BIC: Enzyme Driven Autonomous Biomolecular Computer

The Scripps Research Institute, La Jolla CA

Investigators

Abstract

This project involves connections between formal language theory, finite state machines and biomolecular protocols, and consists of three main tasks: 1.Developing an autonomous read-write transducer and automata with unbounded memory encoded on circular plasmids. 2.Scaling up the computational process allowing these finite state machines to perform parallel computation while immobilized on surfaces. 3.Taking the molecular computing concept one step further by showing that the output can be not just for a specific molecule, but also for a specific biological function, proving that biomolecular computing can be biologically relevant. The two main approaches include: (a) control over the open reading frame (ORF) of an enzyme-encoding gene, and (b) design of biologically meaningful output signals such as bacteria possessing either fluorescent proteins or antibiotic-resistance properties. The project prototypes a molecular machine that is autonomous and produces an output that can potentially serve as an input for a new molecular automaton or as a template for biological organization and regulate gene expression. Methods include real time observation of the automaton dynamics and has a potential for an algorithmic control and modification of DNA strands and genes. Theoretically, the design of the automaton calls for investigations of new types of splicing systems. The process for scaling up the computations may lead to a new crypto system as well as more rapid tests for genetic disorders that are triggered by a combination of mutations. Very few individuals enter the field of DNA-based computation with proper preparation. We will attempt to provide some solutions to this problem during the course of the project. All graduates, undergraduates and high school students who participate in this work will be trained and prepared as unique interdisciplinary research scientists. We anticipate that three graduate students will receive graduate training through this award.