluorescent Dyes ◽  
Agarose Gel ◽  
Agarose Gel Electrophoresis ◽  
Dna Staining

AbstractEthidium bromide (EB) is a mutagen and toxin that is widely used in the laboratory for visualization of nucleic acids. Safer nucleic acid stains, such as SYBR

Recovery of the Nucleic Acids of Tobacco Mosaic and Potato X Viruses from Polyacrylamide Gel and Evidence for a Single Infectious Component in Each of the Two Viruses

1973 ◽  
Vol 28 (9-10) ◽  
pp. 618-625 ◽  
Author(s):  
Satyabrata Sarkar
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Tobacco Mosaic Virus ◽  
Ribonucleic Acid ◽  
Gel Electrophoresis ◽  
Glass Tube ◽  
Polyacrylamide Gel ◽  
Biologically Active ◽  
Viral Rnas ◽  
Infectivity Assay

Abstract RNA, tobacco mosaic virus, potato X virus, gel-electrophoresis, infectivity A simple device is standardised for the elution of biologically active ribonucleic acid from polyacrylamide gel after electrophoresis. The pieces of gel containing the nucleic acid to be re­ covered are held in position by two short cylinders of foam rubber in a glass tube and the nucleic acid is concentrated over a sucrose-containing buffer layer by electrophoresis in a standard electro­ phoretic equipment. Using this method nucleic acids can be recovered undamaged almost quanti­ tatively, as shown for microgram quantities of two viral RNAs by infectivity assay. The results offer additional experimental support to the single-component character of tobacco mosaic and potato X viruses.

scholarly journals A lab-on-a-chip for preconcentration of bacteria and nucleic acid extraction

RSC Advances ◽  
2018 ◽  
Vol 8 (36) ◽  
pp. 20124-20130 ◽  
Author(s):  
M. Hügle ◽  
G. Dame ◽  
O. Behrmann ◽  
R. Rietzel ◽  
D. Karthe ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Gel Electrophoresis ◽  
Lab On A Chip ◽  
Free Flow ◽  
Acid Extraction ◽  
Nucleic Acid Extraction

A lab-on-a-chip combining free-flow electrophoretic preconcentration and thermoelectric lysis of bacteria as well as purification of nucleic acids by gel-electrophoresis.

Nucleic Acid Molecules Prepared by Monolayer Techniques

1972 ◽  
Vol 30 ◽  
pp. 178-179
Author(s):  
Dimitrij Lang
Keyword(s):  
Electron Microscopy ◽  
Standard Deviation ◽  
Nucleic Acid ◽  
Cytochrome C ◽  
Nucleic Acids ◽  
Contour Length ◽  
Sample Standard Deviation ◽  
Molecular Weights ◽  
Length Measurements ◽  
Protein Monolayer

The success of the protein monolayer technique for electron microscopy of individual DNA molecules is based on the prevention of aggregation and orientation of the molecules during drying on specimen grids. DNA adsorbs first to a surface-denatured, insoluble cytochrome c monolayer which is then transferred to grids, without major distortion, by touching. Fig. 1 shows three basic procedures which, modified or not, permit the study of various important properties of nucleic acids, either in concert with other methods or exclusively:1) Molecular weights relative to DNA standards as well as number distributions of molecular weights can be obtained from contour length measurements with a sample standard deviation between 1 and 4%.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

The Analyst ◽  
2021 ◽  
Author(s):  
Qingteng Lai ◽  
Wei Chen ◽  
Yanke Zhang ◽  
Zheng-Chun Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acids ◽  
Dna Probes ◽  
Highly Sensitive ◽  
Increased Sensitivity ◽  
Acid Sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensor due to their higher stability and increased sensitivity than common DNA probes....

scholarly journals Validating DNA Extraction Protocols for Bentonite Clay

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Katja Engel ◽  
Sara Coyotzi ◽  
Melody A. Vachon ◽  
Jennifer R. McKelvie ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Community ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Bentonite Clay ◽  
Dna Recovery ◽  
Blocking Agents ◽  
Clay Matrix ◽  
Microbial Dna

ABSTRACT Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material “spiked” with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination. IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

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