Electrophoresis of DNA through gels of agarose or polyacrylamide (PA) has been one of the most widely used techniques of molecular biology during the past decade, serving both analytical and preparative purposes. The molecular theory of this process has been developing slowly over the same period of time as the result of the efforts of a small but expanding group of people. Initially simple, the theory has grown in ways that no one anticipated at the beginning, partly in response to unexpected experimental discoveries. In this review we describe its current state, including both solved and unsolved problems.

The fundamental relationship between structure and function has served to guide investigations into the workings of living systems at all levels - from the whole organism to individual cells on down to individual molecules. When X-ray crystallography began to reveal the three-dimensional structures of proteins like myoglobin, lysozyme and RNase A, protein chemists were well prepared to draw inferences about functional mechanisms from the precise positioning of amino acid residues they could see. The close proximity between an amino acid side chain and a chemical group on a bound ligand strongly suggests a functional role for that side chain in binding affinity and specificity. Likewise, the nearly universal finding of large clusters of hydrophobic side chains buried in the core of proteins strongly supports a major functional role of hydrophobic interactions in protein folding and stability. Even though eminently plausible hypotheses like these, grounded in the most fundamental principles of chemistry and the logic of structure–function relationships, become widely accepted and make their way into textbooks, protein chemists have felt compelled to search for ways to test them and put them on a more quantitative basis.