About the image
The figure shown is of the conserved protein-water-DNA interaction observed by Dr. Jacobs during his studies of zinc-finger—DNA interactions (Ph.D. thesis, 1992). Several CCHH zinc fingers with a conserved asparagine—adenosine interaction have been superimposed, superimposing the sidechain and nucleotide base atoms. The superimposition reveals that there is a larger co-operative protein-DNA interaction unit than just the sidechain-base interaction. This larger unit includes flanking waters (solid spheres), phosphate groups (purple) and neighbouring protein hydroxyl groups (from serine/threonine). Note that the conserved water on the left has a "fixed" orientation (in terms of hydrogen bond donors and acceptors), emphasising this water molecule can be considered an extended part of the protein in its interaction with DNA. Even though the serine and asparagine are too distant to make direct interaction with eachother, they form part of a strongly co-operative unit in binding DNA.

Dr. Jacobs has studied protein-DNA interactions for many years. From this detailed analysis, he has developed a number of ideas of how to improve the prediction of DNA-binding sites within DNA sequences and on the surface of proteins. These ideas are being translated into BioinfoTools products.