Nucleic Acids Research, 2003, Vol. 31, No. 1 483-485
© 2003 Oxford University Press
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0
Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
*To whom correspondence should be addressed. Tel: +852 26096257; Fax: +852 26035057; Email: scfau-yeung{at}cuhk.edu.hk
Received September 15, 2002; Accepted September 27, 2002
ABSTRACT
The second release of Thermodynamic Database for Nucleic Acids, NTDB 2.0, includes more than 4600 entries (250% increase over release 1.0). It contains sequence types and details of several thermodynamic parameters (enthalpy, 
H; entropy, S; Gibbs free energy, G; melting temperature, Tm), experimental models and methods for extracting thermodynamic parameters, buffer conditions as well as all relevant literature information. In addition, the database statistics and references related to NTDB are included. Information on normal and modified nucleobases and nucleosides are collected in a new section ‘Nucleoside’ whereby data collected thus far will be release in NTDB 2.0. The NTDB is freely available at http://ntdb.chem.cuhk.edu.hk.
INTRODUCTION
Thermodynamic properties of nucleic acids have a deciding role in the binding of normal and modified oligonucleotides to nucleic acids. Not only are thermodynamics values important in exploring the folding and stability of nucleic acids, but their availability are essential in the design and modification of novel oligonucleotides suitable for antisense therapeutics (1). Thus, they have attracted considerable attention since the early 1960s but there is no rapid way of disseminating this important information efficiently. Recent explosion in the development of information technology has made it possible that valuable information on the sequence, structural, functional and their relevant literatures could be delivered through the use of websites. However, most web accessible biological databases are focused on sequences [such as SWISS-PROT (2)] and structures [such as PDB (3) and NDB (4)] and no similar web database whereby the thermodynamic information of normal and modified nucleic acids have been categorically collected. We designed the Thermodynamic Database for Nucleic Acids (NTDB) (5), which includes a collection of thermodynamic and structural data, experimental methods, conditions and the corresponding references since 2000. Moreover, a form-based interface has been provided to make easy searching of the database searching and results visualization. This article reports the infrastructure, current status and recent developments of NTDB.
DATABASE INFRASTRUCTURE
Under each unique NTDB identity number, information on: (i) sequence; (ii) structural type (e.g. DNA or RNA) with or without mismatches, dangling ends, bulge loop and modification information on the base, sugar and/or phosphate position; (iii) thermodynamic data (i.e. H, S, G and Tm); (iv) methods of measurement and analysis (e.g. curve fitting or log Ct method); (v) strand concentration and composition of the buffer used; as well as (vi) all relevant reference information of normal and modified nucleic acids are provided. The references for all entries in NTDB are linked to the NCBI PUBMED literature database (6). The details of the thermodynamic properties of normal and modified nucleic acids can be obtained through a user-friendly web interface with search options available. In addition, a set of useful tools relevant to the study of nucleic acids, and web links connected to some valuable related articles as well as information on scientific groups active in this field are described in the NTDB web site.
DATABASE STATISTICS AND DEVELOPMENT
In this release, the number of entries of NTDB has been increased to 4640, which is about a 2.5 times increase in the number of entries reported compared to the first release (5) and the database statistics is summarized in Table 1. Thermodynamics data determined by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR) are included and these categories are added as search items under ‘experimental method’. Moreover, both methods and models (e.g. the two-state model) are included for extraction of thermodynamic parameters from experiments. Furthermore, a new ‘Nucleoside’ section, which shows the structure, its IUPAC and common names, the NTDB notation, the molecular formula as well as links retrieving chemical and physical properties [NIST Webbook (7)] and cancer screening data [Developmental Therapeutics Program, DCTD, National Cancer Institute (8)], are added where all relevant information associated with normal and modified nucleobases and nucleosides are collected (see Fig. 1). The database statistics and the references related to NTDB are included in NTDB.
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AVAILABILITY AND CITATION OF NTDB
Every effort has been made to verify the registered data as well as the web links to minimize errors. According to received feedbacks, suggestions and comments from authors and users of NTDB, we have redesigned to provide for the best functionality possible for NTDB. NTDB can be freely accessed at http://ntdb.chem.cuhk.edu.hk. NTDB users are encouraged to cite this article in their publication including the URL address. Any comments, suggestions and contributions are welcome and should be addressed to the corresponding author.
ACKNOWLEDGEMENTS
This work is partially supported by two Direct Grants from: The Chinese University of Hong Kong (CUHK) Direct Grants from (Grant nos: 2060156 and 2060179) and the Goldlion Fund (Ref. no.: G01125) of Hong Kong SAR. W.L.A.K.C acknowledges the financial support from the Research Grant Council of Hong Kong SAR, Central Allocation Scheme 2001/2002 and a Faculty of Science Special Grant, CUHK.
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[Abstract/Free Full Text] - Berman,H.M., Olson,W.K., Beveridge,D.L., Westbrook,J., Gelbin,A., Demeny,T., Hsieh,S.-H., Srinivasan,A.R. and Schneider,B. (1992) The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751–759.[Web of Science][Medline]
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[Abstract/Free Full Text] - Wheeler,D.L., Church,D.M., Lasn,A.E., Leipe,D.D., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Tatusova,T.A., Wagner,L. and Rapp,B.A. (2002) Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res., 30, 13–16.
[Abstract/Free Full Text] - Linstrom,P.J. and Mallard,W.G. (eds), NIST Chemistry WebBook, NIST Standard Reference Database Number 69, July 2001, National Institute of Standards and Technology, Gaithersburg MD, 20899 (http://webbook.nist.gov).
- Developmental Therapeutics Program NCI/NIH, National Cancer Institute, (http://dtp.nci.nih.gov).
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