scholarly journals Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps

2013 ◽  
Vol 117 (14) ◽  
pp. 3738-3746 ◽  
Author(s):  
Harish Vashisth ◽  
Georgios Skiniotis ◽  
Charles L. Brooks
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Enhanced Sampling ◽  
Structural Refinement

Electron Microscopy of Nucleic Acids

1974 ◽  
Vol 32 ◽  
pp. 302-303
Author(s):  
Norman Davidson
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Basic Protein ◽  
Molecular Biologist ◽  
Topological Properties ◽  
Protein Film ◽  
Polynucleotide Chain

The basic protein film technique for mounting nucleic acids for electron microscopy has proven to be a general and powerful tool for the working molecular biologist in characterizing different nucleic acids. It i s possible to measure molecular lengths of duplex and single-stranded DNAs and RNAs. In particular, it is thus possible to as certain whether or not the nucleic acids extracted from a particular source are or are not homogeneous in length. The topological properties of the polynucleotide chain (linear or circular, relaxed or supercoiled circles, interlocked circles, etc. ) can also be as certained.

mRNA localization by Electron microscopic in situ hybridization

1991 ◽  
Vol 49 ◽  
pp. 430-431
Author(s):  
J. A. Pollock ◽  
M. Martone ◽  
T. Deerinck ◽  
M. H. Ellisman
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Nucleic Acids ◽  
Recombinant Dna ◽  
Light And Electron Microscopy ◽  
Electron Microscopic ◽  
High Voltage Electron Microscopy ◽  
Functional Sites ◽  
Voltage Electron

Localization of specific proteins in cells by both light and electron microscopy has been facilitate by the availability of antibodies that recognize unique features of these proteins. High resolution localization studies conducted over the last 25 years have allowed biologists to study the synthesis, translocation and ultimate functional sites for many important classes of proteins. Recently, recombinant DNA techniques in molecular biology have allowed the production of specific probes for localization of nucleic acids by “in situ” hybridization. The availability of these probes potentially opens a new set of questions to experimental investigation regarding the subcellular distribution of specific DNA's and RNA's. Nucleic acids have a much lower “copy number” per cell than a typical protein, ranging from one copy to perhaps several thousand. Therefore, sensitive, high resolution techniques are required. There are several reasons why Intermediate Voltage Electron Microscopy (IVEM) and High Voltage Electron Microscopy (HVEM) are most useful for localization of nucleic acids in situ.

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%.

Ultrastructural analysis of the spatial distribution of MRNA

1992 ◽  
Vol 50 (1) ◽  
pp. 552-553
Author(s):  
Gary Bassell ◽  
Robert H. Singer
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Nucleic Acids ◽  
Colloidal Gold ◽  
Dna Probe ◽  
Nucleotide Analogs ◽  
Gold Particles

We have been investigating the spatial distribution of nucleic acids intracellularly using in situ hybridization. The use of non-isotopic nucleotide analogs incorporated into the DNA probe allows the detection of the probe at its site of hybridization within the cell. This approach therefore is compatible with the high resolution available by electron microscopy. Biotinated or digoxigenated probe can be detected by antibodies conjugated to colloidal gold. Because mRNA serves as a template for the probe fragments, the colloidal gold particles are detected as arrays which allow it to be unequivocally distinguished from background.

Aerosol Synthesis of Pure and Pt-Doped ZnO Particles Using Nitrate and Pdda-Pt(IV) Complex Solutions

2005 ◽  
Vol 20 (1) ◽  
pp. 102-113 ◽  
Author(s):  
Vesna M. Djinovic ◽  
Lidija T. Mancic ◽  
Goran A. Bogdanovic ◽  
Predrag J. Vulic ◽  
Gilberto del Rosario ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Diffraction ◽  
Complex Structure ◽  
Structural Refinement ◽  
Cell Parameters ◽  
Jcpds Card ◽  
Selected Area Electron Diffraction ◽  
Primary Particles ◽  
Zno Particles ◽  
Doped Zno

