Roland Hager1, Andreas Arnold2, Eva Sevcsik2, Gerhard J Schütz2, Stefan Howorka1,3. 1. Center for Advanced Bioanalysis GmbH . Linz , 4020 , Austria. 2. Institute of Applied Physics , TU Wien , Wien , 1040 , Austria. 3. Department of Chemistry, Institute for Structural and Molecular Biology , University College London (UCL) , London , WC1E 6BT , U.K.
Abstract
The controlled immobilization of biomolecules onto surfaces is relevant in biosensing and cell biological research. Spatial control is achieved by surface-tethering molecules in micro- or nanoscale patterns. Yet, there is an increasing demand for temporal control over how long biomolecular cargo stays immobilized until released into the medium. Here, we present a DNA hybridization-based approach to reversibly anchor biomolecular cargo onto micropatterned surfaces. Cargo is linked to a DNA oligonucleotide that hybridizes to a sequence-complementary, surface-tethered strand. The cargo is released from the substrate by the addition of an oligonucleotide that disrupts the duplex interaction via toehold-mediated strand displacement. The unbound tether strand can be reloaded. The generic strategy is implemented with small-molecule or protein cargo, varying DNA sequences, and multiple surface patterning routes. The approach may be used as a tool in biological research to switch membrane proteins from a locally fixed to a free state, or in biosensing to shed biomolecular receptors to regenerate the sensor surface.
The controlled immobilization of biomolecules onto surfaces is relevant in biosensing and cell biological research. Spatial control is achieved by surface-tethering molecules in micro- or nanoscale patterns. Yet, there is an increasing demand for temporal control over how long biomolecular cargo stays immobilized until released into the medium. Here, we present a DNA hybridization-based approach to reversibly anchor biomolecular cargo onto micropatterned surfaces. Cargo is linked to a DNA oligonucleotide that hybridizes to a sequence-complementary, surface-tethered strand. The cargo is released from the substrate by the addition of an oligonucleotide that disrupts the duplex interaction via toehold-mediated strand displacement. The unbound tether strand can be reloaded. The generic strategy is implemented with small-molecule or protein cargo, varying DNA sequences, and multiple surface patterning routes. The approach may be used as a tool in biological research to switch membrane proteins from a locally fixed to a free state, or in biosensing to shed biomolecular receptors to regenerate the sensor surface.
Anchoring bioactive
molecules onto surface micro- or nanopatterns
is important in sensing as well as for biophysical and cell biological
research.[1−13] Spatially immobilized bioactive small-molecules or proteins can
miniaturize biosensing or biophysical assays, such as to increase
in microarray format the throughput of investigation, and minimize
sample consumption. In biology, microclusters of biomolecular receptors
can mimic cell–cell contact by binding cognate cellular membrane
proteins and thereby probe how the proteins’ distribution in
cells and function is influenced by their defined localization.[1,2]Reversible anchoring of biomolecules onto surfaces is of increasing
interest. In cell biological research, controllable release of receptors
can switch membrane proteins from a fixed to an unbound state and
thereby elucidate cell adhesion,[14] cell
migration,[15] signaling,[16−18] protein–protein
interactions,[19] or lateral diffusion of
membrane proteins.[1,20] Outside cell biology, the controllable
shedding of protein-coated surfaces may be used to regenerate biomaterial
activity.Generating arrays for controllable release can utilize
classical
patterning routes in which biochemically adhesive surface-patches
are top-down fabricated and then linked to biomolecular cargo.[21−24] However, controllable release requires cleavable linkers that respond
to an external trigger by severing the bond between cargo and surface.
Specialized photolytic linkers have been developed.[25] Yet, avoiding intense light can be beneficial in cell biology
to minimize cytotoxicity. Of similar advantage would be a chemically
simple route with readily available components.Here we use
deoxyribose nucleic acid (DNA) association and dissociation
as a means to spatiotemporally control the reversible attachment of
biomolecules onto surfaces. DNA-directed immobilization of molecular
cargo was pioneered by the Niemeyer group[26] and further developed for use in biosensing and biomedical diagnostics,
and for fundamental studies in biology and medicine.[27−29] Our approach for controlled immobilization and release relies on
competitive hybridization/dehybridization[30] as shown in Figure A. Anchor strand A-DNA (Figure A, black) is bound to the substrate surface.
