Investigating DNA-recognition by proteins

Many proteins recognize specific sequence motifs in DNA and form stable protein-DNA complexes to perform a range of biological functions associated with transcription, repair and packaging. Although, DNA sequences recognized by most proteins are relatively easily described by small sequence motifs, similar motif-like alphabet in proteins is rarely observed. Sequence and structural elements of proteins interact with DNA in a complex, cooperative and dynamic manner. We have been investigating sequence, structural, evolutionary and thermodynamic patterns of DNA-binding proteins to establish the broad principles of DNA-recognition by them. Our studies have revealed several interesting features useful for understanding and predicting DNA-binding proteins, their binding sites and pinpoint the most significant players in the stability of these complexes.We have developed these leads into novel algorithms and web-based tools for public use.