O04_05

Integrated web user interface for DNA nanotechnology including coarse-grained molecular dynamics simulation

Ibuki KAWAMATA *

School of Science, Kyoto University
( * E-mail: kawamata.ibuki.8p@kyoto-u.ac.jp)

DNA nanotechnology is an expanding field of research that aims to fabricate nanoscale architectures and machineries in nanoscale precision using DNA as a building block. The advantage of using DNA is its programmability by which one can rationally design the interaction among DNA molecules by defining base sequences of DNA. Among several design strategies to build nanoscale objects, DNA origami methodology is receiving much attention thanks to its versatility and robustness. In a standard DNA origami structure, circular single-stranded DNA with more than 7000 nucleotides and more than 200 short single-stranded DNAs are used as materials. Because it is not practical to design a DNA structure by human trails and errors using pen and pencil, computer aided design tools and standardized file formats play important roles. Although many useful file formats and software have been developed, file conversion between different formats or graphical user interface to operate software such as molecular dynamics simulation is lacking. Here, we built a set of web user interface to accelerate the computational design, visualization, simulation, and analysis of DNA nanostructures. In the presentation, our research using the software will be discussed along with the introduction of the web user interface.