Micro air bubble formation and its control during polymerase chain reaction (PCR) in polydimethylsiloxane (PDMS) microreactors

Air bubble formation during polymerase chain reaction (PCR) thermocycling in microreactors has been reported as one of the major causes for PCR failure. In this paper we investigate the locations, mechanisms and other characteristics of the micro bubble formation inside a PCR microreactor array chip made by polydimethylsiloxane (PDMS) bonded with glass. The bubble formation is found to be strongly related to the micro features inside the microreactors and inside the chip bonding interface, especially near the inner corners of the microreactors, which are dependent on the micro-fabrication methods used. Gas permeability of PDMS and the wetting property of PCR sample also have influence on the air bubble formation. After investigation of various methods to control the bubble formation, we present the two most viable ones through micro bubble absorption and chip bonding interface modification. Finally, a bubble-free PCR in PDMS microreactors is demonstrated, in which the micro bubbles are suppressed with a bonding interface cladding technique.

[1]  S. Spearing,et al.  Effect of process parameters on the surface morphology and mechanical performance of silicon structures after deep reactive ion etching (DRIE) , 2002 .

[2]  Z. Osawa,et al.  Dynamics of Polymeric Solid Surfaces Treated with Oxygen Plasma: Effect of Aging Media after Plasma Treatment , 1998 .

[3]  Yuzuru Takamura,et al.  Circumventing air bubbles in microfluidic systems and quantitative continuous-flow PCR applications , 2006, Analytical and bioanalytical chemistry.

[4]  T. Merkel,et al.  Gas sorption, diffusion, and permeation in poly(dimethylsiloxane) , 2000 .

[5]  Zongyuan Chen,et al.  Thermally-actuated, phase change flow control for microfluidic systems. , 2005, Lab on a chip.

[6]  H. Wolf,et al.  Hydrophilic Poly(dimethylsiloxane) Stamps for Microcontact Printing , 2001 .

[7]  C. Brenan,et al.  High throughput, nanoliter quantitative PCR. , 2005, Drug discovery today. Technologies.

[8]  Wenyuan Chen,et al.  DNA amplification on a PDMS–glass hybrid microchip , 2006 .

[9]  Kagan Kerman,et al.  Microchamber array based DNA quantification and specific sequence detection from a single copy via PCR in nanoliter volumes. , 2005, Biosensors & bioelectronics.

[10]  Y. Hsu.  On the Size Range of Active Nucleation Cavities on a Heating Surface , 1962 .

[11]  A Manz,et al.  Miniaturised nucleic acid analysis. , 2004, Lab on a chip.

[12]  Hye Jung Cho,et al.  Precise temperature control and rapid thermal cycling in a micromachined DNA polymerase chain reaction chip , 2002 .

[13]  Zongyuan Chen,et al.  A disposable microfluidic cassette for DNA amplification and detection. , 2006, Lab on a chip.

[14]  Gwo-Bin Lee,et al.  Integrated microfluidic systems for cell lysis, mixing/pumping and DNA amplification , 2005 .

[15]  Dong-Chul Han,et al.  PDMS-based micro PCR chip with Parylene coating , 2003 .

[16]  P. H. Yap,et al.  Microfluidic handling of PCR solution and DNA amplification on a reaction chamber array biochip , 2006, Biomedical microdevices.

[17]  Robin H. Liu,et al.  Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. , 2004, Analytical chemistry.

[18]  D. Beebe,et al.  PDMS bonding by means of a portable, low-cost corona system. , 2006, Lab on a chip.

[19]  G. Peterson,et al.  Microscale heterogeneous boiling on smooth surfaces—from bubble nucleation to bubble dynamics , 2005 .

[20]  Ernesto Occhiello,et al.  On the aging of oxygen plasma-treated polydimethylsiloxane surfaces , 1990 .

[21]  P. Cheng,et al.  Bubble cavitation in a microchannel , 2004 .

[22]  Stephen R Quake,et al.  Solving the "world-to-chip" interface problem with a microfluidic matrix. , 2003, Analytical chemistry.

[23]  Patrick M. Pilarski,et al.  Small volume PCR in PDMS biochips with integrated fluid control and vapour barrier , 2006 .

[24]  Steven A Soper,et al.  Electrokinetically synchronized polymerase chain reaction microchip fabricated in polycarbonate. , 2005, Analytical chemistry.

[25]  R. Zare,et al.  Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding. , 2005, Lab on a chip.

[26]  R. Mathies,et al.  Multichannel reverse transcription-polymerase chain reaction microdevice for rapid gene expression and biomarker analysis. , 2006, Analytical chemistry.

[27]  S. Quake,et al.  Monolithic microfabricated valves and pumps by multilayer soft lithography. , 2000, Science.

[28]  James P Landers,et al.  Advances in polymerase chain reaction on microfluidic chips. , 2005, Analytical chemistry.

[29]  Q. Xiang,et al.  Real Time PCR on Disposable PDMS Chip with a Miniaturized Thermal Cycler , 2005, Biomedical microdevices.

[30]  Nathaniel C. Cady,et al.  Real-time PCR detection of Listeria monocytogenes using an integrated microfluidics platform , 2005 .

[31]  J P Landers,et al.  Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds. , 2001, Analytical biochemistry.

[32]  Thomas R Gingeras,et al.  Fifty years of molecular (DNA/RNA) diagnostics. , 2005, Clinical chemistry.

[33]  Patrick J. Smith,et al.  Plasma treatment of polydimethylsiloxane , 1994 .

[34]  W. Miles Clift,et al.  Removal of SU-8 photoresist for thick film applications , 2002 .

[35]  Igor L. Medintz,et al.  Single-molecule DNA amplification and analysis in an integrated microfluidic device. , 2001, Analytical chemistry.