Preparation, Single-Molecule Manipulation, and Energy Transfer Investigation of a Polyfluorene-graft-DNA polymer

Article abstract of DOI:10.1002/chem.201702780

Conjugated polymers have been intensively studied due to their unique optical and electronic properties combined with their physical flexibility and scalable bottom up synthesis. Although the bulk qualities of conjugated polymers have been extensively utilized in research and industry, the ability to handle and manipulate conjugated polymers at the nanoscale lacks significantly behind. Here, the toolbox for controlled manipulation of conjugated polymers was expanded through the synthesis of a polyfluorene-DNA graft-type polymer (poly(F-DNA)). The polymer possesses the characteristics associated with the conjugated polyfluorene backbone, but the protruding single-stranded DNA provides the material with an exceptional addressability. This study demonstrates controlled single-molecule patterning of poly(F-DNA), as well as energy transfer between two different polymer–DNA conjugates. Finally, highly efficient DNA-directed quenching of polyfluorene fluorescence was shown.

Full text of DOI:10.1002/chem.201702780

A Journal of
Accepted Article
Title: Preparation, single-molecule manipulation and energy transfer
investigation of a polyfluorene-graft-DNA polymer
Authors: Mikael Madsen, Rasmus S Christensen, Abhichart
Krissanaprasit, Mette R Bakke, Camilla F Riber, Karina S
Nielsen, Alexander Zelikin, and Kurt Vesterager Gothelf
This manuscript has been accepted after peer review and appears as an
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of the final Version of Record (VoR). This work is currently citable by
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To be cited as: Chem. Eur. J. 10.1002/chem.201702780
Link to VoR: http://dx.doi.org/10.1002/chem.201702780
Supported by

Chemistry - A European Journal
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COMMUNICATION
Preparation, single-molecule manipulation and energy transfer
investigation of a polyfluorene-graft-DNA polymer
[
a]
[a]
[a]
[a]
Mikael Madsen , Rasmus S. Christensen , Abhichart Krissanaprasit , Mette R. Bakke , Camilla F.
[
b]
[a]
[b]
[a],[b]
Riber , Karina S. Nielsen , Alexander N. Zelikin and Kurt V. Gothelf*
Abstract: Conjugated polymers have been intensively studied due
to their unique optical and electronic properties combined with their
physical flexibility and scalable bottom up synthesis. While the bulk
qualities of conjugated polymers have been extensively utilized in
research and industry, the ability to handle and manipulate
conjugated polymers at the nanoscale lacks significantly behind.
Here we extend the toolbox for controlled manipulation of conjugated
polymers through the synthesis of a polyfluorene-DNA graft type
polymer (poly(F-DNA)). The polymer possesses the characteristics
associated with the conjugated polyfluorene backbone, but the
protruding single-stranded DNA provides the material with an
exceptional addressability. This allows us to demonstrate controlled
single polymer patterning, as well as energy transfer between two
different polymer-DNA conjugates. Finally, we demonstrate highly
efficient DNA directed quenching of the polyfluorene fluorescence.
is however extremely challenging, and although single molecule
fluorescence spectroscopy and STM studies have provided
valuable insight, the ability to investigate and utilize single
[
6],[7]
molecule CPs remains underdeveloped.
In an attempt to overcome this, our group recently
presented platform for positioning individual alkoxy-p-
a
phenylene vinylene polymers carrying single-stranded DNA
brushes (poly(APPV-DNA)) in designed patterns on DNA
nanostructures, and we further showed that we could switch the
polymer conformation in
a controlled fashion via strand
[
8]
displacement reactions. We envisioned that this platform could
be of great use for studying the optical properties of individual
CP molecules, as well as the interaction between different types
of dyes and CPs at the single molecule level. The poly(APPV-
DNA) of our previous studies, however, contains inherent
defects which limit the conjugation length, while photooxidative
degradation of the polymer upon irradiation tends to impede
optical studies preventing us from investigating effects such as
Conjugated polymers (CPs) are intriguing molecules with a wide
variety of applications. They can be produced at low cost, and
their physical properties such as band gaps, solubility and
optical behavior can be tuned by rational chemical design of the
[9]
hybridization-controlled quenching. The fact that we only had
access to one type of CP-DNA conjugate further excluded the
possibility of investigating inter-polymer energy transfer. To meet
these challenges, we have prepared a polyfluorene-graft-DNA
polymer (poly(F-DNA)) that provides continuous conjugation,
improved stability and good fluorescence quantum yield. The
results on the quenching and energy transfer studies, along with
details on the synthesis and single molecule immobilization of
poly(F-DNA) are outlined below.
[
1]
polymer structure.
