DNA Computing in Microreactors
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
Journal of Computer Science and Technology - Special issue on bioinformatics
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The paper demonstrates experimentally the basic principle of DNA transfer between magnetic bead based selection stages, which can be used in steady flow microreactors for DNA Computing [McCaskill, J.S.: Biosystems, 59 (2001) 125-138] and molecular diagnostics. Short DNA oligomers, which can be attached covalently to magnetic beads by a light programmable photochemical procedure [Penchovsky et.al.: Nucleic Acids Res., 22 (2000) e98], are used to bind matching ssDNA from a flowing solution. The beads are restrained in two reaction chambers (modules) by etched ledges in a bonded microreactor made of silicon and glass, with the solutions flowing in closed micro-channels. The action of a steady flow network of selection modules is studied in this two chamber microreactor using a succession of different buffer solutions at alternate pH to simulate the transfer between parallel flows in the former system. The pH changes cause successive hybridisation and dissociation of ssDNA to matching sequences on the beads. Detection of DNA is by fluorescence from rhodamine-labelled target DNA. The results demonstrate the successful selection of specific DNA in one module and its subsequent transfer to and pickup on the magnetic beads of a second module. This verifies the biochemical operation of the basic processing step for optically programmable DNA Computing in micro-flow reactors.