Figure 1
(A) Schematic
overview of DNA-mediated binding, release, and rebinding
of molecular cargo to a surface. Steps: capturing of biotin-tagged
anchor strand A-DNA to surface-bound streptavidin (gray) followed
by hybridization of cargo-strand C-DNA, release of cargo (yellow circle)
by toehold-mediated strand displacement with release strand R-DNA,
rebinding of C-DNA to A-DNA. (B) Schematic overview of the microstructured
surface featuring a dense poly(ethylene glycol) (PEG) film on a glass
slide. The PEG film is microstructured and features biotin–PEG
patches that bind streptavidin protein.
(A) Schematic
overview of DNA-mediated binding, release, and rebinding
of molecular cargo to a surface. Steps: capturing of biotin-tagged
anchor strand A-DNA to surface-bound streptavidin (gray) followed
by hybridization of cargo-strand C-DNA, release of cargo (yellow circle)
by toehold-mediated strand displacement with release strand R-DNA,
rebinding of C-DNA to A-DNA. (B) Schematic overview of the microstructured
surface featuring a dense poly(ethylene glycol) (PEG) film on a glass
slide. The PEG film is microstructured and features biotin–PEG
patches that bind streptavidin protein.Cargo strand C-DNA (Figure A, red) hybridizes to A-DNA thereby forming a short
duplex
with a single-stranded overhang (Figure A, capturing). The terminus of C-DNA carries
molecular cargo (Figure , yellow circle) which is tethered via the duplex to the anchoring
site. However, the cargo can be released from the surface by the addition
of release strand R-DNA (blue)(Figure A). R-DNA is complementary to the entire length of
C-DNA, thereby leading via toehold-mediated strand displacement[30−32] to a long nontethered duplex (Figure A, release). The liberated anchor strand can be reloaded
with C-DNA (Figure A, rebinding). The approach is related to the previous use of strand
displacement for release of DNA-bound cargo from DNA-assembled supramolecular
protein conjugates[33] and the release of
DNA-bound cells from solid substrates by means of restriction endonucleases.[34]We implement our approach of triggered
release of molecular cargo
with a micropatterned substrate, relevant for many applications including
cell biology. Our approach is demonstrated with patterns produced
by photolithography and by microcontact printing. Photolithography
has the advantage of being automatable, whereas microcontact printing
is cheaper and more flexible in its applications.[35] We expect that the combination of DNA-mediated controllable
immobilization on micropatterns will enable new research in cell biology
such as on the formation of the immunological synapse.[36]
Results and Discussion
Generation of Micropatterned
Surfaces
The substrate
surfaces for our DNA-based release strategy featured a homogeneous
poly(ethylene glycol) (PEG) film grafted to a glass slide (Figure B). The dense layer
of end-tethered PEG chains fulfilled two functions. It avoided the
nonspecific adhesion of DNA and protein. In addition, part of the
layer’s polymer chains carried the biotin tag to form a grid-like
micropattern. The biotin bioaffinity pattern served to bind streptavidin
(Figure B) and thereby
anchor biomolecular cargo onto the surface.The biochemically
patterned substrate surfaces were generated using a method shown in Figure S1 by (i) grafting PEG diamine (MW 600
D) onto epoxy-functionalized glass surfaces. The quality of the PEG
layer was confirmed with atomic force microscopy (Figure S2). (ii) The free amine end of the PEG chains was
then modified with biotin using activatedester chemistry. The pattern
of biotinylated vs nonbiotinylated areas was attained by photolithography.
Therefore, the biotin–PEG film was (iii) embedded within a
layer of positive photoresist. The resist was (iv) illuminated with
UV light and a grid-mask featuring round holes of 3 μm diameter
separated by a distance of 3 μm. (v) Illuminated photoresist
was removed using photolithographic developer solvent, followed by
plasma-etching to oxidatively breakdown the now no-longer photoresist-embedded
biotin-PEG within the round features. Incubation with others organic
solvents stripped off the nonilluminated photoresist to yield a grid-patterned
biotin-PEG surface. The generation of micropatterns of round holes
within the biotin-PEG layer was demonstrated by AFM analysis (Figure S2). (vi) Exposed glass surface within
the round holes was backfilled by grafting with nonbiotinylated methoxy-PEG-silane
thereby yielding the micropattern featuring the round features of
nonbiotinylated PEG surrounded by biotin-PEG (Figure B).The functionality of the biotin-micropatterned
PEG surface was
demonstrated by adding fluorophore-labeled streptavidin protein. It
was expected that the protein would bind via specific biomolecular
recognition to the biotin-grid pattern but not to the protein-repelling
PEG discs without biotin. Indeed, fluorescence microscopy visualized
the expected grid-like pattern of bound Cy5-tagged streptavidin (Figure S3). The contrast between biotin and nonbiotin,
as judged by the fluorescence signals, was 0.98 ± 0.02. The contrast
was calculated by using the formula: contrast = (Fmax – Fmin)/(Fmax – BG) whereby Fmax and Fmin are fluorescence counts
in the bright, Cy5-streptavidin-coated biotin-PEG areas and in the
dim, nonbiotin-PEG areas of the pattern, respectively. BG refers to
background which is the glass surface that had not been exposed to
Cy5-streptavidin.
