ABSTRACT
I. INTRODUCTION Gel electrophoresis is without a doubt one of the most important analytical tools in molecular biology and biochemistry, and it is invaluable in predict ing conformation and structural changes of nucleic acids upon their inter action with proteins and small ions [la-d]. While this technique is used daily in hundreds of laboratories, the physical mechanisms underlying gelbased electrophoresis are still poorly understood at best. That this lack of understanding does not involve merely minutiae is demonstrated amply by the recent discovery that size-dependent electrophoretic mobility of small ss DNA fragments exhibits behavior that is exactly opposite to that of larger fragments [le]. A quantitative theoretical understanding of the mechanism of gel-retardation of biologically significant macromolecules such as bentDNA sequences and protein-induced DNA are needed since they will sim plify the interpretations of what are now considered to be unusually complex phenomena. The bending of DNA by proteins is important in the control of replication and recombination processes, the packaging of DNA into nucleosomes, and transcriptional regulation phenomena [2-6].
