[Analysis of distribution of ligands adsorbed on DNA fragments]

The effect of finite fragment length on the distribution pattern of bound protein along the DNA fragment is considered. If the size of the binding site for a ligand on DNA is comparable with the length of the DNA fragment fluctuations in the amount of ligand bound to the fragment create some difficulties for evaluating the distribution pattern of ligand on DNA. A mathematical approach is developed which enables one to calculate the distribution pattern of ligand on DNA provided that the number of bound ligand on the DNA fragment is known. Expression are also obtained to treat the effects of fluctuations in the number of ligand molecules bound to the DNA fragment on the distribution pattern of ligand. A new procedure is proposed which may be useful for locating the preferable binding sites for ligand on DNA on the basis of footprinting experiments.