DNA-directed synthesis of aniline and 4-aminobiphenyl oligomers: Programmed transfer of sequence information to a conjoined polymer nanowire

Article abstract of DOI:10.1021/ja0726106

A new class of materials was prepared from aniline-containing oligomers that are covalently linked to the nucleobases of duplex DNA. Oligomers composed of repeating aniline (PANI) or 4-aminobiphenyl (PAB) units having the properties of conducting polymers conjoined to the DNA were prepared by the reaction of horseradish peroxidase and H₂O₂ with DNA having the appropriate monomers aligned within the major groove. These oligomers exhibit the spectral and chemical properties typical of para-linked polyanilines. This method of preparation enables utilization of the unique self-recognizing properties and sequence programmability of DNA to create tailored oligomers. This ability was demonstrated experimentally by preparation of PAB oligomers from alternating benzene and aniline monomers. Conjoined conducting polymers carrying the sequence information of DNA may have applicability as nanowires.

Full text of DOI:10.1021/ja0726106

Published on Web 02/12/2008
DNA-Directed Synthesis of Aniline and 4-Aminobiphenyl
Oligomers: Programmed Transfer of Sequence Information to
a Conjoined Polymer Nanowire
Bhaskar Datta and Gary B. Schuster*
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, 30332
Received April 14, 2007; E-mail: Gary.Schuster@cos.gatech.edu
Abstract: A new class of materials was prepared from aniline-containing oligomers that are covalently
linked to the nucleobases of duplex DNA. Oligomers composed of repeating aniline (PANI) or 4-aminobi-
phenyl (PAB) units having the properties of conducting polymers conjoined to the DNA were prepared by
the reaction of horseradish peroxidase and H2O2 with DNA having the appropriate monomers aligned within
the major groove. These oligomers exhibit the spectral and chemical properties typical of para-linked
polyanilines. This method of preparation enables utilization of the unique self-recognizing properties and
sequence programmability of DNA to create tailored oligomers. This ability was demonstrated experimentally
by preparation of PAB oligomers from alternating benzene and aniline monomers. Conjoined conducting
polymers carrying the sequence information of DNA may have applicability as nanowires.
templates that control formation and structure.5 Polyanilines have
attracted enormous interest as components of nanometer scale
Introduction
There is a rapidly growing awareness that the self-recognizing
and self-organizing properties of biomolecules, particularly
nucleic acids, can be exploited for the creation of new nanoscale
materials with unique properties and capabilities. In a recent
example, Seeman has cleverly exploited the highly selective
nucleobase recognition properties that are inherent in DNA to
create a nanomechanical device that operates as a fully
functional robot arm.1
devices because of their wide range of conductivity, their
stability, and the ease of synthesis. In particular, PANI can be
prepared enzymatically under mild conditions in aqueous
solution using DNA as a template.6 In this process, anilinium
ions bound electrostatically to the negatively charged phosphate
groups of the DNA are converted to PANI by reaction with
horseradish peroxidase and H2O2. This procedure is limited to
producing only aniline homopolymers that do not take advantage
of the sequence information inherent in DNA.
We recently reported a fusion of the templating and scaf-
folding roles of DNA in the DNA-directed assembly of PANI.7
In this approach, cytosine nucleotides are covalently linked to
aniline moieties that are subsequently polymerized to create
DNA-conjoined PANI oligomers. Significantly, this process
provides a method to utilize the sequence programmability of
DNA to prepare any number of unique conducting polymers
tailored to have desired structural or electronic properties.
In this work, we report the further development of conjoined
PANI-DNA oligomers and demonstrate the sequence program-
mability of these polymers by preparing conjoined poly(4-
aminobiphenyl)-DNA oligomers (PAB-DNA). In comparison
with PANI, the PAB oligomers possess distinct structural and
electronic properties, which affect their state of oxidation.
However, irrespective of the structural difference in the
monomers, our results show that the covalently linked PANI
and PAB oligomers are formed predominantly by a para-
directed, head-to-tail process. Finally, we used this approach
DNA is also being used as a template for the fabrication of
nanowires. These are one-dimensional structures that are
anticipated to be suitable for forming self-organizing connections
between functional electronic components.2 A popular method
for the creation of these nanowires is DNA-templated metal-
lization. In this approach, the chemical reduction of metal ions
bound electrostatically to DNA creates nanometer-sized metallic
aggregates that act as catalysts for further metal deposition along
the path defined by the DNA.3 A recent refinement of this
method allows for directed metallization of selected DNA
segments.4 This modification offers the prospect of sequence
selective metallization, which could enable the creation of
uniquely alloyed nanowires.
Nanowires may also be created from conducting organic
polymers such as polyaniline (PANI) by a self-assembly process
in the presence of surfactants or DNA, which act as “soft”
(1) Ding, B.; Seeman, N. C. Science 2006, 314, 1583-1585.
(2) Gu, Q.; Cheng, C.; Gonela, R.; Suryanarayanan, S.; Anabathula, S.; Dai,
K.; Haynie, D. T. Nanotechnology 2006, 17, R14-R25. Fischler, M.;
Simon, U.; Nir, H.; Eichen, Y.; Burley, G. A.; Gierlich, J.; Gramlich, J.;
Carell, T. Small 2007, 3, 1049-1055.
(3) Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. Nature 1998, 391, 775-
778.
(5) Zhang, G.; Wang, Y. Mater. Sci. Eng. B 2006, 134, 9-14.
(6) Liu, W.; Kumar, J.; Tripathy, S.; Senecal, K. J.; Samuelson, L. J. Am.
Chem. Soc. 1999, 121, 71-78.
