Self-assembly of DNA into nanoscale three-dimensional shapes

A key challenge for biomolecular nanotechnologists is to develop methods to use nanoscale primitives for "bottom-up fabrication" of structures that rival the size and complexity of those found in nature. In 1982, Nadrian Seeman laid the theoretical framework for using DNA as a nanoscale building material by suggesting that stable branched motifs could be created out of synthetic DNA oligonucleotides. Subsequently, DNA has been used to make increasingly complex shapes and lattices. In 2006, Rothemund introduced "scaffolded DNA origami", a versatile method that he used to construct diverse planar shapes with dimensions of 100 nm in diameter and 6 nm spatial resolution. The method uses hundreds of short oligonucleotide "staple" strands to direct the folding of a long, single strand of DNA into a programmed arrangement. We have extended Rothemund's method to building three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We constructed several shapes with precisely controlled dimensions ranging from 10 to 100 nm, and found that proper assembly requires weeklong folding times and calibrated monovalent and divalent cation concentrations. Expanding on previous work that has focused primarily on pure oligo-based DNA nanostructures, or variations on planar DNA origami similar to Rothemund's original designs, we have developed caDNAno, an open-source software package for designing 3D DNA origami shapes.;For each advance in fabrication methods, a second key challenge is to realize demand-meeting applications. We have developed the first detergent-compatible liquid crystal for NMR structure determination of membrane proteins. Membrane proteins comprise approximately one-third of the human genome but represent less than 1% of known structures. By weakly aligning membrane proteins under a strong magnetic field, orientation constraints in the form of NMR dipolar couplings can be measured and used for structure determination. Previously known liquid-crystalline alignment media (such as concentrated Pf1 phage) worked for soluble proteins, but were incompatible with detergents necessary for solubilization of membrane proteins. Our DNA-nanotube-based alignment medium was validated by measurements on transmembrane domain of the zeta-zeta chain of the T-cell receptor complex and a 40 kD truncated version of the influenza B virus BM2 channel.