William M. Shih
Professor, Department of Cancer Biology, Dana-Farber Cancer Institute
Founding Core Faculty, Wyss Institute at Harvard University
We explore design principles for self-assembling molecular machines, primarily usinge structural DNA nanotechnology as our model system.
Tools For Molecular Biophysics:
NMR Structure Determination of Membrane Proteins An outstanding problem in biology is the efficient structure determination of transmembrane proteins. Residual dipolar couplings (RDCs), commonly measured for biological macromolecules weakly aligned by liquid-crystalline media, are important global orientation restraints for NMR structure determination. However, none of the existing liquid-crystalline media used to align water-soluble proteins are compatible with the detergents required to solubilize membrane proteins. In collaboration with James Chou at Harvard Medical School, we generated detergent-resistant liquid crystals of 0.8-μm-long DNA nanotubes that enable weak alignment of detergent-reconstituted membrane proteins. This DNA-nanotube liquid crystal will introduce the advantages of weak alignment to NMR structure determination for a number of membrane proteins.
To generalize further the method (e.g. compatibility with positively-charged protein-micelle complexes) and to facilitate measurement of linearly-independent restraints (i.e. more structural information), we are working to generate additional DNA-nanostructure based alignment media.
Single-Molecule Biophysics Single-molecule approaches provide a powerful tool for mechanistic investigation of biomolecular systems. Compared to bulk methods, analysis of individual molecules allows more direct measurement of microscopic forces and a more direct observation of changes in microscopic state, oftentimes obviating the need for technically challenging system synchronization. We seek to take advantage of the fine positional control afforded by DNA nanostructures to constrain and report on biomolecular complexes in ways that facilitate their study using single-molecule approaches. For example, exerting forces with nanoscale devices (as oppose to top-down devices such as optical traps or atomic-force microscopes) can be used to produce a system that in many cases is more amenable to study by single molecule fluorescence.
Tools for Therapeutics:
Drug Delivery DNA nanotechnology affords unprecedented control over macromolecular shape and site-specific functionalization. We are investigating the effect of DNA nanostructure shape, size, and chemical functionalization on the rate of uptake of such particles into cells. We are especially interested in delivery of antigens and danger signals to dendritic cells towards improved cancer vaccines. As a longer-term challenge, we also seek to design DNA-scaffolded molecular machines that enable controlled passage through biological membranes, by either triggered membrane fusion or triggered membrane pore formation.
Enabling Technology Development for DNA Nanoconstruction:
The complexity of integrated circuits has doubled every eighteen months or so over the past 40 years. This staggering increase in computing capability has transformed society. Our field seeks a similar trajectory of exponential advancement for programmable self-assembling systems. We try to maintain subnanometer positional control while constructing DNA scaffolds that are ever larger and more complex. At the same time, we think about how we could scale up the mass quantities of scaffolds that we could produce, towards constructing macroscale objects from these materials. We also are interested in generating dynamic molecular machines and devices.
Tian Y, Wang T, Liu W, Xin HL, Li H, Ke Y, Shih WM, Gang O. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. Nat Nanotechnol 10, 637–644, 2015.
Shih WM. Materials Science. Exploiting weak interactions in DNA self-assembly. Science 347, 1417–1418, 2015.
Kocabey S, Kempter S, List J, Xing Y, Bae W, Schiffels D, Shih WM, Simmel FC, Liedl T. Membrane-assisted growth of DNA origami nanostructure arrays. ACS Nano 9, 3530–3539, 2015.
Ke Y, Ong LL, Sun W, Song J, Dong M, Shih WM, Yin P. DNA brick crystals with prescribed depths. Nat Chem. 6, 994–1002, 2014.
Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM. Self-assembly of DNA into nanoscale shapes. Nature 459, 414–418, 2009.
Longwood Center, LC3313
360 Longwood Avenue, Boston, MA 02215
Ctr. for Life Science Bldg. Room 541,
3 Blackfan Circle, Boston MA 02115