ARTICLE: DNA in computers

The self-assembly of DNA Holliday junctions studied with a minimal model

• Physically rich DNA structures are vital in biology and genetics, and valuable in nanotechnology: we show that they can be studied with coarse-grained computer models, which are simple enough to simulate but rich enough to match real-world behaviour

DNA is a fascinating and flexible model. In our cells, it forms a famous "double helix" structure, but lots of other structures too, including "Holliday junctions", four-armed crosses that occur when DNA molecules meet and exchange genetic information. DNA is also used in nanotechnology, where our ability to design DNA molecules which interact in designed ways is harnessed to produce tiny molecular structures and machines. Holliday junctions also play important roles in this DNA nanotechnology, forming the corners of rigid structures.

To understand the physics of how DNA behaves in both these biological and nanotechnological contexts, we explored whether a simple model of DNA simulated in a computer can describe and predict its behaviour in the real world. DNA is made of many atoms and interacts in a complicated way with its environment: we aimed to reduced these complications as far as possible while retaining the necessary information to describe the physics of interest.

In a paper in the Journal of Chemical Physics here (free here), we build a model of DNA using common pieces of "kit" from a physicists' toolbox: model sticky particles linked in a chain, with interactions limiting how much the chain can be bent and twisted. The model is simple enough to simulate easily on a computer, but correctly forms duplexes and Holliday junctions analagous to those we see in the real world. It's a demonstration that so-called "coarse-grained" models (as opposed to modelling in fine detail) can be of use in simplifying and understanding complicated structures and physical systems.

Model DNA molecules forming four-armed Holliday junctions in a computer simulation.

This philosophy has since been developed and expanded hugely, leading to the highly influential oxDNA project, which has been used to explore how DNA nanomachines move and function and has led to a wide range of insights in chemical physics and nanotechnology. Iain