Analysis of Protein-DNA Interactions

Abstract

By analyzing specific protein-DNA interactions, molecular recognition processes can be better understood. How do distinct proteins recognize specific DNA sequences? Prokaryotic restriction endonucleases, for example, are characterized by highly specific DNA interactions and therefore are excellent models to study recognition events. More than 3,300 type II restriction endonucleases are known, recognizing about 200 distinct DNA specificities (Roberts and Macelis 2001). Among this large group of functionally related enzymes is a considerable number of isoschizomers, proteins isolated from different microbial species that interact with the same DNA sequence. However, there does not appear to be noteworthy homology in amino acid sequence among these enzymes (for a review see Pingoud and Jeltsch 2001). Did enzymes that interact with the same DNA sequence develop independent structures or mechanisms to interact with a specific target site? Are there any as yet unknown common rules of DNA recognition? To date, X-ray crystallography of protein-DNA complexes is without doubt the most informative method for understanding specific recognition. However, X-ray crystallography can be slow because obtaining good diffracting crystals is a very time-consuming and unpredictable process. Thus, faster methods are sought to increase the data pool on recognition complexes.