Conference on DNA Computing Liveblog 1

Today is day one of the International Conference on DNA Computing and Molecular Programming (DNA19). The first day is a “tutorial session” which is a conference feature that new to me. I like the idea, though: catch everyone up and get on the same page for the rest of the conference. The sessions were oriented to reviews of the field and introductions to new tools. Prof. Kurt Gothelf discussed primarily structure. Most of this is fairly familiar to me: DNA has been used to build increasingly complex physical and computational designs over the last 10-15 years.

DNA origami was very popular in the scientific media for a while. It has expanded into moving/actuated structures and 3 dimensions. It is starting to go from intellectual curiosity to functional nano-objects. I’m confident we’ll talk more about the functions of these constructs this week, but for today it was essentially a single slide about nanopores.

Fritz Simmel talked about the thermodynamics of nanostructures. The force of water molecules on a dissolved molecule/structure is about 500 pN. Particles are bouncing around in random directions at m/sec speeds even though these objects are angstroms in size. Familiar macro scale objects have opposite properties: smaller ambient vibrations relative to object size. Engineering functional systems is difficult when all of our intuitions are backwards.

Andrew Phillips then talked about a new tool for designing DNA-DNA reactions called Visual DSD. I especially liked this talk. Phillips works for Microsoft Corporation. The software presented allows the user to specify DNA designs at a high level of abstraction. Instead of spelling out ATGC, the user design “domains” of about 8 to 10 bases and give them names. Domains and their complementary sequences have well-defined behavior. So the user can manipulate dozens of domains into more elaborate designs.

The software is capable of taking designed molecules and computing the formulas of the reactions that will happen. Essentially, it will simulate the time course of any reaction that the DNA reactants might undergo. That is actually quite remarkable. I don’t know of any other chemical system where you can design the reactants and have a computer accurately predict and simulate the full reaction in over time. I’m looking forward to playing with the software.