Optically programming DNA computing in microflow reactors

The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techni ques. A magnetically switchable selective transfer module (STM) is presente d which implements the basic sequence-specific DNA filtering operation unde r constant-flow. Secondly, a single steady flow system of STMs is presented which solves an arbitrary instance of the maximal clique problem of given maximum size N. Values of N up to about 100 should be achievable with curre nt lithographic techniques. The specific problem is encoded in an initial l abeling pattern of each module with one of 2N DNA oligonucleotides, identic al for all instances of maximal clique. Thirdly, a method for optically pro gramming the DNA labeling process via photochemical lithography is proposed , allowing different problem instances to be specified. No hydrodynamic swi tching of flows is required during operation - the STMs are synchronously c locked by an external magnet. An experimental implementation of this archit ecture is under construction and will be reported elsewhere. (C) 2001 Elsev ier Science Ireland Ltd. All rights reserved.