SPECIFICITY, FREE-ENERGY AND INFORMATION-CONTENT IN PROTEIN-DNA INTERACTIONS

Site-specific DNA-protein interactions can be studied using experiment al and computational methods. Experimental approaches typically analyz e a protein-DNA interaction by measuring the free energy of binding un der a variety of conditions. Computational methods focus on alignments of known binding sites for a protein, and, from these alignments, mak e estimates of the binding energy. Understanding the relationship betw een these two perspectives, and finding ways to improve both, is a maj or challenge of modern molecular biology.