Reversible Anchoring of Small-Molecule Cargo
After
validating the functionality of the biotin-patterns, we applied them
for our reversible anchoring approach. Therefore, the biotin-patterns
were decorated with A-DNA. This was achieved by first coating onto
the biotin pattern unlabeled streptavidin (Figure B) and then binding biotinylated A-DNA (Figure A, capturing). The
molecular interaction of biotin and streptavidin is known to be of
high affinity and very reproducible. The successful decoration of
the grid patterns with A-DNA was demonstrated by hybridizing fluorophore
Cy3-labeled capture oligonucleotide C-DNA. The latter oligonucleotide
comprises the full complementary sequence of A-DNA but carries a single-stranded
5′ extension. Fluorescence microscopic analysis (Figure A) shows that hybridization
via a short duplex was successful leading to a clear fluorescence
grid-like pattern of C-DNA signal that extends over hundreds of micrometers.
The contrast between bound and nonbound areas was 0.52 ± 0.04.
Figure 2
Fluorescence
microscopy confirms the DNA-mediated binding and release
of small-molecule cargo anchored onto microstructured DNA-A surfaces.
Schematic overview and fluorescence microscopic images of microstructured
surfaces (A) after incubation with C-DNA labeled with small-molecule
Cy3 fluorophore, (B) after toehold-mediated strand displacement with
release R-DNA, and (C) after rehybridization of fluorescent labeled
C-DNA. The line profiles of fluorescent microscopic images along the
white lines of the microscopic images are shown to the right. Image
size: 96 μm × 96 μm.
Fluorescence
microscopy confirms the DNA-mediated binding and release
of small-molecule cargo anchored onto microstructured DNA-A surfaces.
Schematic overview and fluorescence microscopic images of microstructured
surfaces (A) after incubation with C-DNA labeled with small-molecule
Cy3 fluorophore, (B) after toehold-mediated strand displacement with
release R-DNA, and (C) after rehybridization of fluorescent labeled
C-DNA. The line profiles of fluorescent microscopic images along the
white lines of the microscopic images are shown to the right. Image
size: 96 μm × 96 μm.We next probed whether targeted release of cargo C-DNA can
be achieved
with competitive hybridization/dehybridization upon addition of R-DNA
(Figure A, release).
In model experiments, DNA release was first demonstrated in solution
using read-out with agarose gel electrophoresis, rather than on the
glass surface (Figure S4). Releasing cargo-carrying
C-DNA by R-DNA was also successful on the surface as shown in fluorescence
microscopic analysis (Figure B). The low fluorescence levels and the virtual absence of
the grid pattern indicate the almost complete removal of C-DNA, as
compared to the pattern before the addition of R-DNA. Quantitative
analysis of the fluorescence signal determined a 300-fold drop of
DNA coverage (Figure S5). This suggests
that R-DNA displaced anchoring A-DNA in the short DNA duplex thereby
forming a new long DNA duplex between R-DNA and C-DNA (Figure A, release). Successful release
and concomitant liberation of anchor strand into a single-stranded
form was also demonstrated by reloading the freed anchor A-DNA with
another charge of fluorophore-labeled C-DNA (Figure A, rebinding). The microscopic image showed
again the grid-pattern (Figure C). However, the total amount of fluorescence was about 30%
lower than in the first round of binding (Figure S5). Several controls confirmed the specificity of the triggered
release (Figure S6). Release conditions
such as incubation time with R-DNA were also optimized to achieve
complete release (Figure S6).
Reversible
Anchoring of Protein Cargo
The DNA-mediated
release principle was next implemented for protein-based molecular
cargo (Figure ). As
a model protein, streptavidin was used. The protein was bound via
biotinylated cargo-DNA to the surface (Figure ). We used streptavidin as cargo as well
as for obtaining the A-DNA micropatterns given the high affinity and
highly reproducible nature of the biotin–streptavidin interaction.
