Microfluidics and Nanofluidics

, Volume 13, Issue 1, pp 1–7 | Cite as

Optofluidic DNA computation based on optically manipulated microdroplets

Research Paper

Abstract

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.

Keywords

Optofluidics DNA computing Microdroplets Optical manipulation DNA logic operation 

References

  1. Benenson Y (2009) Biocomputers: from test tubes to live cells. Mol BioSyst 5:675–685CrossRefGoogle Scholar
  2. Mao C, Labean TH, Reif JH, Seeman NC (2000) Logical computation using algorithmic self-assembly of dna triple-crossover molecules. Nature 407:493–496CrossRefGoogle Scholar
  3. Stojanovic MN, Stefanovic D (2003) A deoxyribozyme-based molecular automaton. Nat Biotechnol 21:1069–1074CrossRefGoogle Scholar
  4. Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429:423–429CrossRefGoogle Scholar
  5. Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585–1588CrossRefGoogle Scholar
  6. Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201CrossRefGoogle Scholar
  7. Yoshida W, Yokobayashi Y (2006) Photonic Boolean logic gates based on DNA aptamers. Chem Commun 14:195–197Google Scholar
  8. Reif JH (2011) Scaling up DNA computation. Science 332:1156–1157CrossRefGoogle Scholar
  9. Huebner A, Sharma S, Srisa-Art M, Hollfelder F, Edel JB, deMello AJ (2008) Microdroplets: a sea of applications. Lab Chip 8:1244–1254CrossRefGoogle Scholar
  10. Teh SY, Lin R, Hung LH, Lee AP (2008) Droplet microfluidics. Lab Chip 8:198–220CrossRefGoogle Scholar
  11. Dittrich PS, Manz A (2006) Lab-on-a-chip: microfluidics in drug discovery. Nat Rev Drug Discov 5:210–218CrossRefGoogle Scholar
  12. Grover WH, Mathies RA (2005) An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. Lab Chip 5:1033–1040CrossRefGoogle Scholar
  13. Zhang Y, Yu H, Qin J, Lin B (2009) A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis. Biomicrofluidics 3:44105CrossRefGoogle Scholar
  14. Gahagan KT, Swartzlander GA (1998) Trapping of low-index microparticles in an optical vortex. J Opt Soc Am B 15:524–534CrossRefGoogle Scholar
  15. Sasaki K, Koshioka M, Misawa H, Kitamura N, Masuhara H (1992) Optical trapping of a metal particle and a water droplet by a scanning laser beam. Appl Phys Lett 60:807–809CrossRefGoogle Scholar
  16. Reiner JE, Crawford AM, Kishore RB, Goldner LS, Helmerson K, Gilson MK (2006) Optically trapped aqueous droplets for single molecule studies. Appl Phys Lett 89:013904Google Scholar
  17. Lorenz RM, Edgar JS, Jeffries GDM, Zhao Y, McGloin D, Chiu DT (2007) Vortex-trap-induced fusion of femtoliter-volume aqueous droplets. Anal Chem 79:224–228CrossRefGoogle Scholar
  18. Ogura Y, Nishimura T, Tanida J (2011) Spatially parallel control of DNA reactions in optically manipulated microdroplets. J Nanophoton 5: 051702Google Scholar
  19. Prentice P, MacDonald M, Frank T, Cuschier A, Spalding G, Sibbett W, Campbell P, Dholakia K (2004) Manipulation and filtration of low index particles with holographic Laguerre–Gaussian optical trap arrays. Opt Express 12:593–600CrossRefGoogle Scholar
  20. Eriksen R, Daria V, Gluckstad J (2002) Fully dynamic multiple-beam optical tweezers. Opt Express 10:597–602Google Scholar
  21. Bengtsson J (1994) Kinoform design with an optimal-rotation-angle method. Appl Opt 33:6879–6884CrossRefGoogle Scholar
  22. Nkodo AE, Garnier JM, Tinland B, Ren H, Desruisseaux C, McCormick LC, Drouin G, Slater GW (2001) Diffusion coefficient of DNA molecules during free solution electrophoresis. Electrophoresis 22:2424–2432CrossRefGoogle Scholar
  23. Ogura Y, Kazayama Y, Nishimura T, Tanida J (2011) Large-area manipulation of microdroplets by holographic optical tweezers based on a hybrid diffractive system. Appl Opt 50:H36–H41CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Graduate School of Information Science and TechnologyOsaka UniversitySuita,Japan

Personalised recommendations