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Updated: Aug 2, 2026
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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
Conformational and physicochemical DNA features specific for transcription factor binding sites
J V Ponomarenko1, M P Ponomarenko, A S Frolov
1Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru
Bioinformatics (Oxford, England)
|September 17, 1999
Summary
This study introduces B-DNA-VIDEO, an activated database for identifying transcription factor binding sites by analyzing DNA conformational and physicochemical properties. It enables the creation of custom recognition programs for specific DNA sequences.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Accurate identification of transcription factor binding sites is crucial for understanding gene regulation.
- Experimental evidence highlights the importance of DNA's conformational and physicochemical properties in site function.
- Existing online tools lack the capability to identify these critical DNA features and utilize them for site recognition.
Purpose of the Study:
- To develop a novel approach for identifying significant conformational and physicochemical properties of functional DNA sites.
- To implement this approach in an accessible database and toolset for researchers.
- To facilitate the recognition of transcription factor binding sites based on their unique DNA feature profiles.
Main Methods:
- Development of the B-DNA-VIDEO database and associated web tools.
- Implementation of a system to reveal significant conformational and physicochemical DNA properties for specific sites.
- Generation of custom C-programs for site recognition based on identified features, integrated within the database.
Main Results:
- The B-DNA-VIDEO database successfully identifies specific sets of significant conformational and physicochemical DNA properties characterizing transcription factor binding sites.
- The system allows for the generation, testing, and storage of custom site recognition programs (C-programs).
- Each database entry links to a web applet for immediate site recognition, creating a novel 'activated database' resource.
Conclusions:
- B-DNA-VIDEO provides a unique resource for both data searching and active computation in the field of genomic sequence analysis.
- The 'activated database' concept integrates data storage with functional computational tools for enhanced usability.
- This system advances the ability to analyze and recognize regulatory genomic sequences by leveraging specific DNA properties.
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