Signal-amplifying conjugated polymer-DNA hybrid chips

Article abstract of DOI:10.1002/anie.200700419

Expand on that: Signal-amplifying DNA chips have been fabricated by a light-directed on-chip DNA synthesis on a thin film of a photostable conjugated polyoxadiazole derivative. The fluorescence signal from a hexachlorofluorescein- labeled target DNA was i

Full text of DOI:10.1002/anie.200700419

Angewandte
Chemie
DOI: 10.1002/anie.200700419
DNA Microarrays
Signal-Amplifying Conjugated Polymer–DNA Hybrid Chips**
Kangwon Lee, Jean-Marie Rouillard, Trinh Pham, Erdogan Gulari, and Jinsang Kim*
Bio-/synthetic hybrid materials have recently received con-
siderable attention owing to their potential biomedical
applications.[1] The most reliable way of identifying any
biological target is through its genetic code.[2] However,the
current commercial DNA microarray requires costly and
time-consuming PCR to multiply the number of analyte DNA
molecules and label the analyte DNA with a fluorescent dye
because of the low detection limit. In this context,devising
self-signal-amplifying DNA microarrays can realize low-cost,
fast,and reliable detection of nucleic acids. Herein,we report
signal-amplifying DNA chips fabricated by on-chip DNA
synthesis on a thin film of a newly developed conjugated
polymer (Figure 1 and the chemical structure in Figure 2a).
in a parallel fashion,is flexible in sequence design,easy to
manufacture,and has a high sequence fidelity compared with
other recently developed methods,such as the pin micro-
dotting method,[2c] the ink-jet microdropping method,[5] and
the electrostatic addressing method.[6] Almost all the on-chip
DNA synthesis technologies,however,require harsh condi-
tions such as long exposure to UV light and/or to strong acids.
Under these harsh conditions,conventional conjugated
polymers will be photobleached or chemically degraded.
We have developed a novel conjugated polymer with a
strong fluorescence emission and unique stability under the
above-mentioned harsh conditions. Figure 2a shows the
chemical structure of the poly(oxadiazole-co-phenylene-co-
fluorene) P1 with oxadiazole units and amine side chains. All
monomer units of P1 were designed to have their own
contribution to the final property of P1 and synthesized
through multiple synthetic steps (see the Supporting Infor-
mation). Oxadiazole is an electron-poor heterocyclic mole-
cule that has been used in polymer design in which the
improvement of electron transport and/or stability of the
polymer is required.[7] We designed an oxadiazole-containing
monomer (M3) and incorporated this unit into the conjugated
polymer backbone by using a Pd-based Suzuki coupling
method.[8] The oxadiazole-containing monomer unit M3 of P1
has an intense blue fluorescence emission at 413 nm in a
chloroform solution and is stable when exposed to strong UV
irradiation and a strong acidic environment. The amine
groups on the phenylene unit (M1) of P1 serve as functional
groups for immobilization of P1 on a glass substrate as well as
linkers for direct on-chip synthesis of oligonucleotides on the
resulting thin-layer film of P1. The fluorene unit (M2) of P1 is
incorporated to provide good solubility in organic solvents
and to ensure a good spectral overlap with commonly used
organic dyes for an efficient fluorescence resonance energy
transfer (FRET). Figure 2b shows the absorption (UV) and
photoluminescence spectra (PL) of P1 in chloroform and
incorporated in the film. The absolute quantum yield of P1
solution in chloroform (1 mgLÀ1),measured in an integrating
sphere (PTI technologies,Inc.),was 94%. We investigated the
stability of P1 compared with commonly used conjugated
polymers,such as poly( p-phenylene-ethynylene)s and poly(3-
hexylthiophene),under strong UV irradiation and highly
acidic conditions. None of the compounds except P1 survived
these tests (data not shown). The fluorescence of the conven-
tional conjugated polymers was completely quenched by
degradation of polymers under these harsh conditions. How-
ever, P1 showed unique stability against the exposure to UV
irradiation and acid treatments both in the solution and solid
state. The unique stability of P1 made possible on-chip DNA
synthesis directly on a thin film of the conjugated polymer.
The preparation of P1-coated glass substrates is described
in Figure 3a. We covalently linked P1 to a glass substrate to
Figure 1. Schematic representation of the signal-amplifying conjugated
polymer-based DNA chip. a) P1-coated glass slide by covalent bond-
ing; b) light-directed on-chip oligonucleotide synthesis; c) hybridiza-
tion with a target DNA results in large emission enhancement of the
fluorescent dye through efficient Förster resonance energy transfer.
Conjugated polymer-based biosensors are an attractive
approach to improve the detection limit because an environ-
mental change at a single site can affect the properties of the
[3]
collective system,producing large signal amplification.
Therefore,if one devises a strategy combining the signal-
amplification scheme of conjugated polymers and efficient
on-chip DNA synthesis,signal-amplifying DNA microarrays
can be conveniently prepared. On-chip oligonucleotide
synthesis[2d,4] has the unique advantage of being performed
[*] K. Lee, Prof. J. Kim
Department of Materials Science and Engineering
University of Michigan
2300 Hayward St., Ann Arbor, MI 48109 (USA)
Fax: (+1)734-936-4681
E-mail: jinsang@umich.edu
Dr. J.-M. Rouillard, T. Pham, Prof. E. Gulari, Prof. J. Kim
Department of Chemical Engineering
University of Michigan
2300 Hayward St., Ann Arbor, MI 48109 (USA)
[**] We appreciate financial support from the National Science Foun-
dation (BES 0428010) and the equipment grant from the University
of Michigan College of Engineering. J.K. and K.L. also acknowledge
