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Cecile Dueymes, Jean Luc Decout,* Philippe Peltie,
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Arrays of oligonucleotide probes (DNA chips) immobilized
on glass or silicon surfaces have emerged as powerful new
tools for the analysis of DNA and RNA.[1] These specific
DNA sensors operate through hybridization reactions which
are based on the mutual recognition of two complementary
nucleic acid strands that establish hydrogen bonds between
their nucleic bases. Hybridization is most commonly assayed
by fluorescence, and hence requires that fluorophore labels
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This technology, however, is still fraught with a number of
drawbacks and requires new developments. For example, it is
still difficult to assess the quality of the oligonucleotides
attached to the surface. The homogeneity and the reprodu-
cibility of the procedures for preparing the DNA-functional-
ized surfaces, and consequently the DNA surface density, are
difficult to control. Furthermore the polymerase chain
reaction (PCR) step, which serves to amplify the DNA
targets, and the subsequent chemical step, for the attachment
of the fluorophore to the target DNA, are responsible for
significant modifications in the relative proportions of the
different populations of the nucleic acids to be analyzed.
We propose that some of these problems might be simply
solved if the detection label (here a fluorophore) is incorpo-
rated on the array capture DNA strand and not on the target
to be detected. This strategy might have many advantages.
First it greatly reduces the number of manipulations of the
targets. Second, it provides a way to control the quality of the
DNA array (by using standard fluorescence scanners) in the
absence of the targets. Such an array requires that: 1) the
fluorescence is not quenched by interaction of the fluoro-
phore with the surface; 2) the label on the probe does not
affect its affinity for its complementary oligonucleotide; and
3) the fluorescence is significantly changed as a specific
consequence of hybridization of the functionalized DNA
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[*] Prof. J. L. Decout
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Departement de Pharmacologie Moleculaire
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UMR Universite J. Fourier, CNRS no. 5063
Domaine de la Merci, 38706 La Tronche Cedex (France)
Fax : (33)4-76-51-86-67
Prof. M. Fontecave, C. Dueymes
DBMS-CB
¬
UMR Universite J. Fourier, CNRS, CEA no. 5047
CEA Grenoble
17Avenue des Martyrs, 38054 Grenoble Cedex 9 (France)
Fax : (33)4-38-78-91-24
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Dr. P. Peltie
LETI, CEA Grenoble
17Avenue des Martyrs
38054 Grenoble Cedex 9 (France)
Supporting information for this article is available on the WWW under
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¹ WILEY-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002
1433-7851/02/4103-0486 $ 17.50+.50/0
Angew. Chem. Int. Ed. 2002, 41, No. 3