Schematic diagrams of nucleic acids and protein–nucleic acid complexes

1989 ◽  
Vol 22 (6) ◽  
pp. 569-571 ◽  
Author(s):  
V. I. Lesk ◽  
A. M. Lesk
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Complex Structures ◽  
Acid Complex ◽  
Protein Nucleic Acid ◽  
Schematic Diagrams

Simplified representations of components of nucleic acids have been designed and implemented as programs integrated with other software that draws schematic diagrams of proteins. Examples illustrating the structures of oligonucleotides, tRNA and a protein–nucleic acid complex indicate the utility of these representations for making intelligible illustrations of complex structures containing nucleic acids.

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.

Covalent Binding of Modified Nucleic Acids to Proteins as a Method for Investigation of Specific Protein—Nucleic Acid Interactions

ChemInform ◽  
2005 ◽  
Vol 36 (28) ◽  
Author(s):  
T. S. Zatsepin ◽  
N. G. Dolinnaya ◽  
E. A. Kubareva ◽  
M. G. Ivanovskaya ◽  
V. G. Metelev ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Covalent Binding ◽  
Specific Protein ◽  
Modified Nucleic Acids ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Covalent binding of modified nucleic acids to proteins as a method for investigation of specific protein–nucleic acid interactions

2005 ◽  
Vol 74 (1) ◽  
pp. 77-95 ◽  
Author(s):  
Timofei S Zatsepin ◽  
N G Dolinnaya ◽  
Elena A Kubareva ◽  
Marina G Ivanovskaya ◽  
V G Metelev ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Covalent Binding ◽  
Specific Protein ◽  
Modified Nucleic Acids ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

NuProPlot: nucleic acid and protein interaction analysis and plotting program

2015 ◽  
Vol 71 (3) ◽  
pp. 667-674 ◽  
Author(s):  
Lagnajeet Pradhan ◽  
Hyun-Joo Nam
Keyword(s):  
Nucleic Acid ◽  
Interaction Analysis ◽  
Three Dimensional ◽  
Data Bank ◽  
Van Der Waals Interactions ◽  
Acid Complex ◽  
Protein Nucleic Acid ◽  
The Individual ◽  
Nucleic Acid Interactions ◽  
User Friendly

Growing numbers of protein and nucleic acid complex structures are being determined and deposited in the Protein Data Bank and the Nucleic Acid Database. With the increasing complexity of these structures, it is challenging to analyse and visualize the three-dimensional interactions. The currently available programs for such analysis and visualization are limited in their applications. They can only analyse a subset of protein–nucleic acid complexes and require multiple iterations before obtaining plots that are suitable for presentation. An interactive web-based program,NuProPlot(http://www.nuproplot.com), has been developed which can automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein–DNA and protein–RNA interactions can be visualized in simple two-dimensional schematics. Interactive schematic drawing options allow selection of the plotted area and repositioning of the individual interactions for better legibility.NuProPlotis a fully automated and user-friendly program providing various custom options.NuProPlotrepresents a greatly improved option for analysis and presentation of protein–nucleic acid interactions.

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