Microfluidics and Nanofluidics

, Volume 2, Issue 1, pp 37–49 | Cite as

Modeling of coupled momentum, heat and solute transport during DNA hybridization in a microchannel in the presence of electro-osmotic effects and axial pressure gradients

Research Paper

Abstract

An integrated thermofluidic analysis of DNA hybridization, in the presence of combined electrokinetically and/or pressure-driven microchannel flows, is presented in this work. A comprehensive model is developed that combines bulk and surface transport of momentum, heat and solute with the pertinent hybridization kinetics, in a detailed manner. Results confirm that electrokinetic accumulation of DNA occurs within a few seconds or minutes, as compared to passive hybridization that could sometimes take several hours. Further, it is observed that by increasing the accumulation time, significantly higher concentration of DNA can be achieved at the capture probes. However, this eventually tends to attain a saturation state, due to a lesser probability of successful hybridization on account of a prior accumulation of target DNA molecules on the capture probe strands. While favorable pressure gradients augment DNA hybridization rates that are otherwise established by the electro-osmotic transport, adverse pressure gradients of comparable magnitude may turn out to be much less consequential in retarding the same. Such effects can be of potential significance in the designing of a microfluidic arrangement to achieve the fastest rate of DNA hybridization.

References

  1. Axelrod D, Wang MD (1994) Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. Biophys J 66:588–600PubMedGoogle Scholar
  2. Bousse L, Cohen C, Nikiforov T, Chow A, Kopfsill AR, Dubrow R, Parce JW (2000) Electrokinetically controlled microfluidic analysis systems. Annu Rev Biophys Biomo Struct 29:155–181CrossRefGoogle Scholar
  3. Chan V, Graves DJ, McKenzie SE (1995) The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys J 69:2243–2255PubMedGoogle Scholar
  4. Chan V, Graves D, Fortina P, McKenzie SE (1997) Adsorption and surface diffusion of DNA oligonucleotides at liquid/solid interfaces. Langmuir 13:320–329CrossRefGoogle Scholar
  5. Chan V, McKenzie SE, Surrey S, Fortina P, Graves DJ (1998) Effect of hydrophobicity and electrostatics on adsorption and surface diffusion of DNA oligonucleotides at liquid/solid interfaces. J Colloid Int Sci 203:197–207CrossRefGoogle Scholar
  6. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA (1996) Accessing genetic information with high-density DNA arrays. Science 274:610–614CrossRefPubMedGoogle Scholar
  7. Cheng J, Sheldon EL, Wu L, Uribe A, Gerrue LO, Carrino J, Heller M, O’Connell J (1998) Preparation and hybridization analysis of DNA/RNA from E-coli on microfabricated bioelectronic chips. Nat Biotechnol 16:541–546CrossRefPubMedGoogle Scholar
  8. Dutta P, Beskok A (2001) Analytical solution of combined electroosmotic/pressure driven flows in two-dimension straight channels: finite debye layer effects. Anal Chem 73:1979–1986CrossRefPubMedGoogle Scholar
  9. Edman FE, Raymond DE, Wu DJ, Tu E, Sosnowski RG, Butler WF, Nerenberg M, Heller MJ (1997) Electric field directed nucleic acid hybridization on microchips. Nucleic Acid Res 25:4907–4914CrossRefPubMedGoogle Scholar
  10. Edman CF, Swint RB, Gurtner C, Formosa RE, Roh SD, Lee KE, Swanson PD, Ackley DE, Coleman JJ, Heller MJ (2000) IEEE 12:1198–1200Google Scholar
  11. Erickson D, Li D, Krull UJ (2003) Dynamic modeling of DNA hybridization kinetics for spatially resolved biochips. Anal Biochem 317:186–200CrossRefPubMedGoogle Scholar
  12. Eugene T, Forster AH, Heller MJ (2000) Active microelectronic chip devices which utilize controlled electrophoretic fields for multiplex DNA hybridization and other genomic applications. Electrophoresis 21:157–164CrossRefPubMedGoogle Scholar
  13. Harrison DJ, Fluri K, Seiler K, Fan Z, Effenhauser, DF, Manz A (1993) Micromaching a miniaturized capillary electrophoresis-based chemical-analysis system on a chip. Science 261:895–897CrossRefGoogle Scholar
