Design, synthesis, characterization and property study of topological structures of DNA

Abstract

It has been recognized in the past that alteration of writhe of DNA in prokaryotic and eukaryotic cells is maneuvered solely by histone proteins and topological enzymes such as gyrase, reverse gyrase, topo I and topo II. It is demonstrated in the current studies for the first time that the shapes of DNA writher (toroidal and interwound forms) can be precisely created sheerly through maneuvering the sequence of DNA and with no involvement of topological enzymes. It is also shown unprecedentedly in our investigation that the size of DNA writhe could be accurately engineered by altering T-rich and A-rich segments in the target duplex DNAs. In addition, the results of our studies confirmed that the intrinsic curvatures of organismal DNAs alone could lead to the generation of duplex backbone self-crossings in their relaxed forms and the backbone self-crossings of those organismal DNAs could be readily confirmed through atomic force microscopic examination. “DNA Topological Conservation Law (Lk - Tw = Wr)” was formulated by Professor F. B. Fuller in 1971 and further elucidated by Professor F. H. C. Crick in 1976 in order to describe the superhelical molecular architectures of DNA that had been discovered in nucleosomes in the eukaryotic cells at an earlier time. This law has since been widely cited in textbooks and taken as the fundamental principle that governs the topological behaviors of DNA in both prokaryotic and eukaryotic cells.