What is DNA?

DNA is a molecule that acts as a library of genetic information. DNA consists of hundreds of thousands to billions of chemicals called nucleotides attached in a long chain. Specific sequences of these nucleotides describe genes, the instructions for how and when to create specific proteins. Via another molecule, RNA, the genes encoded in DNA are turned into the proteins that organisms are built from and kept alive by. In Nanocrafter, you use DNA as a building block rather than for its normal genetic function.

What is synthetic biology?

The past few decades have seen incredible advances in biology that have allowed us to look deeper into the systems of life and understand them better - and to go beyond that to start building our own systems. Scientists racing to catalog the genetic material of the organisms living on Earth developed new technologies: technologies that allow them to identify molecules of DNA easily and cheaply, and produce new ones in custom patterns. This has lead to the use of DNA for something besides their natural purpose: when removed from their normal place within cellular machinery, DNA can act as a building block.

In the 1990s, scientists discovered that certain specially-designed DNA molecules, called DNA circuits, can be used to solve logic problems in much the way computers can. In 2006, the Seelig Lab at the University of Washington discovered a new way of constructing these DNA circuits, using only a few simple rules that we think even non-scientists can learn. So the Center for Game Science and the Seelig Lab teamed up to build Nanocrafter: a game that lets you build DNA circuits to solve problems, share them with your friends, and eventually invent new structures that may be of scientific value.

Why build things with DNA?

Nucleic acids - DNA and RNA - are the ideal molecules for creating many types of biomolecular systems; they can be easily programmed by logically designing their base sequences. Nucleic acids are a uniquely promising substrate for a molecular programming approach because the base sequence and the rules of Watson Crick base pairing predictably determine how single-stranded nucleic acids interact with one another. For decades, RNA has been engineered to play functional roles within the cell and in biotech applications. More recently and perhaps more impressively, DNA has been used as a material for the self-assembly of complex two- and three-dimensional structures, as a substrate for molecular computation and for the rational design of molecular devices and motors with moving parts.

Many of these devices rely on a phenomenon know as strand displacement. Strand displacement is the process through which two strands with partial or full complementarity hybridize to each other, displacing one or more pre-hybridized strands in the process. This is a key mechanism for the dynamic DNA systems that you can design in Nanocrafter, and part of what makes it such a good molecule for synthetic biology: not only is it inexpensive to produce, relatively hearty, and chemically well-understood, strand displacement gives DNA a predictable, dependable reaction to harness.

Why is this game important?

The key to Nanocrafter is to allow humans to do what they are good at, and computers to do what they are good at. In this case, humans exceedingly outperform computers with their creativity. The space of all possible bio-molecular systems is vastly larger than what a computer can search - yet human creativity and insight to build systems can lead to focused discoveries in this space. However, computers can quickly simulate, verify, and potentially perform local optimizations on player designs - something that would be tedious and inefficient for humans to perform. By designing new inventions and then simulating them in the game, we hope that players will come up with new ideas that can be applied to ongoing research in the field.