(7) Datta, B.; Schuster, G. B.; McCook, A.; Harvey, S. C.; Zakrzewska, K. J.
Am. Chem. Soc. 2006, 128, 14428-14429.
(4) Burley, G. A.; Gierlich, J.; Mofid, M. R.; Nir, H.; Tal, S.; Eichen, Y.;
Carell, T. J. Am. Chem. Soc. 2006, 128, 1398-1399.
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J. AM. CHEM. SOC. 2008, 130, 2965-2973
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A R T I C L E S
Datta and Schuster
Figure 2. A structural model showing aniline modifications on cytosines
extending into the major groove of a DNA duplex.
Figure 1. DNA sequences used in this work. The structural modifications
incorporate modified nucleotides X,Y, Z, X′, and Y′, as indicated. The DNA
oligomers used in these experiments are duplexes formed from appropriate
complementary strands.
to prepare conjoined copolymers of aniline and benzene
monomers positioned on alternating cytosine residues of DNA
duplexes. These results demonstrate the potential of using
variously modified nucleotides in preparing conjoined polymers
with non-recurring, irregular structures.
Experimental Section
Figure 3. UV-vis absorption spectra of duplexes of DNA(X2) and DNA-
Materials. All reagents were used as received without further
purification. 4-Bromobiphenyl, p-bromotoluene, phenylethylamine,
ethylenediamine, sodium t-butoxide, ammonium persulfate, phenylhy-
drazine, and 1,4-dioxane were obtained from Acros Organics, Morris
Plains, NJ. 1,1′-Bis(diphenylphosphino)ferrocene and 1,1′-bis(diphe-
nylphosphino)ferrocene-palladium(II) dichloride were obtained from
Strem Chemicals, Inc., Newburyport, MA. The O4-Triazolyl-deox-
yuridine phosphoramidite along with the PAC phosphoramidites
(phenoxyacetyl-dA, isopropyl-phenoxyacetyl-dG and acetyl-dC) were
purchased from Glen Research Corporation, Sterling, VA.
Preparation of Modified DNA Oligomers. Aniline, 4-aminobi-
phenyl, 4-methylaniline, and 4′-methoxy-4-aminobiphenyl modified
DNA oligomers were synthesized by the convertible nucleotide
approach8 using the O4-triazolyl-deoxyuridine phosphoramidite for
coupling the desired monomer. For this purpose, N-phenylethylenedi-
amine, N-[(1,1′-biphenyl)-4-yl]ethane-1,2-diamine, N-(4-methylphenyl)-
ethane-1,2-diamine and N-[4′-methoxy-(1,1′-biphenyl)-4-yl]ethane-1,2-
diamine were synthesized following a previously published report.9 The
resin-bound oligonucleotides containing the convertible nucleotide were
treated with 500-750 µL of 5 M (in CH3CN) solutions of the
appropriate amines for 24 h at 60 °C. The yield of modified oligomers
is similar to that of regular unmodified DNA sequences based upon
(X6) after treatment with HRP and H2O2.
data from the trityl monitor during automated DNA synthesis. The
oligonucleotides were deprotected by treatment with 4 mL of concen-
trated aqueous ammonium hydroxide at room temperature for 8-10 h.
The ammonium hydroxide solution was dried on a Speed Vac and the
samples reconstituted with water for purification by HPLC. The
oligomers were purified by reversed phase HPLC on a Hitachi
preparative HPLC system using a Dynamax C18 column. Purified DNA
sequences were desalted using Waters Sep-Pak cartridges and charac-
terized by ESI-Mass spectrometry.
Synthesis of Oligoanilines and Oligo(4-aminobiphenyl). Horserad-
ish Peroxidase (HRP), type II (200 units/mg) was purchased from Sigma
Aldrich Chemical Co., St. Louis MO. A solution of HRP was prepared
(2 mg in 2 mL) and used as a stock solution for the polymerization.
Hydrogen Peroxide (H2O2; 30%) was purchased from Fisher Scientific,
Pittsburgh, PA and diluted to 0.15% in deionized water for use. The 5
µM DNA duplexes were prepared in 10 mM citrate buffer (pH 4.5)
containing 500 mM of NaCl. These conditions were used and
maintained consistently after ensuring the stability of the corresponding
DNA duplexes. After addition of HRP to DNA samples, polymerization
was initiated by the addition of 2-5 µL of H2O2. UV-vis spectra were
recorded 30 min after addition of H2O2 and at 10 min intervals thereafter
to confirm the completion of reaction. For mass spectral characteriza-
tion, samples were prepared at a concentration of ∼100 uM. Addition
(8) Min, C.; Verdine, G. L. Nucleic Acids Res. 1996, 24, 3806-3810.
(9) Beletskaya, I. P.; Bessmertnykh, A. G.; Averin, A. D.; Denat, F.; Guilard,
R. Eur. J. Org. Chem. 2005, 261-280.
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DNA-Directed Synthesis of Oligomers
A R T I C L E S
Figure 4. UV-vis absorption spectra of PANI-DNA(X6) after treatment with different amounts of (A) APS and (B) phenylhydrazine. Arrows indicate
loss or gain of absorbance.
of H2O2 was followed by raising the pH of the solution to 7.0 (by
addition of triethylamine). Ethanol precipitation of the samples was
then performed followed by desalting using Waters Sep Pak cartridges
and the samples were subjected to Electrospray Mass spectrometry.
