A Sticker Based Model for DNA Computation

Abstract

We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is represented and of separation by hybridization as a central mechanism. However, unlike previous models, the stickers model has a random access memory that requires no strand extension, uses no enzymes, and (at least in theory) its materials are reusable. The paper describes computation under the stickers model and discusses possible means for physically implementing each operation. We go on to propose a specific machine architecture for implementing the stickers model as a microprocessor-controlled parallel robotic workstation. Finally, we discuss several methods for achieving acceptable overall error rates for a computation using basic operations that are error prone. In the course of this development a number of previous general concerns about molecular computation [Smith, Hartmanis, Letters to Sci..