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Nucleic Acids Research Pages 184-185  

The Database of Ribosomal Cross-links: an update
Introduction
New Features Of The DRC
Acknowledgements
References

The Database of Ribosomal Cross-links: an update

The Database of Ribosomal Cross-links: an update

Pavel V. Baranov, Andrew V. Kubarenko, Olga L. Gurvich1, Tatyana A. Shamolina and Richard Brimacombe2,*

A. N. Belozersky Institute of Physico-Chemical Biology, Department of Chemistry, Moscow State University, Moscow 119899, Russia, 1Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USAand 2Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestrasse 73, 14195 Berlin, Germany

Received September 8, 1998; Accepted September 10, 1998

ABSTRACT

The Database of Ribosomal Cross-links (DRC) was created in 1997. Here we describe new data incorporated into this database and several new features of the DRC. The DRC is freely available via World Wide Web at http://visitweb.com/database/ or http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/

INTRODUCTION

The Database of Ribosomal Cross-links (DRC) was created one year ago (1). This database includes data on more than 1000 published cross-links between different Escherichia coli ribosomal components. During the past year new cross-linking data have appeared, namely intra-RNA cross-links within 16S rRNA (2) and 23S rRNA (3), inter-RNA cross-links between 5S rRNA and 23S rRNA (4), and protein-protein cross-links to L7/L12 (5). All these data are now included in the updated version of the DRC.

NEW FEATURES OF THE DRC

Because some research publications do not provide full information concerning the chemical and photochemical reagents used to generate the cross-links, we have created a brief description of the basic features of almost all the reagents mentioned in the DRC. This description includes: (i) most common names of the reagent; (ii) chemical structure of the molecule; (iii) maximum extended length of the cross-link formed after treatment with the reagent; (iv) method of incorporation of the reagent into the ribosomal component or ligand; (v) methods or conditions for cross-link generation; (vi) specificity of the reagent; and (vii) relevant literature referenced.

In order to make this database available for the different software on almost all computer platforms, we have created a counterpart of the DRC in dBASE IV format. These files are available in zip archive in the DRC. Users can freely download these files, and edit the data for their own purposes. Figure 1 illustrates the interface of the DRC in dBASE IV format for Windows 95/NT.


Figure 1. Windows 95/NT interface for the DRC in dBASE format.

In order to make the information search in the DRC simpler and faster, we are planning to create a search system based on the secondary structure maps of rRNA. At the moment a demonstration version is available for the data concerning 5S rRNA cross-links. In order to get full information about a particular nucleotide within the 5S rRNA, the user simply needs to click onto the corresponding nucleotide with the left key of his mouse. For next year we are planning to create similar search systems for the 16S and 23S rRNA.

ACKNOWLEDGEMENTS

We are grateful to Prof. Steve Harvey (University of Alabama), Petr Sergiev (Moscow State University) and Ingolf Sommer (MPI für Molekulare Genetik) for very useful suggestions and comments during the update of the DRC. We also thank all those users who have drawn our attention to mistakes within the DRC.

REFERENCES

1. Baranov,P.V., Sergiev,P.V., Dontsova,O.A., Bogdanov,A.A. and Brimacombe,R. (1998) Nucleic Acids Res., 26, 187-189. MEDLINE Abstract

2. Mundus,D. and Wollenzien,P. (1998) RNA, 4(11), in press. MEDLINE Abstract

3. Baranov,P.V., Gurvich,O.L., Bogdanov,A.A., Brimacombe,R. and Dontsova,O.A. (1998) RNA, 4, 658-668. MEDLINE Abstract

4. Sergiev,P., Dokudovskaya,S., Romanova,E., Topin,A., Bogdanov,A., Brimacombe,R. and Dontsova,O. (1998) Nucleic Acids Res., 26, 2519-2525. MEDLINE Abstract

5. Dey,D., Bochkariov,D.E., Jokhadze,G.G. and Traut,R.R. (1998)J. Biol. Chem., 273, 1670-1676. MEDLINE Abstract

*To whom correspondence should be addressed. Tel: +49 30 8413 1592; Fax: +49 30 8413 1690; Email: sommer@mpimg-berlin-dahlem.mpg.de

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Last modification: 9 Dec 1998
Copyright©Oxford University Press, 1998.
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