Possible consequences of the double use of streptavidin, such as nonspecific
binding of cargo streptavidin to any residual biotin-PEG was avoided
by the high-quality of the streptavidin micropatterns[37](Figures S6 and S9).
Figure 3
Schematic overview
of DNA strand-mediated binding, release, and
rebinding of protein-based molecular cargo. Steps: capturing of biotin-tagged
anchor strand A-DNA to surface-bound streptavidin (gray) followed
by hybridization of conjugate C-DNA and streptavidin; release of protein
cargo by toehold-mediated strand displacement with release strand
R-DNA; rebinding of C-DNA onto A-DNA.
Schematic overview
of DNA strand-mediated binding, release, and
rebinding of protein-based molecular cargo. Steps: capturing of biotin-tagged
anchor strand A-DNA to surface-bound streptavidin (gray) followed
by hybridization of conjugate C-DNA and streptavidin; release of protein
cargo by toehold-mediated strand displacement with release strand
R-DNA; rebinding of C-DNA onto A-DNA.The protein–DNA conjugate was obtained by mixing Atto550-labeled
streptavidin to the biotinylated cargo-DNA at a molar ratio of 1:4.
Ratios ranging from 2:1 to 1:20 were also prepared and analyzed
via gel electrophoresis (Figure S7). The
protein–DNA conjugate was successfully hybridized onto the
anchor-DNA modified surface (Figure , capturing), as shown by fluorescence microscopy analysis
(Figure A for a streptavidin:
DNA ratio of 1:4; Figure S8 for a ratio
of 1:10).
Figure 4
Fluorescence microscopic analysis of DNA-mediated binding, release,
and rebinding of streptavidin–DNA conjugates at microstructured
A-DNA surfaces. Schematic overview and fluorescence microscopic images
of microstructured surfaces (A) after incubation with C-DNA-streptavidin
conjugates labeled with Cy3, (B) after toehold-mediated strand displacement
with release R-DNA, and (C) after rehybridization of C-DNA-streptavidin
conjugates. The molar ratio for C-DNA and streptavidin was 4:1. The
line profiles of fluorescent microscopic images along the white lines
of the microscopic images are shown to the right. Image size: 96 μm
× 96 μm.
Fluorescence microscopic analysis of DNA-mediated binding, release,
and rebinding of streptavidin–DNA conjugates at microstructured
A-DNA surfaces. Schematic overview and fluorescence microscopic images
of microstructured surfaces (A) after incubation with C-DNA-streptavidin
conjugates labeled with Cy3, (B) after toehold-mediated strand displacement
with release R-DNA, and (C) after rehybridization of C-DNA-streptavidin
conjugates. The molar ratio for C-DNA and streptavidin was 4:1. The
line profiles of fluorescent microscopic images along the white lines
of the microscopic images are shown to the right. Image size: 96 μm
× 96 μm.Microscopic analysis
(Figure B, Figure S8) also confirmed
that the surface-tethered protein cargo could be released from the
surface by adding R-DNA (Figure , release). As implied by the experimental results,
release DNA led to the competitive dehybridization of C-DNA from A-DNA,
and concomitant hybridization of cargo to release strand to form the
long duplex (Figure , release).Single-stranded A-DNA could be reloaded with cargo
by adding fresh
Atto550-streptavidin-tagged C-DNA (Figure , rebinding), as indicated by the grid-like
fluorescence pattern (Figure C, Figure S8). The extent of loading
was, however, lower than for the first capturing (Figure S9). Quantitative analysis of fluorescence brightness
yielded 1450 ± 150 counts compared to 1800 ± 170 counts
for the first hybridization (for a streptavidin/DNA ratio of 1:4).
For a streptavidin/DNA ratio of 1:10, the corresponding counts were
903 ± 126 and 1080 ± 110, respectively.
Universality
of the Anchoring Principle
To demonstrate
its universality, the principle of DNA-mediated anchoring of molecular
cargo was extended to a non-PEG micropatterned surface. An additional
aim was to probe whether the orientation and sequence design of DNA
strands can be altered without affecting the release efficiency. The
redesigned DNA duplexes and DNA strands are schematically shown in Figure . As a first difference,
A′-DNA is longer than C′-DNA; the opposite was the case
in the previous design. Furthermore, R′-DNA binds to the free
distal 3′ terminus of the A′-DNA. In the previous design,
R-DNA binds to the 5′ which is close to streptavidin. Finally,
R′-DNA hybridizes to the A′-DNA to form the long duplex,
thereby displacing C′-DNA. A consequence of duplex formation
between anchor and release strand is that A′-DNA cannot be
reloaded with C′-DNA. We tested the new DNA release design
with the fluorophore-labeled cargo strand.
