PDMS valves in DNA computers

Abstract

DNA computing is an interdisciplinary field accessing the possibility for the use of biomolecules, such as DNA, RNA and proteins, as a computational or control tool. Traditionally, DNA computers were thought to compete with electronic computers to solve, for example, NP-complete problems. However recently, there has been a focus shift to biomedical applications. One form of DNA computing is performed in microfluidics. A network of microreactors decides the computational aspects and DNA is the tool for selection procedures. To control complex microflow systems like this, a series of pneumatic valves are used to control the flow direction, i.e. the information direction, and to contain DNA functionalised beads in the microreactors.

Abstraction layers for scalable microfluidic biocomputing

“…Apart from being amenable to computer control, microfluidics drastically reduces the volumes of samples, thereby reducing costs and improving capture kinetics. Using microfluidics, DNA hybridization times can be reduced from 24 hours to 4 minutes [van Noort and Zhang, 2004] and the number of bases needed to encode information can be decreased from 15 bases per bit to 1 base per bit [Braich et al, 2002, van Noort, 2005.…”

“…For example, a 20-variable 3-SAT problem required 96 hours to complete [Braich et al, 2002], not counting the considerable time needed for setup and evaluation. To automate and optimize this process, researchers have turned to microfluidic devices [Farfel and Stefanovic, 2005, Gehani and Reif, 1999, Grover and Mathies, 2005, Livstone et al, 2006, McCaskill, 2001, Somei et al, 2005, van Noort, 2005, van Noort et al, 2002, van Noort and Zhang, 2004. Microfluidics offers the promise of a "lab on a chip" system that can individually control picoliter-scale quantities of fluids, with integrated support for operations such as mixing, storage, PCR, heating/cooling, cell lysis, electrophoresis, and others [Breslauer et al, 2006, Erickson and Li, 2004, Sia and Whitesides, 2003.…”

A proposed modularized DNA computer, based on biochips

“…Such reports refer to multiple steps on one sample being carried out simultaneously or in a step wise fusion. Continuous or online assays for different samples are referenced far less [15], [16], [17], [18], [19], [20], [21], [22], [23]. The reason for this is that most systems lack an efficient method to exchange samples, thus this becomes the bottleneck in the application.…”

Abstraction Layers for Scalable Microfluidic Biocomputers

“…Apart from being amenable to computer control, microfluidics drastically reduces the volumes of samples, thereby reducing costs and improving capture kinetics. Using microfluidics, DNA hybridization times can be reduced from 24 hours to 4 minutes [10] and the number of bases needed to encode information can be decreased from 15 bases per bit to 1 base per bit [1,8]. Thus has emerged a vision for creating a hybrid DNA computer: one that uses microfluidics for the plumbing (the control paths) and biological primitives for the computations (the ALUs).…”

“…For example, a 20-variable 3-SAT problem required 96 hours to complete [1], not counting the considerable time needed for setup and evaluation. To automate and optimize this process, researchers have turned to microfluidic devices [2][3][4][5][6][7][8][9][10]. Microfluidics offers the promise of a "lab on a chip" system that can individually control picoliter-scale quantities of fluids, with integrated support for operations such as mixing, storage, PCR, heating/cooling, cell lysis, electrophoresis, and others [11][12][13].…”