DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction

The session explores computational approaches to understanding the fundamental cycle of DNA $ Protein $ DNA by which DNA and proteins co-exist, co-regulate, and co-create each other. There is mounting evidence that DNA structural properties beyond the double helix signiicantly aaect its interactions with proteins and play an important role in a number of biological phenomena ranging from gene regulation to triplet repeat expansion diseases. The selected papers address the underlying structural and functional basis by which these interactions can be understood, modeled, and predicted. The study of DNA structure, protein-DNA interactions, and DNA-protein expression addresses the structural and functional basis underlying many areas of current signiicance, such as gene expression arrays, gene networks, genetic regulation, motif discovery, molecular recognition, and ultimately the regulated control of all life processes. As examples, the protein-DNA interactions of regulatory proteins provide the physical basis for the expression patterns studied by gene expression arrays; triplet repeat expansion diseases such as Hunting-ton's disease are due to the abnormal expansion of DNA triplets which h a ve very extreme structural properties; and the viral packaging of nucleotides into the protein shell provides the physical basis for some of the most virulent o f human pathogens. The interplay b e t ween DNA and proteins is the most fundamental of biological interactions, and has pervasive implications in biology, medicine, pharmacology, and biotechnology. The DNA$Protein$DNA cycle, by which DNA and proteins co-exist, co-regulate, and co-create each other, is a delicate balance between string and structure. The heteropolymer nature of both DNA and proteins allows for their compact representation and manipulation as sequences of characters drawn from alphabets of four and twenty c haracters respectively. Sequence analysis has been one of the most fruitful areas of computational biology, and much of our knowledge in areas as diverse as phylogenetic ancestry and DNA binding has been obtained by clever string manipulations. On the other hand,