The construction of DNA helical duplexes along prescribed 3-D curves

Curved DNA structures can be either intrinsic or induced through interaction with proteins. Large DNA molecules can adopt complex curved shapes in space. Many curved DNA structures (e.g., Cro-operator, Cap-operator, nucleosomal DNA, etc.) are believed to have important biological functions. To model curved DNA molecules is a challenging task. In this work, we introduce a method for the computer generation of DNA structures having any prescribed 3-D shape in space. The approach is purely geometrical and highly efficient. This method is used successfully to construct an atomic level nucleosomal DNA that is consistent with the experimental data. The smallest closed DNA circle we are able to construct with the method is a 51 bp DNA duplex.