Pure and Pt-doped ZnO nanophase particles were synthesized by ultrasonic spray pyrolysis. The particles were obtained through the decomposition of zinc nitrate and with a newly developed Pt(IV) complex with 1,3-propylenediamine-N,N′-diacetate tetradentate class ligand (pdda). The complex was characterized by elemental analysis, electronic absorption and infrared spectroscopy. The form of the determined complex structure {trans-[Pt(pdda)Br2]·H2O} implies that Pt(IV) ion has a distorted octahedral coordination due to intramolecular N–H···Br interaction. The results of structural refinement (cell parameters, bond lengths, and ion occupancy) of ultrasonically derived pure and Pt-doped ZnO particles suggest either the formation of Zni interstitials or platinum ion incorporation into the ZnO lattice in octahedral interstitial positions, respectively. A well-crystallized hexagonal wurtzite structure of ZnO was pronounced in all investigated samples [JCPDS card 36-1415, Joint Committee on Powder Diffraction Standards, defined by International Centre for Diffraction Data (www.icdd.com)]. Phase determination also indicated the presence of a nitrate hydroxide hydrate phase (JCPDS card 24-1460), as a result of incomplete precursor decomposition and a spinel Zn2PtO4 phase (below 1.0 wt%) located in the boundary region for a Pt-doped ZnO sample. Based on x-ray diffraction, scanning electron microscopy, and energy-dispersive spectroscopy analyses, it was shown that the different particle growingmorphologies, which were either spheroidally or pyramidally shaped, were influenced by the precursor chemistry, processing parameters and the presence of platinum ions. The composite internal particle structure revealed by transmission electron microscopy and selected area electron diffraction analyses, implied that the secondary particles represent an assembly of primary particles sized under 60 nm aroused during the processes of nucleation, growth and aggregation. Both hexagonal and spheroidal shape of primary particles was evident. The particle morphology, primarily particle size and the mechanism of Pt4+ ion introduction into the ZnO cell was discussed based on the structural refinement and selected area electron diffraction analysis.

scholarly journals Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus

2020 ◽  
Vol 94 (24) ◽  
Author(s):  
Álvaro Ortega-Esteban ◽  
Carlos P. Mata ◽  
María J. Rodríguez-Espinosa ◽  
Daniel Luque ◽  
Nerea Irigoyen ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Atomic Force Microscopy ◽  
Nucleic Acids ◽  
Capsid Protein ◽  
Cycle Phase ◽  
Human Virus ◽  
Double Stranded Rna ◽  
Force Microscopy ◽  
Atomic Force ◽  
Cryo Electron Microscopy

ABSTRACT Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an in vitro reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo. IMPORTANCE Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans.

Monospecific Antibody against 5-Methyl-Cytidine for the Structural Analysis of Nucleic Acids

1982 ◽  
Vol 37 (5-6) ◽  
pp. 399-404
Author(s):  
Sofia K. Mastronicolis ◽  
Vassilios M. Kapoulas ◽  
Hans Kröger
Keyword(s):  
Electron Microscopy ◽  
Nucleic Acids ◽  
Density Gradient ◽  
Cross Linking ◽  
Density Gradient Ultracentrifugation ◽  
Disk Electrophoresis ◽  
Detection And Localization ◽  
Hydrolysis Of ◽  
Gel Diffusion ◽  
Drop Technique

Abstract Anti 5-methyl-cytidine antibodies might be useful agents for the detection and localization of 5-methyl-cytidine of nucleic acids, but only if the antibodies recognize this nucleoside with sufficient specificity. A conjugate containing 18 moles of 5-methyl-cytidine per mole of BSA was prepared and antibodies directed against this nucleoside hapten were produced by immunization of rabbits (as determined by gel diffusion in agar containing excessive amounts of the carrier). A slight crossreaction of cytidine-BSA was eliminated by adsorption on the cross-reacting antigen. Further purification of the antibodies was effected by chromatography on DEAE-Sephadex A-50 and a method for the rapid quantitation of the antibodies showed that 12.7% of the IgG protein are monospecific against 5-methyl-cytidine-BSA. Hydrolysis of antibodies with insolubilized pa­pain produced monovalent Fab fragments which were identified by SDS-Disk-electrophoresis. A two stage method for cross linking the immunoproteins to ferritin by glutaraldehyde was used. The isolation of immunoferritin conjugates by Bio-Gel A 1.5 m column chromatography is described. The identification of the effluents was made by glycerin density gradient ultracentrifugation. The results were visualized by electron microscopy after the treatment of immunoferritin conjugates with (methylated and unmethylated) denaturated DNA, fractionation on the glycerine density gradient, and the spreading by a modification of drop technique.

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