DNA Computing – Introduction

Our interest in DNA computing was sparked by a presentation which Dr Jack Lutz of Iowa State University gave at Simpson in the Fall of 2010. Dr Lutz was invited to Simpson by Dr Lydia Sinapova of the Computer Science Department. The presentation was extremely well attended by faculty and students. It was the first time many in the audience were exposed to molecular self-assembly and DNA computing, and many were clearly fascinated by the ideas and possibilities of this area of research.

The talk led to discussions between Iowa State and Simpson concerning collaborative work and the establishment of a joint research project. The main goal from Simpson’s perspective was to expose our students, who are undergraduates, to this exciting field. It is important to show our students what the future may hold, and to enable them to learn the skills needs to engage with and create that future.

The basic idea behind DNA computing is quite simple, elegant and beautiful: Use DNA to encode information and implement computational algorithms using biological and chemical operations. The discipline is inherently inter-disciplinary, blending research in computer science, biology, chemistry, physics and mathematics. Making it possible for undergraduates to master such a topic is a highly challenging pedagogical task.

Firstly, many researchers are confined within the perspective of their own discipline, and face difficulties communicating with researchers in other disciplines. Entirely new vocabularies, subject matter, and methodologies have to be learned in order to create a fertile collaborative environment across multiple disciplines. It is perhaps fair to say that research in DNA computing is currently primarily multi-disciplinary rather than inter-disciplinary. Researchers in each discipline that make up the field communicate using their own vocabulary, which they have to explain to researchers in the other disciplines before effective communication can occur.

Creating a common vocabulary that all the disciplines can utilize would greatly facilitate inter-disciplinary collaboration. This objective may be easier to achieve at a small liberal arts college, like Simpson, because our faculty sizes are small, and faculty from different departments are continually interacting and collaborating. In addition, in some ways undergraduate students, who have not yet become deeply entrenched in their own discipline’s perspective, may find inter-disciplinary communication easier than more experienced faculty. This can only happen if they are exposed to the subject in an integrated, inter-disciplinary way, rather than learning bits and pieces of information from separate disciplines.

A second challenge in teaching DNA computing to undergraduates is that research in the area is done primarily by graduate students at large institutions. Here our close connection with Iowa State University’s Laboratory for Nanoscale Self-Assembly has been invaluable, since it has enabled our students to spend time working at Iowa State, gaining experience in a research laboratory while being mentored by graduate students and faculty.

A third challenge is that expensive and sophisticated equipment is needed for successful practical work in DNA computing. Fortunately, Simpson has an atomic-force-microscope (AFM). Our faculty and students have learned to use the AFM to successfully explore the world of DNA computing. We have benefited greatly from our collaboration with Iowa State, which has enabled us to improve our capabilities with the AFM.