DNA Nanotechnology

Biology uses chemicals with complex interfaces, whether they be shape charge, hydrophobicity / hydrophilicty in order to encode its programs. I use synthetic DNA, which has simple, well-understood chemistry and a combinatorial number of interfaces, in the form of sequences of base pairs. Short DNA (< 100 base pairs) with any desired sequence can be mail-ordered and is relatively cheap, and biological DNA with a pre-specified sequences of a length of about 7000 base pairs is also cheaply available commercially. DNA physical chemistry is well understood and there is an energy model that allows one to predict the energy by which two strands add given their sequences, concentrations and the temperature and buffer conditions.
B-form DNA is a right-handed helix with 10.5 bases (A,T,G or C) per turn.
"Crossover points," where one strand is part of 2 adjacent helices, allow us to weave structures consisting of many helices.

The above image is a "ribbon diagram" of a DNA structure consisting of 4 strands (each in a single color). Each strand spans two helices, "crossing over" from one to another at crossover points. The sequences of the strands are designed such that the double helical regions of the assembly above have complementary base pairs, and that the assembly represents the maximal amount of complementary bases achievable.

Above is a more elaborate structure consisting of many DNA strands, using the same crossover motif. Reuse of the motif and the use of strands with specific sequences allow us to create designed, extended structures.

The use of synthetic DNA for nanoscale construction was pioneered by Nadrian Seeman. Some past highlights that give an idea of what is possible with DNA assembly include the assembly of a DNA cube, assembly of designed two-dimensional crystal lattices and the assembly of nanoscale shapes using the scaffolded DNA origami technique in 2 dimensions and 3 dimensions.

I am interested in the possibilities of active assembly, where instead of simply statically creating structures, we produce processes of controlled assembly and disassembly in response to the environment. Details of my work can be found here.