Revisiting DNA with Single Molecule Methods

Abstract

DNA contains information that defines life phenomena and is a biomolecule found repeatedly in consistent form at all levels of life. Through the discovery of the double helix structure 70 years ago, the discovery of the human genome sequence 20 years ago, and the recent completion of the complete human genome sequence, its physicochemical properties and biological functions have been studied in detail. But recent single-molecule measurements and computational simulations are revealing new facts that were not known about this molecule that was thought to be well understood. For example, it still remains controversial how flexible DNA is and what determines its bending flexibility. In this talk, our recent finding on how the base sequence and chemical modification determine the condensation and looping properties of DNA based on single-molecule fluorescence measurements, atomic force microscopy, and all-atom molecular dynamics simulations. It was found that the C5 methyl group of thymine is critical in the polycation-induced DNA compaction, which relates to the cysteine methylation, an important epigenetic marker. Deformation energy of neighboring stacks of bases was found to heavily depend on the base sequence, which results in a large variation in the looping propensity of short DNA, more than an order of magnitude. These findings suggest a biophysical mechanism for spatiotemporal regulation of chromatin structure, and also can be utilized for gene therapy through sequence manipulation.