scholarly journals Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

2014 ◽  
Vol 70 (2) ◽  
pp. 354-361 ◽  
Author(s):  
Rob Abdur ◽  
Oksana O. Gerlits ◽  
Jianhua Gan ◽  
Jiansheng Jiang ◽  
Jozef Salon ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Complex Structure ◽  
Rnase H ◽  
Acid Complex ◽  
Mad Phasing ◽  
Sad Phasing ◽  
Protein Nucleic Acid ◽  
Dna Complex ◽  
Dna Substrate ◽  
Structural Insights

The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteinsviaMAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

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.

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.

Dark field EM of the RNA of the small subunit of the E. coli ribosome

1983 ◽  
Vol 41 ◽  
pp. 596-597
Author(s):  
A. P. Korn ◽  
D. Elson ◽  
P. Spitnik-Elson ◽  
F. P. Ottensmeyer
Keyword(s):  
Nucleic Acid ◽  
Recent Experiment ◽  
Small Subunit ◽  
Dark Field ◽  
Single Individual ◽  
Field Mode ◽  
Acid Complex ◽  
Digestion Product ◽  
E Coli ◽  
Protein Nucleic Acid

We have embarked on a series of EM experiments using the dark field mode in an attempt to ascertain how much of a role the ribonucleic acid (RNA) component of the ribosome has in determining the structure of the protein-nucleic acid complex. We have observed that treatment of specimens of the smaller subunit enhances the visibility of band-like structures on the "back" of the subunit. In total, though not necessarily all appearing at once on a single individual, three parallel bands of 20 Å diameter are seen (Fig. 2). We have speculated that these are double stranded sections of the RNA that emerge on the surface. This does not preclude external single stranded sections that are not as prominent, however. The identification of the bands with double stranded external RNA is still subject to further testing. In a very recent experiment we have examined a heated RNAase digestion product that has been shown to lack a section of its RNA.

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