Information content of binding sites on nucleotide sequences

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Macromolecules like repressors and polymerases bind to specific DNA sequences.
• Recognition of these binding sites relies on identifiable sequence patterns.

Purpose of the Study:

• To define and apply a quantitative measure for information content in DNA binding site sequences.
• To investigate information distribution within binding sites and compare different sites.
• To calculate the information required to locate binding sites based on their genomic frequency.

Main Methods:

• Defined and calculated 'R sequence' as a measure of information in sequence patterns at binding sites.
• Defined and calculated 'R frequency' as the information needed to locate sites given their genomic occurrence.
• Empirically analyzed Escherichia coli and bacteriophage T7 RNA polymerase binding sites using these measures.

Main Results:

• For most analyzed Escherichia coli binding sites, R sequence and R frequency were similar.
• Bacteriophage T7 RNA polymerase binding sites showed approximately twice the information necessary for recognition.
• This excess information at T7 promoters correlated with a strong symmetry element, potentially indicating a second protein binding site (operator).

Conclusions:

• The information content at most DNA binding sites is generally sufficient for distinguishing them from the broader genome.
• T7 RNA polymerase promoters possess excess information, suggesting a regulatory mechanism involving an additional protein.
• The identified symmetry element at T7 promoters may function as an operator, distinct from the primary promoter recognition site.