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Signals in DNA sequences and their potential properties.
1Laboratory of Mathematical Biology, NCI, NIH, Bethesda, MD 20892.
Computer Applications in the Biosciences : CABIOS
|July 1, 1991
Summary
Regulatory proteins recognize DNA and RNA signals through nucleotide sequences or structural changes. This study highlights the importance of DNA oligomer properties and detection algorithms in regulatory regions.
Area of Science:
- Molecular Biology
- Genetics
- Bioinformatics
Background:
- DNA and RNA recognition by regulatory proteins/enzymes relies on nucleotide sequences or induced structural changes.
- Current research primarily focuses on sequence recurrences, neglecting structural and flexibility aspects of recognition elements.
Purpose of the Study:
- To review methods for searching DNA/RNA signals, focusing on nucleotide sequences and structural properties.
- To investigate the asymmetric distribution of complementary oligomers near biological features, particularly in transcription initiation regions.
Main Methods:
- Review of existing methods for identifying sequence-specific and structure-dependent recognition signals.
- Analysis of oligomer distributions, focusing on G-rich and A-tracts upstream of transcription initiation.
- Examination of DNA bending mechanisms influenced by G-tracts and A-tracts.
Main Results:
- G-rich oligomers and A-tracts are frequently found upstream of transcription initiation sites.
- Guanine tracts, but not cytosine tracts, enhance A-tract-directed DNA bends.
- DNA G-tracts can induce bends via major groove compression, potentially without protein involvement.
Conclusions:
- DNA oligomer properties, such as G-tracts and A-tracts, play a crucial role in DNA conformation and regulation.
- Structural properties of DNA, beyond mere sequence, are vital for biological recognition.
- Development of algorithms for detecting these properties in regulatory regions is important for understanding gene regulation.