  14. Heller MJ (1996) An active microelectronics device for multiplex DNA analysis. IEEE Eng Med Biol 15:100–104CrossRefGoogle Scholar
  15. Kassegne SK, Resse H, Hodko D,Yang JM, Sarkar K, Smolko D, Swanson P, Raymond DE, Heller MJ, Madou MJ (2003) Numerical modeling of transport and accumulation of DNA on electronically active biochips. Sensors Actuators B 94:81–98CrossRefGoogle Scholar
  16. Livshits MA, Mirzabekov AD (1996) Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligos. Biophys J 71:2795–2801PubMedCrossRefGoogle Scholar
  17. Mala GM, Li DQ, Dale JD (1997) Heat transfer and fluid flow in microchannels. Int J Heat Mass Transfer 40:3079–3088CrossRefMATHGoogle Scholar
  18. McKnight TE, Culbertson CT, Jacobson SC, Ramsey JM (2001) Electroosmotically induced hydraulic pumping with integrated electrodes on microfluidic devices. Anal Chem 73:4045–4049CrossRefPubMedGoogle Scholar
  19. Melcher JR (1981) Continuum electromechanics. MIT Press, CambridgeGoogle Scholar
  20. Ozkan M (2001) PhD Dissertation, Department of Electrical Engineering, University of California, San Diego, CAGoogle Scholar
  21. Paces M, Lindner J, Havlica J, Kosek J, Snita D, Marek M (2000) Mathematical modeling of complex chemical microsystems in electric field. Proceedings of the fourth international conference on microreaction technology (IMRET 4) AtlantaGoogle Scholar
  22. Patankar SV (1980) Numerical heat transfer and fluid flow. Hemisphere, New YorkMATHGoogle Scholar
  23. Qu W, Li D (2000) A model for overlapped EDL fields. J Colloid Interface Sci 224:397–407CrossRefPubMedGoogle Scholar
  24. Radtkey R, Feng L, Muralhider M, Duhon M, Canter D, DiPierro D, Fallon S, Tu E, McElfresh K, Nerenberg M, Sosnowski R (2000) Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res 28:17CrossRefGoogle Scholar
  25. Reif F (1965) Fundamentals of statistical and thermal physics. McGraw-Hill, New YorkGoogle Scholar
  26. Sadana A, Ramakrishnan A (2001) A fractal analysis approach for the evaluation of hybridization kinetics in biosensors. J Colloid Interface Sci 234:9–18CrossRefPubMedGoogle Scholar
  27. SantaLucia J Jr, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting dna duplex stability. Biochemistry 35:3555–3562CrossRefPubMedGoogle Scholar
  28. Sosnowski RG, Tu E, Butler WF, O’Connell JP, Heller MJ (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc Natl Acad Sci USA 94:1119–1123CrossRefPubMedGoogle Scholar
  29. Tang GY, Yang C, Chai JC, Gong HQ (2004) Joule heating effect on electroosmotic flow and mass species transport in a microcapillary. Int J Heat Mass Transfer 47:215–227CrossRefMATHGoogle Scholar
  30. Vainrub A, Pettitt BM (2000) Thermodynamics of association to molecule immobilized in an electric double layer. Chem Phys Lett 323:160–166CrossRefGoogle Scholar
  31. Wetmur JG, Davidson N (1968) Kinetics of renaturation of DNA. J Mol Biol 31:349–370CrossRefPubMedGoogle Scholar
  32. Yang C, Li DJ (1997) Electrokinetic effects on pressure-driven liquid flows in rectangular microchannels. J Colloid Interface Sci 194:95–107CrossRefPubMedGoogle Scholar
  33. Yang RJ, Fu LM, Hwang CC (2001) Electroosmotic entry flow in a microchannel. J Colloid Interface Sci 244:173–179CrossRefGoogle Scholar
  34. Yarmush ML, Patankar DB, Yarmush DM (1996) An analysis of transport resistances in the operation of BIACORE: implications for kinetic studies of biospecific interactions. Mol Immunol 33:1203–1214CrossRefPubMedGoogle Scholar
  35. Zeng J, Almadidy A, Watterson J, Krull UJ (2002) Interfacial hybridization kinetics of oligonucleotides immobilized onto fused silica surfaces. Sensors Actuators B 90:68–75CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  1. 1.Department of Mechanical EngineeringIndian Institute of TechnologyKharagpurIndia
  2. 2.Department of Biotechnology and Biochemical EngineeringIndian Institute of TechnologyKharagpurIndia

Personalised recommendations