Optically programming DNA computing in microflow reactors

Abstract

The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techniques. A magnetically switchable selective transfer module (STM) is presented which implements the basic sequence-specific DNA filtering operation under 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 current lithographic techniques. The specific problem is encoded in an initial labeling pattern of each module with one of 2N DNA oligonucleotides, identical for all instances of maximal clique. Thirdly, a method for optically programming the DNA labeling process via photochemical lithography is proposed, allowing different problem instances to be specified. No hydrodynamic switching of flows is required during operation -the STMs are synchronously clocked by an external magnet. An experimental implementation of this architecture is under construction and will be reported elsewhere.

PDMS valves in DNA computers

“…However, beads have to be somehow fixed in the microfluidic system. One way to trap beads in a certain location, or microreactor, is to use bead barriers [10]. Barriers are elevated sections in the microchannel which leaves a gap between the device cover and barrier which is smaller than the bead's diameter.…”

A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem

“…These microfluidic devices can implement a dataflow-like architecture for processing DNA (see [6] and [12]) and could be a good support for the distributed biomolecular computing model called tissue P systems (or tP systems for short) [11]. The underlying computational structure of tP systems are graphs or networks of connected processors that could easily be translated to microchambers (cells or processors) connected with microchannels.…”

“…There are several previous works on DNA computing using microfluidic systems [6,12,4,8,9]. One [8] describes the design of a linear time DNA algorithm for the Hamiltonian Path Problem (HPP) suited for parallel implementation using a microfluidic system (this bioalgorithm shares some features with the algorithm for the Shortest Common Superstring Problem presented in this paper).…”

“…In another paper, Gehani and Reif [6] study the potential of biomolecular microflow computation, describe methods to efficiently route strands between chambers, and determine theoretical lower bounds on the quantities of DNA and the time needed to solve a problem in the microflow biomolecular model. Two other works [12,4] solve the Maximum Clique Problem with microfluidic devices. This is an NP-complete problem.…”

“…This is an NP-complete problem. McCaskill [12] takes a brute-force approach codifying every possible subgraph in a DNA strand. The algorithm uses the so-called Selection Transfer Modules (STM) to retain all possible cliques of the graph.…”