Ammonium Persulfate and Phenylhydrazine Titrations. Aniline
and 4-aminobiphenyl modified DNA duplexes were first treated with
HRP and H2O2 to prepare DNA-conjoined oligomers. Then, 2 µL
aliquots of 1 M ammonium persulfate or phenylhydrazine, respectively
were added to 1 mL solutions of the DNA duplexes (5 µM) and the
UV-vis absorption spectra were recorded. The additions were con-
tinued until no further change in absorbance was observed. Treatment
of an unmodified DNA duplex with ammonium persulfate or phenyl-
hydrazine under similar conditions did not show any changes in
absorbance at 260 nm.
Equipment. UV-visible absorption spectra were recorded on a Cary
1E spectrophotometer, UV melting and cooling curves were recorded
using a multicell block and temperature controller on the spectropho-
tometer. CD spectra were recorded on a JASCO J-715 spectropola-
rimeter. ESI-MS spectra were recorded on a Applied Biosystems
QSTAR-XL in negative ion mode.
spectrum of DNA(X6) is similar to that of DNA(1), and this
indicates that it maintains an overall B-form structure.
The treatment of duplex DNA(X6) with HRP and H2O2 under
conditions known to cause aniline polymerization leads to the
formation of a conjoined PANI oligomer characterized by
absorption bands at ∼420 and 730 nm, see Figure 3.7 This
absorption spectrum shows that the conjoined PANI-DNA
oligomer is formed primarily in the “pseudo-proton doped”
emeraldine oxidation state. Melting temperature data and CD
spectroscopy show that the PANI-DNA oligomer maintains a
duplex structure. However, molecular modeling indicates that
the DNA duplex is severely distorted in the region of the PANI.7
As expected, the conjoined PANI oligomer has a circular
dichroism spectrum with an apparent peak at 680 nm.7
Significantly, ESI mass spectrometric analysis of DNA(X6),
before reaction of the duplex [DNA(X6)/DNA(1)] with HRP
and H2O2, reveals that it has the expected mass to charge ratio
(m/e, e ) 1) of 7300 amu (see Supporting Information). The
complete oligomerization of DNA(X6) should result in conver-
sion of its six covalently linked aniline monomers to PANI-
DNA(X6) with the formation of five new carbon-nitrogen bonds
and a concomitant reduction in mass of 10 amu. Mass
spectrometric analysis of the PANI-DNA resulting from this
reaction confirms this expectation. After treatment with HRP
and H2O2, the m/e ratio for the PANI-DNA is found to be
7291 ( 1 (see Supporting Information), which confirms
oligomerization. Moreover, careful analysis of the mass spec-
trum of PANI-DNA(X6) shows that there is no detectable
residual monomer-containing strand and there are no significant
partially oligomerized compounds. That is, based on the mass
spectrometric data, reaction of duplex DNA(X6)/DNA(1) with
HRP and H2O2 results in its essentially complete conversion to
PANI-DNA in which all monomers have reacted. There is no
detectable PANI formation when a DNA oligomer (up to a
concentration of 60 µM) having only one covalently linked
aniline group is treated with HRP/H2O2, which shows that
intermolecular oligomerization does not occur under these
conditions.
Results
DNA-Conjoined PANI Oligomers. A series of DNA oli-
gomers, see Figure 1, comprising cytosines bearing covalently
linked aniline groups was prepared to assess the possibility of
forming conducting PANI oligomers that maintain the sequence
programmability inherent in DNA. The cytosines were modified
by replacement of the 4-amino group by N-(2-aminoethyl)aniline
giving a nucleobase that is abbreviated as X in Figure 1.
DNA(1) is an unmodified 22-mer strand that forms duplex
DNA with its complement (not shown). DNA(X2) and DNA-
(X6) are related to DNA(1) except that they are constructed
with two and six contiguous aniline bearing cytosines (X),
respectively. Molecular modeling10 of the duplex formed from
DNA(X6) and its complement reveals that the covalently linked
aniline groups are positioned in the major groove of the duplex,
see Figure 2. Although the presence of six aniline groups in
the major groove of DNA(X6) results in a melting temperature
that is 18 °C below that of DNA(1), the circular dichroism (CD)
(10) Geometry optimizations were performed in HyperChem 7.5 using standard
molecular mechanics methods based on the amber94 force field and a
conjugate gradient method with a termination value of the RMS gradient
of 0.01 kcal/mol/Å.
The redox properties of the conjoined PANI-DNA oligomer
formed from polymerization of DNA(X6) were probed further
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A R T I C L E S
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Figure 5. UV-vis absorption spectra of 4-methyl-N-(2-aminoethyl)aniline
containing DNA (DNA(X′6)) and DNA(X6) upon treatment with HRP/
H2O2.
Figure 6. UV-vis absorption spectra of DNA(Y1-4) and DNA(Y′4) after
treatment with HRP/H2O2.
by examining the effects of the chemical oxidizing and reducing
agents ammonium persulfate (APS) and phenylhydrazine,
respectively, on the conjoined polymer. Both APS and phenyl-
hydrazine have been used in the preparation of the pernigraniline
base and leucoemeraldine base forms of polyaniline.11 As shown
in Figure 4A, treatment of the PANI-DNA(X6) conjoined
oligomer with APS results in the loss of absorbance at 730 nm
and the concomitant increase in absorbance at ∼550 nm. The
loss of the 730 nm band by reaction with a strong oxidizing
agent such as APS is indicative of the further oxidation of the
emeraldine form.12 Alternatively, the reduction of PANI-DNA-
(X6) with phenylhydrazine results in the complete disappearance
of the absorbance at 730 nm without the appearance of any
additional bands (Figure 4B). This is the expected result for
reduction of PANI to the leucoemeraldine form of polya-
niline.12,13 These results are consistent with the conclusion that
the PANI-DNA(X6) conjoined oligomer is formed primarily
in the conducting emeraldine oxidation state by the reaction of
duplex DNA(X6) with HRP/H2O2.