the IljuFoundation for the Iljuscholarship.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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Communications
Figure 2. a) Chemical structure of P1. b) UV/PL spectra of P1 in chloroform (black=UV, blue=PL) and solid film (green=UV, red=PL).
prevent any loss of P1 during the on-chip DNA synthesis. To
blocks and each synthesis cycle consists of a deprotection step
by using photogenerated acids,coupling of a DMT-protected
monomer,capping of unreacted terminal OH groups,and
oxidation of the phosphite to phosphatetriester at internu-
cleotide linkages.[4b,10] Various sequences of DNA can be
synthesized at different locations on the chip by generating a
strong acid at the desired locations by UV-induced decom-
position of a photoacid generator (PAG). The photogener-
ated acid (PGA) then catalyzes the deprotection reaction,
producing a 5’-OH group,which is available for the next
monomer. We synthesized two different sequences. The first
sequence was 5’-ACA TCC GTG ATG TGT T-glass-3’ (the 3’
T is a spacer),which was used for hybridization with the
complementary sequence with hexachlorofluorescein (HEX)
dye,and the second sequence was 5-ACAG AAG CAT
TAT TTC T-glass-3’ for the Cy5-labeled complementary
sequence.
do so,isothiocyanate-functionalized glass substrates were
prepared by using a slightly modified literature procedure.[3e]
First,aminopropyl groups were introduced onto a glass
substrate by first cleaning with pirahna solution (H2O2/
H2SO4 3:7 (v/v)) followed by an aminopropyltrimethoxysi-
lane (APTMS) coating. 1,4-Phenylenediisothiocyanate was
then reacted with the amine of APTMS to form a reactive
linker for P1. Finally, P1 was chemically bound onto the glass
substrate. After immobilization of P1,the derived UV
spectrum of the glass substrate showed a new broad band at
350–400 nm,which corresponds to P1 absorption. Fluores-
cence spectroscopy also showed a well-defined fluorescence
emission spectrum of P1 from the glass substrate.
The on-chip DNA synthesis[9] on the P1-coated glass
substrate was conducted by using a modified automatic
oligosynthesizer equipped with a UV patterning device. The
synthesis is carried out by using 5’-(4,4’-dimethoxytrityl)
(DMT) nucleophosphoramidite monomers as the building
Figure 3b shows the fluorescence image of the synthe-
sized DNA on the P1-coated glass substrate after hybrid-
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Angewandte
Chemie
Figure 3. a) Schematic representation of the light-directed parallel on-chip DNA synthesis on P1-immobilized glass: i) APTMS, ii) 1,4-phenyl-
enediisothiocyanate, iii) polymer (P1), and iv) cyclic procedures of oligo synthesis. b) A fluorescence image of a patterned signal-amplifying DNA
microarray with two different DNA sequences after hybridization with a mixture of c-DNA-HEX (green) and c-DNA-Cy5 (red; scale bar: 200 mm).
ization with two different dye-labeled complementary DNA
molecules. Selective fluorescent patterns of green (HEX) and
red (Cy-5) dots are clearly shown in Figure 3b. This result
demonstrates that direct on-chip DNA synthesis onto a P1-
coated glass slide was macroscopically accomplished. More-
over,during the harsh DNA synthesis procedures,the
emissive property of P1 was maintained. We prepared a
control sample to conduct quantitative analysis of signal
amplification by P1. The control sample had the same 16-base
DNA sequence (5’-ACA TCC GTG ATG TGT T-glass-3’) as
was synthesized on an amine-functionalized glass slide,but
without P1. The density of the synthesized oligonucleotide
(2.44 pmolcmÀ2) on the conventional control slide was the
same as that of the oligonucleotide on the P1-coated slide.
This was confirmed by UV absorption at 410 nm (see the
Supporting Information).
ment for efficient FRET. Figure 4a shows the fluorescent
emission spectrum of the P1-coated DNA chip and the
control slide before and after hybridization with the HEX-
labeled complementary DNA (c-DNA-HEX). Upon hybrid-
ization tests with c-DNA-HEX on the signal-amplifying P1-
immobilized DNA chip,one can observe a large signal
amplification. The fluorescence emission of P1 was decreased
when excited at 380 nm,whereas the emission of HEX was
significantly amplified. Direct excitation of HEX at 535 nm
produced only a weak fluorescence emission as shown in
Figure 4a. This large signal amplification clearly indicates an
efficient fluorescence resonance energy transfer from P1 to
HEX. The detection limit of our signal-amplifying DNA
microarray is 10À10 m (see the Supporting Information). We
conducted the same hybridization test on the control slide.
Direct excitation of HEX at its absorption maximum (lmax) of
535 nm produced the same weak fluorescence emission as
obtained from the direct excitation of the P1-immobilized
DNA chip at 535 nm. A selectivity test was also done with
We used a 15-base HEX-labeled complementary DNA
sequence to observe the FRET effect from P1 to HEX dye.
FRET involves a nonradiative transmission of fluorescence
energy from a donor molecule to the acceptor molecule. P1
has a good spectral overlap with HEX,satisfying the require-
HEX-labeled
one-mismatch
DNA
(5’-HEX-ACA
CAT CTC GGA TGT-3’) and HEX-labeled noncomplemen-
Angew. Chem. Int. Ed. 2007, 46, 4667 –4670
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www.angewandte.org 4669

Communications
principle for further development of self-signal-amplifying
DNA microarrays that possibly allow PCR-free DNA detec-
tion through a large signal amplification.
Received: January 30,2007
Revised: April 6,2007
Keywords: conjugated polymers · DNA structures ·
.
FRET (fluorescence resonant energy transfer) · polyoxadiazoles ·
signal amplification
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