Computational Design of Next-generation Nanoscale DNA-based Materials

Project Personnel

Mark Bathe

Principal Investigator

Massachusetts Institute of Technology (MIT)


Hao Yan

Arizona State University


Peng Yin

Harvard University


Funding Divisions

Division of Chemical, Bioengineering, Environmental, and Transport Systems (CBET), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA)

The major goal of this project is to develop general strategies to synthesize programmed DNA architectures based on physical design principles that can be encoded in predictive computational models. Synthetic strategies we are exploring include traditional scaffolded DNA origami that utilizes a single-stranded scaffold to template shorter synthetic oligonucleotides, purely single-stranded DNA and RNA origami in which single-stranded DNA or RNA fold into a complex user-specified shape without the use of helper strands, and single-stranded tiles that self-assemble without the use of a scaffold strand. Additional major goals are to (1) extend single-stranded tile DNA-brick technology to construct robust and diverse nanostructures; (2) develop a versatile sub-micrometer three-dimensional (3D) building blocks, termed Meta-DNA, to construct complex DNA meta-molecules and constructs on the micron scale, and produce 1D and 2D arrays based on a new structural motif: the double T-junction; and (3) convert DNA assemblies into functional materials for a wide range of applications. Based on our understanding of self-assembly and yield, we propose to increase structural complexity and diversity, improve assembly yield and fidelity, and extend scaffold-free assembly to other materials. Meanwhile, we pursue post-assembly modifications of resulting DNA and RNA nanostructures for real-world applications including lithography, therapeutics, structural biology, excitonics, and photonics.