Their semi-conducting behavior and
spectacular optical properties have allowed them to find use in
various devices including field effect transistors (FETs), polymer
solar cells (PSCs), and polymeric light emitting diodes
[
2]
(
PLEDs). Polyfluorenes (PFs) are one type of CP that has
gained particular interest due to their high stability, great
[
3]
quantum yields and blue light emission. PFs have therefore
become a favorite candidate for use in optoelectronic devices
The poly(F-DNA) is a graft type polymer based on a
polyfluorene backbone carrying linkers that are functionalized
with single-stranded DNA. To obtain polymers carrying a large
number of DNA strands, we followed an approach where DNA is
synthesized directly onto the polymer by solid phase
oligonucleotide synthesis. To realize this for a polyfluorene type
construct, we chose a target structure based on repeating
fluorene units carrying protected hydroxyl linkers. This was
obtained through the synthesis of a fluorene based monomer (1)
carrying 2-tetrahydropyranyl (THP) protected triethylene glycol
linkers in two steps from fluorene (Scheme S1 and S2).
[
4]
and mainly PLEDs.
The success of PFs and other conjugated polymers in
such devices is attributed to the bulk polymer properties
prevailing in thin films. Extensive research has evolved around
understanding and tuning the performance of CP thin films
[
5]
through calculations and thin film characterization. Arguably, it
would be of great value to know the behavior of individual
polymer molecules and how it translates into the observed
output of thin film devices. The study of individual CP molecules
Polymerization of the monomer, 1, was carried out through
a
Yamamoto-type reaction. After precipitation from
a
[
a]
M. Madsen, R. S. Christensen, Dr. A. Krissanaprasit, M. R. Bakke,
K. S. Nielsen, Prof. K. V. Gothelf*
Interdisciplinary Nanoscience Center (iNANO)
Aarhus University
MeOH/Acetone (4:1) mixture, polymers with M values of 42, 33,
N
and88 kDa and dispersities in the range of 1.5-1.8 as measured
by SEC-MALS (Size exclusion chromatography coupled to a
multiangle light scattering detector, Table S1 and figure S13)
were obtained for the three batches of polymers used in this
study. To facilitate immobilization of the polymers for solid phase
DNA synthesis, a fraction of the THP groups were removed
using dilute TsOH in a chloroform/MeOH mixture. The partial
deprotection served to maintain masked hydroxyl groups for
oligonucleotide synthesis as well as to keep the polymers
soluble. The exposed hydroxyl groups were functionalized by
reaction with 2-cyanoethyl N,N-diisopropylchlorophosphor-
Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
E-mail: kvg@chem.au.dk
[
b]
c]
Camilla F. Riber, Assoc. Prof. Alexander N. Zelikin and Prof. K. V.
Gothelf*
Department of Chemistry
Aarhus University
Langelandsgade 140, 8000 Aarhus C, Denmark
Dr. A. Krissanaprasit
[
Present address: Department of Materials Science and Engineering,
North Carolina State University, Raleigh, North Carolina 27606,
USA
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Scheme 1. Synthesis of poly(F-DNA). Yamamoto polymerization of 1 followed by partial removal of THP protecting groups affords the hydroxyl functionalized
polyfluorene, P2. Reaction of P2 with 2-cyanoethyl N,N-diisopropylchlorophosphoramidite affords the polymer phosphoramidite intermediate that is immediately
immobilzed by reaction with the dT modified 3000Å CPG beads in the presence of ETT (5-ethylthio-1H-tetrazole). Deprotection of remaining THP groups allows
for oligonucleotide synthesis onto the polymer. poly(F-DNA) is obtained after cleavage and deprotection in AMA followed by size exclusion chromatography.
Further details regarding synthetic procedures are provided in the supporting information.
amidite, and the phosphoramidite of the polymer was directly
used for immobilization on hydroxyl functionalized 3000 Å CPG
beads. After removal of the remaining THP protecting groups,
solid phase oligonucleotide synthesis was performed.
Subsequent cleavage in AMA (1:1 mixture of ammonium
hydroxide and 40% aqueous methylamine) and size exclusion
chromatography afforded poly(F-DNA) (Scheme 1). Compared
to the methods we have previously used for synthesis of
polymers with DNA brushes, the formation of the reactive
phosphoramidite was here performed on the polymer and not on
the solid support. Both strategies were investigated, and
apparently indifferent CP-DNA conjugates were obtained
through both routes. However, higher yield was observed when
the phosphoramidite was formed on the polymer prior to
immobilization on the solid support. Key to obtaining poly(F-
DNA), was also the use of THP as the hydroxyl protecting group.
This protecting group possessed the desired stability under the
highly alkaline conditions used during fluorene alkylation and
allowed deprotection under mild, acidic conditions after
polymerization.
and it shows great fluorescence quantum yields of ~ 0.58 in TAE
and ~ 0.44 in TEAA buffer respectively (Figure S11-12).
