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- Non-interactive : all records sorted by base pair type | authors' names.

- Interactive : search the database.

- Summary table [Single page | Multiple pages].

- Structures of Base Pairs, Base Triples and Base Quadruples.

- "Database of non-canonical base pairs found in known RNA structures" [PDF format. Nucleic Acid Research, 2000 Jan 1; 28(1):375-376].

 

 

RNA World

Informatics

Phylogeny

Database

 

Overview

- The primary objective of this database is to provide rapid access to all the RNA structures in which a particular rare base pair has been found. A secondary objective is to summarize the important properties that have been associated with each non-canonical base pair. A literature survey of RNA structures was performed to obtain information on the non-canonical base pairs.

- A total of over 2000 occurrences of mismatches have been identified to date. Each of these is tabulated in accordance with the classification scheme as described (see "Conventions" section). Interactions that have only one hydrogen bond have been included as a separate category. Each entry provides access to citation information, the immediate 5' and 3' sequence context and a brief common name for the structures in which the base pairs was found. Additional structural information such as melting point, chemical shift, comments etc. is provided when this information is available.

- In addition to several static tables of information, a query system has been setup, which allows browsing of the database in a variety of ways.


Conventions

- Beginning with Donohue's early analysis(1), it has been recognized that many alternative interactions between bases exist in which two hydrogen bonds are possible.

A recent tabulation by Burkard et al.(2) lists 29 possible pairs of this type including the standard pairs. There are two major types of pairs, normal and flipped. In the eleven normal pairs, the strands are antiparallel and the base is in the anti orientation relative to the ribose. In the 18 flipped arrangements either the strands must be parallel or the base must be switched to the syn configuration. Within each category one can further distinguish purine-purine, purine-pyrimidine, and pyrimidine-pyrimidine types.

- Asterisk(*) denotes the information is either currently unavailable or inapplicable to that record.

- In "Sequence context" of each base interaction, asterisk(*) in the sequence means that no base is present at that location and a hyphen(-) denotes a base pair interaction between the two bases. Please note that a space character between the two bases does not imply they are involved in any kind of interaction.

- Units for parameters: temperature scale--Celsius, free energy--kcal/mol, chemical shift--ppm.

 

Database

- Non-interactive : all records sorted by base pair type | authors' names.

- Interactive : search the database

- Summary table.

- Structures of Base Pairs, Base Triplets and Base Quadruplets.

- Database of non-canonical base pairs found in known RNA structures (PDF format. Nucleic Acid Research, 2000 Jan 1;28(1):375-376.)

 

Contributors

- Literature collection and interpretation was done by Uma Nagaswamy and Neil Voss.

- This database was originally designed and input by N.Voss using Access on Windows. It was revised and exported to Mysql DBMS on Linux by Zhengdong Zhang.

- All database-related web pages were designed and made by Z.Zhang. The database web search functionality was implemented by Z.Zhang.

- All figures of base pairs and base triplets except those adapted from the appendix I(2) of the RNA World(2nd edition) were made by U.Nagaswamy.

- Other contributors: Maia-Larios Sanz, Ling Jing, Shakaala Collins, and James Hury

- This work was supervised by Dr. George E. Fox.

 

What's new

- Building this database is an ongoing process. This database and its web site will be refined and updated whenever new information is available.

- Minor corrections and additions (10 entries added, 276p, 286c, 1-24-00).

- The web page showing the structures of all base interactions included in this database was updated (12-22-99).

- Minor corrections to "Sequence Context" field (280p, 276c, 12-22-99).

- The database-related article published in Nucleic Acid Research was added to "Database" section (12-15-99).

- Minor corrections to "Structure" field (283p, 280c, 11-30-99).

- Minor corrections and additions (25 entries added, 258p, 283c, 11-16-99).

- Minor corrections and additions (15 entries added, 243p, 258c, 11-1-99).

- This page was reorganized (10-20-99).

- The PDB link was added to each individual page if it is currently available (10-7-99).

- The major revision and expansion of the database was finished. Currently the database has 243 entries (excluding the duplicates, see "Summary table") of non-canonical base interactions, compared to 74 entries in the previous database (10-4-99).

- The "Terminology" section was added (see below, 10-3-99).

- more...

 

Acknowledgments

- We thank other members of Fox lab for their kind support to make this work possible.

- This work was supported by W.M.Keck Center for Computational Biology and NASA grant NAG5-8140 to GEF.

 

References

1. Donohue, J. (1956) Proc. Natl. Acad. Sci. USA 42, 60-65.

2. Burkard, M. E. , Turner, D. H., and Tinoco, I. Jr. (1999) In Gesteland, R.F., Cech, T.R., and Atkins, J.F. The RNA World -Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 675-680.

Contact

- Please send corrections or information on omitted data to U.Nagaswamy at uma@prion.bchs.uh.edu

- Please send any other correspondence to Dr. G. E. Fox at fox@uh.edu.

 

Links

- Fox Lab Home | Department of Biology and Biochemistry | University of Houston

- W.M.Keck Center for Computational Biology | NASA

 

- NCBI | PDB

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