Figure 7. Structure of poly(4-aminobiphenyl) oligomers in oxidation states
that correspond to (A) the fully reduced (leuco equivalent of PANI), (B)
the partially oxidized (emeraldine equivalent) and (C) the fully oxidized
(pernigraniline equivalent) state. Cytosine nucleobases connecting the
oligomer to DNA are designated by R.
The absorbance spectrum of conjoined PANI-DNA(X6)
suggests that the oligomer is formed by a head-to-tail reaction;
that is, the oligomer is in the benzenoid-quinoid structure.14 We
assessed the role of the DNA template in enforcing the head-
to-tail polymerization by incorporating 4-methyl-N-(2-amino-
ethyl)aniline (nucleobase X′, see Figure 1) in place of the N-(2-
aminoethyl)aniline of DNA(X6). Of course, the 4-methyl
substituent is expected to prevent PANI formation by the head-
to-tail mechanism.15 As shown in Figure 5, HRP/H2O2 treatment
of DNA(X′6) does not result in significant PANI formation as
revealed by the lack of characteristic spectral features in the
visible region. This finding supports the conclusion that HRP/
H2O2 treatment of duplex DNA(X6) gives predominantly the
head-to-tail emeraldine-form polyaniline.
DNA-Conjoined 4-Aminobiphenyl Oligomers. To investi-
gate the range of structures that will form conducting polymers
by this technique, we chose 4-aminobiphenyl as a test reactant.
Clearly, aniline has only one aromatic ring and the 4-amino-
biphenyl has two. Molecular modeling studies indicated that
the covalently linked aminobiphenyl groups would align in the
major groove of the DNA duplex. However, in contrast to
similarly situated aniline groups, the aminobiphenyls are
properly aligned for oligomerization when they are placed on
every other nucleobase in the sequence. We prepared DNA
oligomers containing cytosines modified by replacement of their
4-amino groups by N-[(1,1′-biphenyl)-4-yl]ethane-1,2-diamine
(abbreviated as nucleobase Y, see Figure 1). These oligomers
contain a varying number of Y nucleobases arranged in an
alternating fashion along one strand of the duplex DNA, and in
the case DNA(Y3′) and DNA(Y3′′) the monomers required to
form a PAB oligomer are on two separate pieces of DNA that
are brought together only in the presence of DNA(2) a
(11) Ray, A.; Asturias, G. E.; Kershner, D. L.; Richter, A. F.; Macdiarmid, A.
G. Synth. Met. 1989, 29, E141-E150.
(12) Masters, J. G.; Sun, Y.; MacDiarmid, A. G.; Epstein, A. J. Synth. Met.
1991, 41, 715-718.
(13) Ram, M. K.; Mascetti, G.; Paddeu, S.; Maccioni, E.; Nicolini, C. Synth.
Met. 1997, 89, 63-69.
(14) Kim, S.-C.; Huh, P.; Kumar, J.; Kim, B.; Lee, J.-O.; Bruno, F. F.;
Samuelson, L. Green Chem. 2007, 9, 44-48.
(15) Kitani, A.; Yano, J.; Kunai, A.; Sasaki, K. J. Electroanal. Chem. 1987,
221, 69-82.
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A R T I C L E S
Figure 8. Schematic representation of PAB formation in a ternary complex comprised of DNA(2)-DNA(Y3′)-DNA(Y3′′). Analysis by absorption spectroscopy
after reaction with H2O2/HRP indicates that oligomerization occurs only when all three components are present. UV-vis spectra: (...) DNA(2); (- - -) 1:1
mixture of DNA(Y3′) + DNA(Y3′′); (- ‚ -)1:1 mixture of DNA(Y3′) + DNA(Y2); (s)1:1:1 mixture of with DNA(Y3′) + DNA(Y3′′) + DNA(2).
templating strand that has adjacent sequences complementary
to DNA(Y3′) and DNA(Y3′′), see Figures 1 and 8. The structure
of the DNA oligomers was confirmed by ESI mass spectrometry
and the corresponding duplexes were characterized by their UV
melting (Tm) and CD spectral features (see Supporting Informa-
tion). Duplexes containing 4-aminobiphenyl residues show an
overall B-form structure and display cooperative melting
behavior, albeit at lower Tm compared with the corresponding
unmodified duplexes (see Supporting Information).
The reactions of DNA(2) with complementary components
DNA(Y3′) and DNA(Y3′′) were examined to demonstrate that
formation of these oligomers is an intramolecular process that
requires alignment of the monomers by DNA. DNA(Y3′)
contains one 4-aminobiphenyl monomer attached covalently at
a position one nucleobase from its 3′-terminus. Similarly, DNA-
(Y3′′) has two 4-aminobiphenyl monomers; one attached at its
5′-terminus and the other one base removed. The nucleobases
of DNA(Y3′) and DNA(Y3′′) are complementary to adjacent
sections of DNA(2), which is referred to as the template strand,
see Figure 8. The combination of these three oligomers forms
a ternary complex (Tm ) 70.1 °C, see Supporting Information)
that organizes the 4-aminobiphenyl monomers so that the two
on DNA(Y3′) and the one on DNA(Y3′′) are adjacent to each
other. A series of experiments was carried out on this system
to show that oligomerization of the 4-aminobiphenyl monomers
occurs only when the template strand is present.