The obtained poly(F-DNA) features absorption from
single-stranded DNA with λmax around 260 nm and from the
polyfluorene with λmax at 395 nm. It furthermore shows bright
blue fluorescence with maximum intensity at 420 nm. The
material is readily soluble in buffers such as TAE (Tris-acetate-
EDTA) and TEAA (triethylammonium acetate volatile buffer),
Figure 1. Characterization of poly(F-DNA). A) Topography AFM image of a
fraction containing medium size poly(F-DNA) carrying
a 10mer DNA
sequence. Scale bar = 100 nm. B) Height profile for poly(F-DNA) showing
heights between 2 and 3 nm. C) UV-vis absorption spectrum for poly(F-DNA)
carrying 15T oligonucleotides. D) Excitation (red line, λ(em) = 430 nm ) and
emission (blue line, λ(exc) = 385 nm) spectra for poly(F-DNA).
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[
12]
To further characterize the polymers, tapping mode atomic
force microscopy (AFM) in liquid was performed. In AFM
topography imaging, the polymers are observed as elongated
structures with occasional presence of multi-polymer structures
2-3 nm.
In an approach inspired by our previous work, we
constructed 2D rectangular DNA origami structures carrying
[
8]
patterns composed of extended staple strands. We then
synthesized poly(F-DNA) with DNA sequences complementary
to the extended staple strands. By mixing the polymer with the
nanostructure, we expected that the polymer would align along
the pattern of complementary single-stranded DNA directed by
DNA-hybridization. To verify that we could indeed position
poly(F-DNA) in desired patterns on DNA nanostructures, we
showed that poly(F-DNA) efficiently aligned in 90 degree curves
and U-shape patterns as visualized and analyzed by liquid
phase AFM (Figure S4).
(
Figure S15). Heights between 2 and 3 nm depending on
imaging conditions (Figure 1A and B), are typically observed for
the structures. The fractions expected to contain the largest
polymers as obtained from size exclusion chromatography
mainly contain polymers of lengths larger than 100 nm as
observed from AFM (Figure S15). SEC-MALS analysis of the
isolated fractions shows a clear difference in size between the
polymers from the different fractions (Table S2). To estimate the
amount of DNA attached to the backbone, a literature value for
the extinction coefficient of water soluble polyfluorenes was
To move forward in the direction of creating nanoscale
circuitry, we wanted to enable the positioning of multiple polymer
components on DNA origami. We therefore designed a construct
that would allow positioning of poly(F-DNA) as well as
[
10]
used. This approach suggests that the polymers typically carry
between 0.8 and 1 DNA strands per monomer unit (Table S3).
One of the long-term goals motivating the development of
polymers carrying DNA brushes was to enable characterization
of intra- and intermolecular energy transfer for individual
polymers positioned in controlled conformations at the
nanoscale. To realize this, we wanted to establish a method to
position poly(F-DNA) in controlled patterns on DNA
nanostructures. DNA nanostructures have been successfully
used for precise nanoscale positioning of various nanoobjects
such as gold nanoparticles, carbon nanotubes and biomolecules
poly(APPV-DNA) along individual tracks on
a
single
nanostructure. The construct was based on a flat rectangular
DNA origami structure with linear patterns of extended single-
stranded DNA on both planes of the flat structure (Figure 2). For
ease of visualization we decided to place the two tracks so that
the polymers would form a cross upon immobilization. The
sequences of the tracks were designed to align poly(APPV-
DNA) along the longest axis of the nanostructure, whereas
poly(F-DNA) would align along the shorter axis. To test the
binding specificity, the polymers were individually mixed with the
DNA origami construct and characterized by AFM. We observed
highly specific binding to the desired track for each polymer, and
[
11]
as well as for templating the formation of polymers.
This
success can be attributed to the unique spatial addressability
that these kinds of structures provide. In structures formed by
the DNA origami method all staple strands can be extended and
addressed individually providing a spatial resolution of as low as
Figure 2. Immobilization of poly(F-DNA) and poly(APPV-DNA) in designed patterns on rectangular DNA nanostructures. A) Illustration (top) and AFM
topography image (bottom) for immobilization of poly(APPV-DNA) with sequence complementarity to the longitudinal track. Scale bar = 300 nm B) Illustration
(
top) and AFM topography image (bottom) for immobilization of poly(F-DNA) along the short axis of the rectangular DNA nanostructure. Scale bar = 300 nm C)
Illustration (top) and AFM topography image (bottom) for both polymers positioned on each side of the flat nanostructure in a cross type architecture. Scale bar =
3
00 nm. In general, poly(F-DNA) is observed as higher contrast structures than poly(APPV-DNA) allowing distinction between the two different types of polymers.
