Comparison of Different Strategies on DNA Chip Fabrication and DNA-Sensing: Optical and Electrochemical Approaches

New strategies for the construction of DNA chips and the detection of DNA hybridization will be discussed in this review. The focus will be on the use of polypyrrole as a linker between a substrate and oligonucleotide probes. The modification step is based on the electrochemical copolymerization of pyrrole and oligonucleotides bearing a pyrrole group on its 5′ end. This strategy was employed for the immobilization of oligonucleotides on millimeter-sized electrodes, microelectrode arrays, as well as for the local structuring of homogeneous gold surfaces. Our approaches for the localized patterning of gold surfaces will be also discussed. Localized immobilization was achieved by using an electrospotting technique, where a micropipette served as an electrochemical cell where spot sizes with 800 μm diameters were fabricated. The use of a microcell using a Teflon covered metal needle with a cavity of 100 μm resulted in immobilized probe spots of 300 μm. Scanning electrochemical microscopy (SECM) was also used, and surface modifications of 100 μm were obtained depending on the experimental conditions. Different detection methods were employed for the reading of the hybridization event: fluorescence imaging, surface plasmon resonance imaging (SPRI), photocurrent measurements, and voltamperometric measurements using intercalators. Their advantages concerning the various immobilization strategies will also be discussed.

[1]  G Marrazza,et al.  Detection of human apolipoprotein E genotypes by DNA electrochemical biosensor coupled with PCR. , 2000, Clinical chemistry.

[2]  Hafsa Korri-Youssoufi,et al.  Toward Bioelectronics: Specific DNA Recognition Based on an Oligonucleotide-Functionalized Polypyrrole , 1997 .

[3]  Thierry Delair,et al.  Toward intelligent polymers: DNA sensors based on oligonucleotide-functionalized polypyrroles , 1999 .

[4]  E. Paleček,et al.  Adsorptive stripping square-wave voltammetry of DNA , 1997 .

[5]  Yong Yang,et al.  The photoelectrochemical behavior of polypyrrole films in non-aqueous solutions , 1994 .

[6]  Thierry Livache,et al.  Micro‐Imprinting of Oligonucleotides and Oligonucleotide Gradients on Gold Surfaces: A New Approach Based on the Combination of Scanning Electrochemical Microscopy and Surface Plasmon Resonance Imaging (SECM/ SPR‐i) , 2005 .

[7]  K. Hashimoto,et al.  Sequence-specific gene detection with a gold electrode modified with DNA probes and an electrochemically active dye. , 1994, Analytical chemistry.

[8]  C. Kranz,et al.  Lateral deposition of polypyrrole lines over insulating gaps. Towards the development of polymer-based electronic devices† , 1995 .

[9]  M. Porter,et al.  Self-Assembled Double-Stranded DNA (dsDNA) Microarrays for Protein:dsDNA Screening Using Atomic Force Microscopy , 2000 .

[10]  A. Roget,et al.  Synthesis and use of labelled nucleoside phosphoramidite building blocks bearing a reporter group: biotinyl, dinitrophenyl, pyrenyl and dansyl. , 1989, Nucleic acids research.

[11]  W. Knoll,et al.  Investigating the kinetics of DNA-DNA and PNA-DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy. , 2001, Biosensors & bioelectronics.

[12]  A. Peterson,et al.  Surface Plasmon Resonance Spectroscopy as a Probe of In-Plane Polymerization in Monolayer Organic Conducting Films , 2000 .

[13]  S. P. Fodor,et al.  Multiplexed biochemical assays with biological chips , 1993, Nature.

[14]  Joseph Wang,et al.  New label-free DNA recognition based on doping nucleic-acid probes within conducting polymer films , 1999 .

[15]  T. Matsue,et al.  Patterning and characterization of surfaces with organic and biological molecules by the scanning electrochemical microscope. , 2000, Analytical chemistry.

[16]  Compton,et al.  Laser-activated voltammetry: measurement of the diffusion coefficients of electropassivating species. Application to pyrrole and phenol in aqueous solution , 2000, Analytical chemistry.

[17]  Geunbae Lim,et al.  DNA hybridization electrochemical sensor using conducting polymer. , 2003, Biosensors & bioelectronics.