In a first set of experiments, modified duplexes containing
4-aminobiphenyl groups were treated with HRP and H2O2 to
initiate polymerization, and the reactions were monitored by
absorption spectroscopy. No significant changes are observed
in the absorption spectra of DNA(Y1) or DNA(Y2), which
contain one and two Y-nucleobases, respectively. However,
treatment of DNA(Y3) or DNA(Y4) duplexes with HRP/H2O2
results in the appearance of new absorption bands at ∼415 and
550 nm with a shoulder at 520 nm, see Figure 6. These bands
are indicative of the formation of poly(4-aminobiphenyl).16
Poly(4-aminobiphenyl) prepared by electrochemical oxidation
of the monomer has been shown previously to have unique
absorption bands at 450 and 550 nm.16 These bands correspond
to radical cations and diimine species, respectively, see Figure
7. We showed that similar absorption bands are observed upon
treatment of 4-aminobiphenyl or N-[(1,1′-biphenyl)-4-yl]ethane-
1,2-diamine with HRP/H2O2 in presence of calf thymus DNA
using the procedure shown previously to give polyanilines.17
The similar optical absorption spectra of the conjoined PAB-
DNA oligomers and those of PAB prepared by conventional
techniques is strong evidence for formation of the PAB-DNA
conjoined conducting polymer. CD and melting experiments
reveal that the PAB-DNA maintains a DNA duplex structure
albeit with reduced thermal stability (see Supporting Informa-
tion).
Treatment of a 1:1 mixture of DNA(Y3′) and DNA(Y3′′) with
HRP and H2O2 does not result in the detectable formation of
oligomers as revealed by the absorption spectrum of the reaction
products (see Figure 8). Similarly, treatment of a 1:1 mixture
of DNA(2) and DNA(Y3′′) or DNA(2) with DNA(Y3′) with
HRP/H2O2 does not lead to oligoaniline formation. However,
the reaction of the ternary complex consisting of a 1:1:1 mixture
of DNA(2), DNA(Y3′), and DNA(Y3′′) clearly forms the PAB
oligomer as revealed by its characteristic absorption bands.
These experiments show that oligomer formation is an intramo-
lecular reaction that requires pre-alignment of the aniline
monomers by the self-recognition properties of DNA.
To confirm the state of oxidation of the conjoined PAB
oligomers, the PAB-DNA(Y4) oligomeric duplex was treated
separately with APS and with phenylhydrazine. As shown in
Figure 9A, treatment of the PAB-DNA(Y4) with APS leads
to an increase in intensity of the 520 nm absorption band without
causing any other significant spectral changes. The ∼30 nm
blue-shift in the diimine transition upon treatment of PAB-DNA-
(Y4) with APS is likely due to nominal further oxidation of the
(16) Guay, J.; Leclerc, M.; Dao, L. H. J. Electroanal. Chem. 1988, 251, 31-
39.
(17) Nagarajan, R.; Tripathy, S. K.; Kumar, J.; Bruno, F. F.; Samuelson, L.
Macromolecules 2000, 33, 9542-9547.
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Datta and Schuster
Figure 9. UV-vis absorption spectra of PAB-DNA(Y4) after treatment with (A) APS and (B) phenylhydrazine. Arrows indicate gain or loss of absorbance.
mechanism that requires head-to-tail addition for the formation
of the conjoined PAB-DNA oligomers.
Copolymer of Aniline and Benzene. Utilizing the sequence
information of DNA is a potential advantage for the creation
of unique conducting polymers using the conjoined DNA
template approach. Clearly, the PAB oligomers described above
can be thought of as a copolymer of aniline and benzene. The
applicability of this method to the formation of such DNA-
conjoined copolymers was examined by investigating the
reactions of compounds DNA(XZ) and DNA(ZX), see Figure
1. In these compounds, the relevant cytosines are modified by
replacement of the pertinent 4-amino groups by two different
groups, aniline and benzene. The cytosines that are modified
by covalent linkage to N-phenylethylamine are abbreviated as
nucleobase Z. The alternating Z and X modifications of DNA-
(XZ) and DNA(ZX) have opposite directionality with respect
Figure 10. UV-vis absorption spectra of DNA(XZ) and DNA(ZX) after
to the DNA. It is important to note that the modifications Z
and X were introduced into the DNA by different routes. This
demonstrates the precise structural control possible using DNA
to template creation of conjoined copolymers. In particular, the
Z nucleobase was incorporated as its phosphoramidite during
standard machine synthesis of DNA (see Supporting Informa-
tion), whereas the X nucleobase was introduced postsynthetically
using the convertible nucleotide approach as described previ-
ously.7
treatment with HRP/H2O2 and its comparison with DNA(Y4).
conjoined PAB oligomers. A comparison of these results with
those obtained from similar experiments with PANI-DNA(X6)
indicates that the PAB oligomer being formed by treatment with
HRP/H2O2 is already in the highest oxidation state. In contrast,
treatment of PAB-DNA(Y4) conjoined polymer with phenyl-
hydrazine causes the disappearance of the absorbance bands at
550 and 520 nm, see Figure 9B. The reaction with phenylhy-
drazine, as expected, forms the fully reduced leuco form of the
conjoined PAB-DNA oligomer.
We showed above that polymerization of PANI-DNA(X6)
proceeds by a head-to-tail mechanism; a similar process for
formation of para-directed PAB oligomers is not compulsory.
