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Department of Biology and Biochemistry | University of Houston |
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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.
- 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 References 1. Donohue,
J. (1956) Proc. Natl. Acad. Sci. USA 42, 60-65. 2. Burkard, M. E. , Turner, D. H.,
and Tinoco, 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
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