Localization and characterization of curved DNA in the human erythropoietin receptor gene by experimental and theoretical approaches

Abstract

We report here the locations of curved DNA in the human erythropoietin receptor gene. A total of 13 DNA bend sites were mapped by circular permutation assays, appearing at an average interval of 651.2 ± 214.6 (S.D.) in the 8-kb region. The bend centers in these 13 bend sites were confirmed by oligonucleotide-based assays where most of these centers had bend angles higher than that shown by (AAACCGGGCC)·(A)20 and lower than that shown by (AAACCGGGCC)2·(A)10· DNA curvature mapping by TRIF software, which is based on the distribution of dinucleotides, primarily AA and TT, provided a highly accurate prediction for the locations of the bend sites. They showed approximately 20° to 40° of bend angles demonstrated by the oligonucleotide assays and by computer analysis.