The structure of the conjoined PAB-DNA oligomers was
investigated by modifying the PAB monomers covalently linked
to the cytosines of DNA(Y4) by incorporating a 4′-methoxy
group (nucleobase Y′; 4′-methoxy-N-[(1,1′-biphenyl)-4-yl]e-
thane-1,2-diamine, see Figure 1). For obvious structural reasons,
the head-to-tail para linkage of nucleobase Y′ will be inhibited
compared with that of nucleobase Y. Treatment of DNA(Y′4)
with HRP/H2O2 does not produce any significant spectral
features in the visible region and the absorption bands charac-
teristic of PAB oligomers. This result is consistent with a
DNA(XZ) and DNA(ZX) were treated with HRP/H2O2 and
these reactions were monitored by absorption spectroscopy. As
shown in Figure 10, the absorption bands that result from this
reaction at ∼415, 520, and 550 nm are essentially identical with
those observed for the conjoined DNA-PAB oligomers formed
from the 4-aminobiphenyl modified structures that are described
above. This result demonstrates that the arrangement of aniline
and benzene groups in DNA(XZ) and DNA(ZX) produces
oligomers that are isostructural to the PAB oligomers obtained
from DNA(Y4). Also, comparing the spectra of DNA(XZ) and
DNA(ZX), indicates that this change in directionality does not
affect the nature of the product. Significantly, these results
demonstrate the potential of designing conjoined copolymers
using the sequence information inherent in DNA to control the
unique placement of monomer groups in the resulting polymer.
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DNA-Directed Synthesis of Oligomers
A R T I C L E S
Discussion
monomers and to provide a template for formation of a PANI
oligomer in the emeraldine oxidation state; once this is
completed, the properties of the conducting nanowires should
be largely independent of the structural fate of the conjoined
DNA.
There is rapidly growing interest in the preparation and
investigation of nanowires.18-20 These are structures that have
a lateral dimension in the nm range, longitudinal dimension in
the range from nm to µm, and electrical properties characteristic
of conductors or semiconductors. Similarly, there is growing
awareness that the unique properties of DNA may be exploited
to fabricate nanowires and other electrical and mechanical
objects of this length scale.21-23 We describe here a novel
approach applicable to the fabrication of such devicessthe
synthesis of conducting polymers conjoined to DNA. Specifi-
cally, designed DNA sequences with aniline-containing mono-
mers covalently linked to the nucleobases can be used in directed
self-assembly that takes advantage of the sequence program-
mability properties of DNA to exercise precise control on
polymer formation. Treatment of these aniline-modified du-
plexes with H2O2 in the presence of HRP leads to oligoaniline
formation.
The applicability of this method for formation of DNA-
conjoined polymers to monomers beyond aniline was demon-
strated by showing that the DNA(Y) series, which contains
covalently linked 4-aminobiphenyl groups, forms conjoined
oligomers. The 4-aminobiphenyl oligomers formed in this
reaction possess distinctive chemical and electronic properties
compared with polyaniline, while at the same time PAB and
PANI retain some common structural features such as π-con-
jugation and a preferred head-to-tail orientation.16 Significantly,
the presence of the additional phenyl ring in the 4-aminobiphenyl
monomers requires a change to the pattern for covalent linkage
from contiguous to alternating bases along one strand of the
DNA because the 4-aminobiphenyl spans a larger region of the
major groove. Clearly, structural constraints resulting from the
covalent attachment of these monomers to DNA control the
oligomerization to form poly(4-aminobiphenyl); i.e., the reaction
of DNA(Y4) leads to oligomer formation, but DNA(Y2) does
not. These results highlight again the templating ability of DNA
in controlling the formation of conjoined oligomers.
There are meaningful differences in the properties of PAB-
DNA(Y4) and PANI-DNA(Y6). The diimine transition band
for poly(4-aminobiphenyl) is considerably blue-shifted compared
with PANI-DNA(X6), which appears at 730 nm. This is
attributed to a less delocalized character for the quinoid-imine
in the structure of PAB, see Figure 7. Notably, even tetramers
of aniline in the emeraldine oxidation state exhibit absorption
bands at ca. 750 nm, albeit at shorter wavelengths compared
with long chain polyanilines (∼850 nm).25 In contrast, the
structure of poly(4-aminobiphenyl) restricts delocalization of
quinoid-imines resulting in the blue-shift of the diimine optical
transition.
Structure and Oxidation States of Conjoined PANI and
PAB. One advantage of polyaniline is its wide and controllable
range of oxidation states. These redox states have been
correlated with the electrical properties of these conducting
polymers.26 The absorption spectrum of PANI-DNA(X6)
formed in the reaction with HRP/H2O2 is indicative of the
emeraldine oxidation state. Since the emeraldine oxidation state
of PANI-DNA(X6) lies between the fully reduced (leuco) and
fully oxidized (pernigraniline) forms, it is possible to manipulate
the redox state of these polymers with appropriate reagents.27,28
The addition of ammonium persulfate, a strong chemical
oxidizing agent, to PANI-DNA(X6) causes its absorbance at
730 nm to diminish while causing a simultaneous increase in
the absorbance at 550 nm. The absorbance at 730 nm is
attributed to diimine radical cations and is related to the presence
of similar numbers of reduced and oxidized units that character-
ize the emeraldine oxidation state.27 Further oxidation of the
PANI is expected to yield a larger number of diimine units with
Forming DNA-Conjoined Oligomers of Aniline and 4-Ami-
nobiphenyl. In contrast to the DNA templated polymerization
of free anilines in solution, the covalent attachment of the aniline
monomers to DNA enforces a particular structural orientation
and restricts certain interactions between moieties on different
DNA molecules. This determines the nature of the polymers
that can be formed. In particular, the observation that charac-
teristic oligoaniline absorption bands are formed only when all
three components of the ternary complex DNA(2), DNA(Y3′),
and DNA(Y3′′) are present confirms the role template and
scaffold play in controlling oligomer formation by preventing
the reaction of monomers attached to different DNA molecules.
