Different flexibility of the upstream regulatory regions of two differently expressed pea rbcS genes studied by theoretical evaluation of DNA distortion energy and cyclization kinetics.

Different superstructural features of the upstream regulatory regions of the two pea genes rbcS-3A and rbcS-E9 have been derived using a theoretical method, developed in our laboratory a few years ago, which evaluates the DNA distortion energy from a matrix of the deviations of the 16 possible dinucleotides from the standard B conformation. The theoretical analysis, which predicts different flexibilities of the regulatory regions of the two genes, is in satisfactorily good agreement with experimental evaluations from gel electrophoretic mobility and cyclization kinetics, suggesting a possible model to explain the largely different transcription efficiencies of the two genes.