[18]  H. Korri-Youssoufi,et al.  Direct chemical functionalization of as-grown electroactive polypyrrole film containing leaving groups , 1996 .

[19]  Wolfgang W. Gärtner,et al.  Depletion-Layer Photoeffects in Semiconductors , 1959 .

[20]  D. Verma,et al.  Several nodulins of soybean share structural domains but differ in their subcellular locations. , 1987, Nucleic acids research.

[21]  G. Dodin,et al.  DNA adsorption onto conducting polypyrrole , 1997 .

[22]  Joseph Wang,et al.  Recognition and detection of oligonucleotides in the presence of chromosomal DNA based on entrapment within conducting-polymer networks , 2001 .

[23]  L. Abrantes,et al.  Photoelectrochemical studies of polymer films: Poly(3-methylthiophene) and poly(3-methylthiophene)/Cu systems , 1996 .

[24]  I. Willner,et al.  Liposomes labeled with biotin and horseradish peroxidase: a probe for the enhanced amplification of antigen--antibody or oligonucleotide--DNA sensing processes by the precipitation of an insoluble product on electrodes. , 2001, Analytical chemistry.

[25]  Roger Ekins,et al.  Development of microspot multi-analyte ratiometric immunoassay using dual fluorescent-labelled antibodies , 1989 .

[26]  R. Corn,et al.  Surface Plasmon Resonance Imaging Measurements of Electrostatic Biopolymer Adsorption onto Chemically Modified Gold Surfaces. , 1997, Analytical chemistry.

[27]  F Lesbre,et al.  Characterization and optimization of a real-time, parallel, label-free, polypyrrole-based DNA sensor by surface plasmon resonance imaging. , 2000, Analytical chemistry.

[28]  Armistead,et al.  Modification of indium tin oxide electrodes with nucleic acids: detection of attomole quantities of immobilized DNA by electrocatalysis , 2000, Analytical chemistry.

[29]  T. Livache,et al.  Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group. , 1994, Nucleic acids research.

[30]  Adam Heller,et al.  Screen printing of nucleic acid detecting carbon electrodes. , 2002, Analytical chemistry.

[31]  T. Livache,et al.  Biosensing effects in functionalized electroconducting conjugated polymer layers: addressable DNA matrix for the detection of gene mutations , 1995 .

[32]  W. Schuhmann,et al.  Formation and imaging of microscopic enzymatically active spots on an alkanethiolate-covered gold electrode by scanning electrochemical microscopy , 1997 .

[33]  Thierry Livache,et al.  Electronically conductive polymer grafted with oligonucleotides as electrosensors of DNA: Preliminary study of real time monitoring by in situ techniques , 2001 .

[34]  M. Pirrung.  How to make a DNA chip. , 2002, Angewandte Chemie.

[35]  Jiri Janata,et al.  Label-free DNA hybridization probe based on a conducting polymer. , 2003, Journal of the American Chemical Society.

[36]  J. Dougherty,et al.  Rapid hybridization kinetics of DNA attached to submicron latex particles. , 1987, Nucleic acids research.

[37]  R. Corn,et al.  Surface plasmon resonance imaging measurements of ultrathin organic films. , 2003, Annual review of physical chemistry.

[38]  Wolfgang Knoll,et al.  Surface-Plasmon Optical Techniques , 1999 .

[39]  T. Livache,et al.  New acridone derivatives for the electrochemical DNA-hybridisation labelling. , 2004, Bioelectrochemistry.

[40]  T. Livache,et al.  New approach to writing and simultaneous reading of micropatterns: combining surface plasmon resonance imaging with scanning electrochemical microscopy (SECM). , 2004, Langmuir : the ACS journal of surfaces and colloids.

[41]  Ruedi Aebersold,et al.  Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy. , 2004, Analytical chemistry.

[42]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[43]  W. Schuhmann,et al.  Lateral deposition of polypyrrole lines by means of the scanning electrochemical microscope , 1995 .

[44]  L. Authier,et al.  Gold nanoparticle-based quantitative electrochemical detection of amplified human cytomegalovirus DNA using disposable microband electrodes. , 2001, Analytical chemistry.

[45]  J. Heinze,et al.  Integration of an electrochemical quartz crystal microbalance into a scanning electrochemical microscope for mechanistic studies of surface patterning reactions , 2000 .