Designing complex 3D DNA scaffolds

A new computer model allows the design of the most complex 3D DNA shapes by building DNA scaffold and customised synthetic strands of DNA. Biological engineers from at the Massachusetts Institute of Technology (MIT) have developed a design program that could allow researchers to build DNA scaffolds to anchor arrays of proteins and light-sensitive molecules, or to create new delivery vehicles for drugs or RNA therapies. Professor Mark Bathe, biological engineer at MIT said: "The general idea is to spatially organise proteins, chromophores, RNAs, and nanoparticles with nanometre-scale precision using DNA. The precise nanometre-scale control that we have over 3-D architecture is what is centrally unique in this approach." Bathe’s study, published in Nature Communications, reports that a computer algorithm can take sequences of DNA scaffold and customised synthetic strands of DNA and use them to predict the 3-D structure of arbitrary programmed DNA assemblies. With this model, they can create more complex structures than were previously possible. The basis of the new approach involves virtually cutting apart sequences of DNA into subcomponents called multi-way junctions. After this stage, the model reassembles these multi-way junctions into larger programmed assemblies of nanometre-scale dimensions, such as rings, discs, and spherical containers. Bathe said: "The principal innovation was in recognising that we can virtually cut these junctions apart only to reassemble them in silico to predict their 3-D structure." The researchers are planning to release their algorithm publically within the next few months. In the future Bathe is hoping to create a version of the DNA design programme where the computer model will obtain the sequence and produce the shape of a given specific shape. This would enable true nanometer-scale 3-D printing, where synthetic DNA is applied. Video: https://www.youtube.com/watch?v=K1Rn5gf-8ZE