On-Chip, Real-Time,
Single-Copy Polymerase Chain Reaction in Picoliter Droplets
N.
Reginald Beer, Benjamin J. Hindson, Elizabeth K. Wheeler, Sara B. Hall,
Klint A. Rose, Ian M. Kennedy, and Bill W. Colston
Lawrence
Livermore National Laboratory, 7000 East Avenue, Livermore, California
94551, and Department of Mechanical
and
Aeronautical Engineering, University of California, Davis, California
95616
Anal.
Chem.2007, 79,8471-8475
The first lab-on-chip
system for picoliter droplet generation and PCR amplification with
real-time fluorescence detection has performed PCR in isolated droplets
at volumes 106 smaller than commercial real-time PCR instruments. The
system utilized a shearing T-junction in a silicon device to generate a
stream of monodisperse picoliter droplets that were isolated from the
microfluidic channel walls and each other by the oil-phase carrier. An
off-chip valving system stopped the droplets on-chip, allowing them to
be thermally cycled through the PCR protocol without droplet motion.
With this system, a 10-pL droplet, encapsulating less than one copy of
viral genomic DNA through Poisson statistics, showed realtime PCR
amplification curves with a cycle threshold of 18, 20 cycles earlier
than commercial instruments. This combination of the established
real-time PCR assay with digital microfluidics is ideal for isolating
single-copy nucleic acids in a complex environment.
On-Chip Single-Copy Real-Time Reverse-Transcription PCR in Isolated
Picoliter Droplets
N.
Reginald Beer, Elizabeth K. Wheeler, Lorenna Lee-Houghton, Nicholas
Watkins, Shanavaz Nasarabadi,
Nicole Hebert, Patrick Leung, Don W. Arnold, Christopher G. Bailey, and
Bill W. Colston
Lawrence
Livermore National Laboratory, 7000 East Avenue, Livermore, California
94551, Department of Biological
Engineering,
Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
Department of Electrical and
Computer
Engineering, Purdue University, West Lafayette, Indiana 47907, and
Eksigent Technologies, Dublin, California
94568
Anal.
Chem.2008, 80,1854-1858
The first lab-on-chip
system for picoliter droplet generation and RNA isolation, followed by
reverse transcription, and PCR amplification with real-time
fluorescence detection in the trapped
droplets has been developed. The system utilized a shearing T-junction
in a fused-silica device to generate a stream of monodisperse
picoliterscale droplets that were isolated from the microfluidic
channel walls and each other by the oil-phase carrier. An off-chip
valving system stopped the droplets on-chip, allowing thermal cycling
for reverse transcription and subsequent PCR amplification without
droplet motion. This combination of the established real-time reverse
transcription-PCR assay with digital microfluidics is ideal for
isolating single-copy RNA and virions from a complex environment and
will be useful in viral discovery and gene-profiling applications.
Rapid microfluidic thermal cycler for polymerase chain reaction nucleic
acid amplification
Shadi Mahjoob, Kambiz Vafai, N. Reginald Be
Mechanical
Engineering Department, University of California, Riverside, CA 92521,
USA
Lawrence
Livermore National Laboratory, Center for Micro and Nanotechnology, USA
International
Journal of Heat and Mass Transfer 51 (2008) 2109–2122
Polymerase chain
reaction (PCR) is widely used in biochemical analysis to amplify DNA
and RNA in vitro. The PCR process is highly temperature sensitive, and
thermal management has an important role in PCR operation in reaching
the required temperature set points at each step of the process. The
goal of this research is to achieve a thermal technique to rapidly
increase the heating/cooling thermal cycling speed while maintaining a
uniform temperature distribution throughout the substrate containing
the aqueous nucleic acid sample. In this work, an innovative
microfluidic PCR thermal cycler, which utilizes a properly arranged
configuration filled with a porous medium, is investigated. Various
effective parameters that are relevant in optimizing this flexible heat
exchanger are investigated such as heat exchanger geometry, flow rate,
conductive plate, the porous matrix material, and utilization of
thermal grease. An optimized case is established based on the effects of
the cited parameters on the temperature distribution and the required
power for circulating the fluid in the heat exchanger. The results
indicate that the heating/cooling temperature ramp of the proposed PCR
heat exchanger is considerably higher (150.82 °C/s) than those in
the literature. In addition, the proposed PCR offrs a very uniform
temperature in the substrate while utilizing a low power.
High-Throughput
Quantitative Polymerase Chain Reaction in Picoliter Droplets
Margaret
Macris Kiss, Lori Ortoleva-Donnelly, N. Reginald Beer, Jason Warner,
Christopher G. Bailey,
Bill W. Colston, Jonathon M. Rothberg, Darren R. Link, and John H. Leamon
Raindance
Technologies, 44 Hartwell Avenue, Lexington, Massachusetts 02421, and
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore,
California 94551
Anal.
Chem. 2008, 80, 8975–8981
Limiting dilution PCR
has become an increasingly useful technique for the detection and
quantification of rare species in a population, but the limit of
detection and accuracy of quantification are largely determined by the
number of reactions that can be analyzed. Increased throughput may be
achieved by reducing the reaction volume and increasing processivity.
We have designed a high-throughput microfluidic chip that encapsulates
PCR reagents in millions of picoliter droplets in a continuous oil
flow. The oil stream conducts the droplets through alternating
denaturation and annealing zones, resulting in rapid (55-s cycles) and
efficient PCR amplification. Inclusion of fluorescent probes in the PCR
reaction mix permits the amplification process to be monitored within
individual droplets at specific locations within the micro-fluidic
chip. We show that amplification of a 245-bp adenovirus product can be
detected and quantified in 35 min at starting template concentrations
as low as 1 template molecule/167 droplets (0.003 pg/µL). Thefrequencies of
positive reactions over a range of template concentrations agree
closely with the frequencies predicted by Poisson statistics,
demonstrating both the accuracy and sensitivity of this platform for
limiting dilution and digital PCR applications.
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