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Microfluidics pp 203-260 | Cite as

Integrated Microfluidic Systems for DNA Analysis

  • Samuel K. Njoroge
  • Hui-Wen Chen
  • Małgorzata A. Witek
  • Steven A. SoperEmail author
Chapter
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 304)

Abstract

The potential utility of genome-related research in terms of evolving basic discoveries in biology has generated widespread use of DNA diagnostics and DNA forensics and driven the accelerated development of fully integrated microfluidic systems for genome processing. To produce a microsystem with favorable performance characteristics for genetic-based analyses, several key operational elements must be strategically chosen, including device substrate material, temperature control, fluidic control, and reaction product readout. As a matter of definition, a microdevice is a chip that performs a single processing step, for example microchip electrophoresis. Several microdevices can be integrated to a single wafer, or combined on a control board as separate devices to form a microsystem. A microsystem is defined as a chip composed of at least two microdevices. Among the many documented analytical microdevices, those focused on the ability to perform the polymerase chain reaction (PCR) have been reported extensively due to the importance of this processing step in most genetic-based assays. Other microdevices that have been detailed in the literature include those for solid-phase extractions, microchip electrophoresis, and devices composed of DNA microarrays used for interrogating DNA primary structure. Great progress has also been made in the areas of chip fabrication, bonding and sealing to enclose fluidic networks, evaluation of different chip substrate materials, surface chemistries, and the architecture of reaction conduits for basic processing steps such as mixing. Other important elements that have been developed to realize functional systems include miniaturized readout formats comprising optical or electrochemical transduction and interconnect technologies. These discoveries have led to the development of fully autonomous and functional integrated systems for genome processing that can supply “sample in/answer out” capabilities. In this chapter, we focus on microfluidic systems that are composed of two or more microdevices directed toward DNA analyses. Our discussions will primarily be focused on the integration of various processing steps with microcapillary electrophoresis (μCE) or microarrays. The advantages afforded by fully integrated microfluidic systems to enable challenging applications, such as single-copy DNA sequencing, single-cell gene expression analysis, pathogen detection, and forensic DNA analysis in formats that provide high throughput and point-of-analysis capabilities will be discussed as well.

Keywords

Continuous flow PCR DNA analysis DNA microarrays Genetic analysis Integrated microsystems Microcapillary electrophoresis Microfluidics Micro-PCR devices Solid-phase extraction 

Abbreviations

AOM

Aluminum oxide membranes

BPU

Biochemical processing unit

CAE

Capillary array electrophoresis

CFPCR

Continuous flow polymerase chain reaction

COC

Cyclic olefin copolymer

ddNTPs

Dideoxy nucleoside triphosphates

DNA

Deoxyribonucleic acid

dNTPS

Deoxyribonucleotide triphosphate

DRIE

Deep reactive ion etching

EDTA

Ethylenediaminetetraacetic acid

ELFSE

End-labeled free-solution electrophoresis

EOF

Electroosmotic flow

FPC

Flexible printed circuits

FSCE

Free solution conjugate electrophoresis

HEC

Hydroxyethyl cellulose

HGP

Human genome project

ITO

Indium–tin oxide

LDR

Ligase detection reaction

LPA

Linear polyacrylamides

MDR-TB

Multidrug resistant tuberculosis

MHEC

Methyl hydroxyethyl cellulose

PC

Polycarbonate

PCR

Polymerase chain reaction

PDMS

Poly(dimethylsiloxane)

PEO

Poly(ethylene oxides)

PMMA

Poly(methyl methacrylate)

PPC

Photoactivated polycarbonate

RNA

Ribonucleic acid

RTD

Resistance temperature detector

RT-PCR

Reverse transcription polymerase chain reaction

SGE

Slab gel electrophoresis

SPE

Solid-phase extraction

STRs

Short tandem repeats

TE

Thermoelectric

TTE

tris-Taps-EDTA

μCE

Microcapillary electrophoresis

μTAS

Micro-total analysis systems

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Samuel K. Njoroge
    • 1
  • Hui-Wen Chen
    • 1
  • Małgorzata A. Witek
    • 1
  • Steven A. Soper
    • 1
    • 2
    Email author
  1. 1.Department of ChemistryLouisiana State UniversityBaton RougeUSA
  2. 2.Department of Mechanical EngineeringLouisiana State UniversityBaton RougeUSA

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