The properties of the conjoined PANI oligomers that are
formed in this process indicate both a close similarity to
conventional conducting polymers and unique attributes resulting
from their linkage to DNA. The absorbance bands of PANI-
DNA(X6) at 420 and 730 nm are attributed to π-π* and
diimine radical cations, respectively, and are indicative of the
conducting “pseudo-proton doped” emeraldine oxidation state
of PANI.7 The PANI linked DNA(X6) oligomer maintains a
duplex structure, albeit with reduced thermal stability. This is
expected since the wrapping of polyaniline onto the DNA has
been found to induce changes in the secondary structure of DNA
leading to the formation of an over-wound polymorph.24
Detailed molecular modeling has suggested that while the region
of the DNA duplex bearing the PANI oligomer is distorted and
exhibits reduced inter-base pair hydrogen bonding, the overall
stability of the conjoined system is improved by incorporating
longer flanking duplex DNA regions (“leads”).7 Regardless, the
fate of the DNA duplex after conjoined polymer formation is
of secondary importance for the creation of conducting polymer
nanowires. The role of the DNA is to order the covalently linked
(18) Noll, J. D.; Nicholson, M. A.; Vanpatten, P. G.; Chung, C. W.; Myrick,
M. L. J. Electrochem. Soc. 1998, 145, 3320-3328.
(19) Maynor, B. W.; Filocamo, S. F.; Grinstaff, M. W.; Liu, J. J. Am. Chem.
Soc. 2002, 124, 522-523.
(20) Wu, C.-G.; Bein, T. Science 1994, 264, 1757-1759.
(21) Nickels, P.; Dittmer, W. U.; Beyer, S.; Kotthaus, J. P.; Simmel, F. C.
Nanotechnology 2004, 15, 1524-1529.
(25) Kulszewicz-Bajer, I.; Rozalska, I.; Kurylek, M. New J. Chem. 2004, 28,
669-675.
(22) Ma, Y.; Zhang, J.; Zhang, G.; He, H. J. Am. Chem. Soc. 2004, 126, 7097-
(26) Focke, W. W.; Wnek, G. E.; Wei, Y. J. Phys. Chem. 1987, 91, 5813-
7101.
5818.
(23) Zhu, L.; Lukeman, P. S.; Canary, J. W.; Seeman, N. C. J. Am. Chem. Soc.
2003, 125, 10178-10179.
(24) Nagarajan, R.; Liu, W.; Kumar, J.; Tripathy, S.; Bruno, F. F.; Samuelson,
L. Macromolecules 2001, 34, 3921-3927.
(27) de Albuquerque, J. E.; Mattoso, L. H. C.; Faria, R. M.; Masters, J. G.;
MacDiarmid, A. G. Synth. Met. 2004, 146, 1-10.
(28) Asturias, G. E.; MacDiarmid, A. G.; Mccall, R. P.; Epstein, A. J. Synth.
Met. 1989, E157-E162.
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J. AM. CHEM. SOC. VOL. 130, NO. 10, 2008 2971

A R T I C L E S
Datta and Schuster
concomitantly reduced delocalization throughout the oligomer.
Notably, the fully oxidized form of PANI (pernigraniline) has
been previously prepared by the chemical oxidation of emer-
aldine, and it absorbs at ∼530 nm.29 The absence of a significant
shift in absorbance of the 420 nm band when PANI-DNA-
(X6) is treated with APS is expected since absorptions in the
300-450 nm region are known to be relatively insensitive to
the overall oxidation state of polyaniline. These findings are
fully consistent with the conclusion that the conjoined oligoa-
niline formed by treatment of DNA(X6) with HRP/H2O2 is in
the emeraldine oxidation state and that this material is further
oxidized to the pernigraniline form by reaction with APS.
In contrast to the most oxidized form, the leuco form of
polyaniline is characterized by absorption at ∼330 nm, which
is attributed to π-π* transitions. The leuco form has no
significant features in the visible spectral range.13 Reduction of
PANI-DNA(X6) with phenylhydrazine causes an increase in
absorption intensity in this near-UV region and a decrease in
the absorption that is characteristic of the emeraldine form at
420 nm. These findings are consistent with the conclusion that
the conjoined oligoaniline formed by treatment of DNA(X6)
with HRP/H2O2 is in the emeraldine oxidation state and that
this material is reduced to the leuco form by phenylhydrazine.
In contrast to PANI, the structure of the PAB oligomer
mandates a restricted delocalization of diimines. In addition,
oxidation of the PAB oligomer, especially at the ends, is
unlikely. Thus the diimine delocalization is limited, which results
in significantly blue-shifted absorption bands compared with
PANI. The results of oxidation of PAB-DNA(Y4) with APS
and reduction with phenylhydrazine are consistent with the
chemical structure proposed for conjoined PAB. The absence
of significant spectral features in the visible region after
reduction with phenylhydrazine is reasonable since reduced PAB
is characterized only by π-π* transitions at ∼360 nm.
Evidently, the PAB-DNA(Y4) oligomer is formed in a higher
oxidation state in the reaction with HRP/H2O2 than is PANI-
DNA(X6). This is not a consequence of being conjoined to DNA
because similar results are observed with the DNA templated
PAB formed from free monomers in solution (see Supporting
Information).
Figure 11. Structures of (A) homopolymer of 4-aminobiphenyl and (B)
copolymer of aniline and benzene. Dashed lines in B indicate location of
bond formation between aniline and benzene monomers. Cytosine nucleo-
bases connecting the oligomer to DNA are designated by R.
and 4′-methoxy-N-[(1,1′-biphenyl)-4-yl]ethane-1,2-diamine (nu-
cleobases X′ and Y′ respectively) sheds light on this mechanistic
aspect of polymer formation. Treatment of DNA(X′6) and DNA-
(Y′4) with H2O2 and HRP does not generate the visible
absorbance bands characteristic of para-linked PANI. Evidently,
the “blocking” substituents on the para positions of these
monomers prohibit reaction. In particular, the enzymatic syn-
thesis of polyaniline in the absence of templates has been shown
to result in branched structures that are characterized by
absorption bands at ∼460 nm.31 These findings are indicative
of a preferred head-to-tail reaction in the formation of the
conjoined PANI and PAB oligomers.
