Optofluidic DNA computation based on optically manipulated microdroplets

DNA computing is a promising approach for dealing with biomolecular information. Although several DNA logic circuits which can evaluate biomolecular inputs have been proposed, they have serious drawbacks in the processing speed and the amount of molecules used in implementation. Here, we present optofluidic DNA computation as an effective method for constructing a DNA computing system. By confining the reaction space of DNA computation to the inside of a microdroplet and manipulating a group of droplets with external light signals, we improve usability of DNA computation as well as the processing performance. Optical manipulation is applied to transport the droplets and to initiate DNA computation by forced merging of the droplets. The proposed method has advantages over conventional DNA computation schemes in flexible operations, simultaneous multiplexed evaluation, and processing acceleration. As the first demonstration of optofluidic DNA computation, logical AND and OR operations are performed by optical manipulation of microdroplets which contain either DNA logic gates or input molecules. Also, considerable reduction in the processing time is confirmed on the optofluidic DNA computation owing to reduction of the reaction space to the microdroplet.

[1]  John H. Reif.  Scaling Up DNA Computation , 2011, Science.

[2]  J Bengtsson.  Kinoform design with an optimal-rotation-angle method. , 1994, Applied optics.

[3]  Monpichar Srisa-Art,et al.  Microdroplets: a sea of applications? , 2008, Lab on a chip.

[4]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[5]  Jianhua Qin,et al.  A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis. , 2009, Biomicrofluidics.

[6]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[7]  David McGloin,et al.  Vortex-trap-induced fusion of femtoliter-volume aqueous droplets. , 2007, Analytical chemistry.

[8]  W Sibbett,et al.  Manipulation and filtration of low index particles with holographic Laguerre-Gaussian optical trap arrays. , 2004, Optics express.

[9]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[10]  Michael K. Gilson,et al.  Optically trapped aqueous droplets for single molecule studies , 2006 .

[11]  Jesper Gluckstad,et al.  Fully dynamic multiple-beam optical tweezers. , 2002, Optics express.

[12]  Spatially parallel control of DNA reactions in optically manipulated microdroplets , 2011 .

[13]  Richard A Mathies,et al.  An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. , 2005, Lab on a chip.

[14]  Grover A. Swartzlander,et al.  Trapping of low-index microparticles in an optical vortex , 1998 .

[15]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[16]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

[17]  Laurette C. McCormick,et al.  Diffusion coefficient of DNA molecules during free solution electrophoresis , 2001, Electrophoresis.

[18]  Yaakov Benenson,et al.  Biocomputers: from test tubes to live cells. , 2009, Molecular bioSystems.

[19]  J. Tanida,et al.  Large-area manipulation of microdroplets by holographic optical tweezers based on a hybrid diffractive system. , 2011, Applied optics.

[20]  Hiroshi Masuhara,et al.  Optical trapping of a metal particle and a water droplet by a scanning laser beam , 1992 .

[21]  A. Manz,et al.  Lab-on-a-chip: microfluidics in drug discovery , 2006, Nature Reviews Drug Discovery.

[22]  Wataru Yoshida,et al.  Photonic Boolean logic gates based on DNA aptamers. , 2007, Chemical communications.