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when both polymers were mixed with the construct, efficient
formation of well-formed cross structures was observed (Figure
sequence complementarity between the DNA on the two
polymers, no significant ET was observed upon mixing in
solution (Figure 3B and C). The energy transfer is most likely
not taking place between individual polymers, and a lot of efforts
remain in order to realize nanoscale optical circuitry based on
individual CPs. The ability to have two conjugated polymers
physically interact in this hybridization-controlled fashion is an
important step on the way. Further control experiments and data
concerning energy transfer are provided in the supporting
information (Figure S8-10).
2
). When using the two different polymer-DNA conjugates in
combination it is noticed, that poly(F-DNA) generally appears
with brighter height contrast than poly(APPV-DNA).
In our initial attempts to investigate inter-polymer energy
transfer between poly(F-DNA) and poly(APPV-DNA) on DNA
nanostructures no efficient energy transfer was observed (data
not given). We expect this to be caused by a lack of physical
inter-polymer contact combined with difficulties eliminating
background signals from non-bound polymers. Therefore, in an
attempt to induce significant physical interaction between the
two materials, we moved on to investigate the energy transfer
between the two polymers when directly co-localized by DNA
hybridization. We investigated the emission of poly(APPV-DNA)
upon excitation of poly(F-DNA) in a set-up where the two
different conjugates carried complementary DNA sequences. As
a control, the same experiment was carried out with non-
complementary sequences on the polymers.
Single molecule fluorescence spectroscopy studies have
shown that intramolecular energy transfer of excitons can take
place over significant distances along the backbone of
[
6]
conjugated polymers until a defect site is reached. This also
implies that a single quencher molecule should potentially be
able to quench the emission from an entire polymer molecule
leading to so-called super quenching. Fan et al. elegantly
showed that gold nanoparticles (GNPs) could quench cationic
fluorene based polymers in a hyperefficient manner with Stern-
1
1
-1 [13]
Volmer constants (KSV) approaching 10 M .
.
Figure 3. Energy transfer between poly(F-DNA) and poly(APPV-DNA). A)
Illustration: Sequence complementarity leads to formation of complexes
between poly(F-DNA) and poly(APPV-DNA) via hybridization (top). Without
complementarity of the DNA sequences, the two polymers exist separately in
solution (bottom). B) Quantification of ET from poly(F-DNA) to poly(APPV-
DNA). Error bars denote 1 standard deviation from the mean derived from
triplicates. C) Fluorescence spectra showing the APPV emission upon addition
of non-complementary poly(F-DNA) (red line), complementary poly(F-DNA)
(
blue line), and buffer (black line) to poly(APPV-DNA). Spectra are normalized
at poly(APPV-DNA) maximum intensity before addition of poly(F-DNA) or
buffer.
The two polymers were mixed in 200 mM NaCl solution, and in
the case of sequence complementarity, significant energy
transfer was observed (Figure 3), and a relative energy transfer
efficiency of around 37% was calculated (Equation S1). We
assume that soluble multi-polymer particles are formed bringing
the two different polymers into very close proximity. Without
Figure 4. Quenching studies with poly(F-DNA). A) Illustration of poly(F-DNA)
binding to a complementary DNA strand carrying a dabcyl quencher. B) Data
from titration with complementary quencher strand. 50 nM (5 pmol) of DNA on
poly(F-DNA) was utilized in the experiments. Error bars denote 1 standard
deviation from the mean derived from triplicates C) Stern-Volmer plot from the
titration data.
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We envisioned that using the unique addressability of
poly(F-DNA) arising from the brush of ssDNA, we could obtain
highly efficient quenching in a very controlled manner by adding
complementary ssDNA carrying a quencher molecule. Using a
polymer carrying brushes composed of 15T sequences and a 5’-
dabcyl-15A sequence, we observed efficient quenching even at
a stoichiometry of 1:50 between quencher-DNA and DNA on the
polyfluorene (Figure 4). The Stern-Volmer plot showed decent
Keywords: Conjugated polymers • Polymer-DNA conjugate •
Self-assembly • Single molecule circuitry • Energy transfer
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unique addressability provides
platform.
a very interesting sensing
In conclusion, we have developed the novel hybrid DNA-
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polyfluorene backbone carrying dense brush of ssDNA
a
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This work was supported financially by the Danish National
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Chemistry - A European Journal
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Entry for the Table of Contents
COMMUNICATION
A graft type polyfluorene-DNA
conjugate (poly(F-DNA)) has been
developed. The conjugate shows
interesting features such as efficient
DNA directed quenching, controlled
interpolymer energy transfer and
efficient single-molecule nanoscale
positioning.
M. Madsen, R. S. Christensen, A.
Krissanaprasit, M. R. Bakke, C. F. Riber,
K. S. Nielsen, A. N. Zelikin and K. V.
Gothelf*
Page No. – Page No.
Preparation, single-molecule
manipulation and energy transfer
investigation of a polyfluorene-graft-
DNA polymer
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