DNA Sequence Programmability Applied to the Forma-
tion of Conjoined Conducting Oligomers. In the approaches
discussed thus far for forming conjoined PANI oligomers, each
of the modified cytosine nucleotides is identically substituted.
There is no fundamental reason why this must be the case or
why the covalently conjoined monomers are restricted to
cytosines. To demonstrate this principle experimentally, we
prepared oligomers having cytosines modified with two different
moieties suitably arranged to form copolymers corresponding
to PAB-DNA. This approach effectively demonstrates the
power of this technique to use the sequence programmability
of DNA to generate conducting copolymers having a wide range
of possible, non-regular structures.
The order of the aromatic rings associated with 4-aminobi-
phenyl modifications in DNA(Y4) can be mimicked by an
appropriate pattern of aniline and benzene substitutions. This
was accomplished by preparing DNA(XZ) and DNA(ZY),
which have modified cytosines carrying the two monomers in
an alternating fashion. The treatment of these compounds with
HRP/H2O2 results in the formation of oligomers that have the
same absorption spectra as that of the PAB-DNA(Y4) con-
joined oligomer. This is indicative of the formation of oligomers
of similar structures by these two routes, see Figure 11. The
oligomers formed from DNA(XZ) and DNA(ZX) have lower
intensity absorbance bands compared with that from DNA(Y4),
which may be due to lower yields. Finally, it should be noted
that absorbance bands of similar intensity are observed inde-
pendent of the directionality of the X and Z nucleobases with
Head-to-Tail Directionality and Copolymer Formation.
The DNA templated enzymatic polymerization of aniline is
known to promote a preference for para-directed, head-to-tail
polymerization30 thereby improving the electrical properties of
the polymers compared with those formed in untemplated
reactions. In comparison to the chemical or enzymatic polym-
erization of anilines in solution, duplexes such as DNA(X6)
offer greater control of the arrangement of substituent anilines.
Nevertheless, the aniline groups still enjoy some flexibility in
their movement due to the alkyl tethers linking them to DNA.
Thus, the possibility of branching in PANI oligomer formation
cannot be precluded. Also, for the PAB oligomers, the presence
of the second aromatic ring provides additional positions for
reactions and branching. We wished to confirm that para-
direction of oligomer formation is enforced in the conjoined
oligomers reported here.
The cytosines incorporating 4-methyl-N-(2-aminoethyl)aniline
(29) Sun, Y.; MacDiarmid, A. G.; Epstein, A. J. J. Chem. Soc. Chem. Commun.
1990, 529.
(30) Samuelson, L. A.; Anagnostopoulos, A.; Alva, K. S.; Kumar, J.; Tripathy,
S. K. Macromolecules 1998, 31, 4376-4378.
(31) Alva, K. S.; Kumar, J.; Marx, K. A.; Tripathy, S. K. Macromolecules 1997,
30, 4024.
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DNA-Directed Synthesis of Oligomers
A R T I C L E S
respect to the DNA since they are reversed in DNA(ZX) from
that in DNA(XZ).
structures by taking advantage of the sequence programmability
of the templating DNA. The oligoanilines formed in this process
may be useful in the development of nanowires that take
advantage of the self-recognizing and self-organizing properties
of DNA to create unique structures.
The important conclusion from these findings is that two
distinct covalently linked monomers can be programmed by the
DNA sequence to form unique oligomers with non-recurring,
irregular structures. The modification of more than one nucleo-
base in a DNA oligomer with appropriate monomers is expected
to further expand the range and complexity of polymers that
can be formed by this technique.
Acknowledgment. This work was supported by the National
Science Foundation and the Vassar Woolley Foundation, for
which we are grateful. Dr. Joshy Joseph assisted with the
synthesis of the DNA oligomers.
Conclusions
Supporting Information Available: ESI mass spectrometric
characterization of modified DNA sequences, HPLC purification
profile of DNA(Y4), UV-thermal melting temperatures of
modified DNA duplexes and melting profile of ternary complex
DNA(Y3′)-DNA(Y3′′)-DNA(Y2), synthetic scheme and pro-
cedure for the preparation of the Z phosphoramidite, CD spectra
of DNA(Y4) before and after HRP/H2O2 treatment, UV thermal
melting behavior of DNA(Y4) before and after HRP/H2O2
treatment, comparative CD spectra of DNA(X6), DNA(Y4),
DNA(X′6), and DNA(Y′4) and mass spectrometric characteriza-
tion of conjoined PANI formation. This material is available
free of charge via the Internet at http://pubs.acs.org.
Aniline monomers covalently attached to DNA nucleobases
can be converted to conjoined oligoanilines having the properties
of conducting polymers by treatment with HRP/H2O2. The DNA
acts as a soft template that restricts the reaction to monomers
aligned along one strand of the duplex DNA and inhibits the
intermolecular reaction of monomers on separate DNA mol-
ecules. The covalent attachment of the monomers enforces a
head-to-tail, para linkage that generates the more desired, higher
conducting form of the polyaniline. The oligomers formed in
this process are in the emeraldine oxidation state, but they can
be oxidized or reduced by chemical reagents. Monomers of
diverse structures can be converted to oligomers in this reaction.
The oligomers that result may be tailored to have unique
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