This invention is a method to produce varied DNA nanostructures useful in applications including drug delivery, immune stimulations for vaccines, sensing, or to mimic biological structures.
The field of DNA nanotechnology has been vastly expanded in recent years allowing target shapes to be programmed from the bottom-up using complementary Watson-Crick base pairing. For instance, scaffolded DNA origami is a powerful means of creating structured DNA assemblies, but it requires complex scaffold routing and staple design to realize a limited scope of target geometries. Furthermore, only one approach offers a solution to the inverse problem of sequence design based on specification of target geometry, but it is only semi-automated and relies on single duplex DNA arms and multi-junctions to represent polyhedral geometries, which may result in compliant and unstable assemblies that are unsuitable for many applications. This invention is a top-down design algorithm for programming arbitrary 3D geometries using DNA.
This method provides the nucleic acid sequences required to form a specific geometric form. A user inputs the geometric parameters of the desired structure and may also optionally define the physical size or template sequence of the object. This strategy can produce any geometric surface including non-spherical topologies such as a torus, provided that it can be rendered using polyhedral surface meshes. File formats containing specifications of the target object are converted into a set of arrays, providing input to a scaffold routing and staple design procedure. A polyhedral mesh is created and used to make a graph of the targeted structure to which equations are applied to determine scaffold routing. Ultimately, positions and orientations of each nucleotide are modeled to predict the 3D structure with full control over DNA sequence. This method produces high fidelity structures which are stable under low salt conditions, an important feature for in vitro applications.
No reliance on user feedback; effiecient
Not limited to spherical topologies as with
other methods; can produce any geometric surface
Control over physical size and DNA sequence
High fidelity structures; stable under low salt