Computer Model Enables the Most Complex 3D DNA Shapes Ever Produced

Because DNA is so stable and can easily be programmed by changing its sequence, many scientists see it as a desirable building material for nanoscale structures. MIT biological engineers have created a new computer model that allows them to design the most complex three-dimensional DNA shapes ever produced, including rings, bowls, and geometric structures such as icosahedrons that resemble viral particles. The computer algorithm can take sequences of DNA scaffold and staple strands and predict the 3D structure of arbitrary programmed DNA assemblies. This design program could allow researchers to build DNA scaffolds to anchor arrays of proteins and light-sensitive molecules called chromophores that mimic the photosynthetic proteins found in plant cells, or to create new delivery vehicles for drugs.

Transcript

00:00:06 Deoxyribonucleic acid more commonly known as DNA is a molecule that encodes the genetic instructions used in the develop- ment and functioning of all known living organisms and many viruses. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. Because DNA is so stable and can

00:00:26 easily be programmed by changing its sequence, scientists see it as a desirable building material for nanoscale structures. In the past, using a strategy called DNA Origami scientists were able to construct two- dimensional structures from DNA and later three-dimensional structures. But now MIT biological

00:00:44 engineers have created a new computer model that allows them to design the most complex three- dimensional DNA shapes ever produced. The new approach relies on virtually cutting apart sequences of DNA into components called multi-way junctions which are the fundamental building blocks of DNA structures.

00:01:03 These junctions which form naturally during DNA replication consist of two parallel DNA helices in which the strands unwind and cross-over the binding strand to a strand of the adjacent DNA helix. After virtually cutting the DNA into smaller sections the new computer program resembles them into larger structures, such as

00:01:23 rings, discs and other shapes. By changing the sequences of these DNA components, designers can also easily create arbitrarily complex architectures including symmetric cages such as tetrahedrons, octahedrons and dodecahedrons. This new design program could allow researchers to build DNA scaffolds to anchor arrays of

00:01:45 proteins that mimic the photosynthetic proteins found in plant cells or create new delivery vehicles for drugs or RNA therapies. The researchers also hope to create a version of the model that allows the designer to specify a shape and obtain the sequence that will produce the shape. This would enable true

00:02:03 nanometer-scale 3-D printing, where the "ink" is synthetic DNA.