Figure 5
Schematic overview of
DNA strand-mediated binding and release of
small-molecule cargo from microstructured A′-DNA surfaces.
Steps: Biotinylated A′-DNA is bound to surface-bound streptavidin
(gray) and hybridizes C′-DNA carrying small-molecule cargo
(yellow circle, fluorophore); release of cargo by toehold-mediated
strand displacement with release strand R′-DNA. The biotin
and the fluorophore tags are attached to the 5′ termini of
the DNA strands.
Schematic overview of
DNA strand-mediated binding and release of
small-molecule cargo from microstructured A′-DNA surfaces.
Steps: Biotinylated A′-DNA is bound to surface-bound streptavidin
(gray) and hybridizes C′-DNA carrying small-molecule cargo
(yellow circle, fluorophore); release of cargo by toehold-mediated
strand displacement with release strand R′-DNA. The biotin
and the fluorophore tags are attached to the 5′ termini of
the DNA strands.The micropatterned non-PEG
substrate surface is shown in Figure S10. It features streptavidin-coated patches
that are surrounded by a nonadsorptive layer of BSA protein. Both
proteins are directly linked to the epoxy-coated glass surface. To
micropattern the surface with streptavidin and BSA, microcontact printing
was used (Figure S10). A microstructured
stamp composed of polydimethylsiloxane (PDMS) was first “inked”
with a solution of streptavidin. After removing streptavidin that
did not adhere to the PDMS surface, the stamp was inverted and placed
onto the glass slide. Consequently, protein adherent to the elevations
of the stamp were transferred onto the glass surface. Residual areas
of the slide not coated with streptavidin were covered with BSA by
adsorption from solution.The functionality of the micropatterned
surfaces with the new DNA
duplex design was tested using fluorescence microscopy read-out (Figure ). The streptavidin
surfaces specifically bound biotinylated A′-DNA (Figure , capturing) because subsequent
hybridization of fluorophore-labeled C′-DNA yielded micropatterns
with the expected shape and dimensions (Figure A). The contrast between bound and nonbound
areas was 0.94 ± 0.08.
Figure 6
Fluorescence microscopy images of streptavidin
micropatterned surfaces
after incubation with (A) A′-DNA and Atto488-labeled C′-DNA,
and (B) after toehold-mediated strand displacement with R′-DNA.
Corresponding line profiles of fluorescence microscopy images are
shown on the right. Image size: 96 μm × 96 μm.
Fluorescence microscopy images of streptavidin
micropatterned surfaces
after incubation with (A) A′-DNA and Atto488-labeled C′-DNA,
and (B) after toehold-mediated strand displacement with R′-DNA.
Corresponding line profiles of fluorescence microscopy images are
shown on the right. Image size: 96 μm × 96 μm.Releasing cargo-carrying C′-DNA
by R′-DNA was also
successful on the surface as shown in fluorescence microscopic analysis
(Figure B). After
incubation with release-DNA the contrast between bound and nonbound
areas reduced to 0.23 ± 0.03.
Conclusions
In
this report, we have described a generic route to temporarily
immobilize small-molecule and protein cargo via DNA hybridization
onto micropatterned surfaces. Releasing cargo can be tuned via the
well-understood toehold-mediated strand displacement to control the
extent of release. Furthermore, only readily available components
such as DNA oligonucleotides are used. The approach can therefore
be easily adopted by other researchers. In future experiments, the
predictability of DNA hybridization could help tune the duration of
the release step such as by shortening the DNA duplex. As a further
advantage, the sequence-specificity of DNA interaction could be exploited
to anchor different cargo to different surface areas. Examples include
antibodies or natural ligands directly conjugated to the C-DNA but
also DNA aptamers. Furthermore, cargo-freed surfaces can be reloaded
with biomolecular cargo. The rebinding efficiency is, however, lower
and probably allows for the loading of cargo for no more than 2–3
times even though the contrast in the micropatterns is not impaired
by the reloading. When applied to biological experiments, DNA’s
negatively charged nature may bias the interaction with cells, but
the effect could be minimized by altering the salt concentration of
the buffer. Similarly, adhesion of cells to the patterns can be enhanced
by supplementing surface-passivating BSA with fibronectin.[38] In conclusion, we expect that DNA-mediated release
of protein cargo will enable exciting research in cell biology.
Materials and Methods
All chemicals
were obtained from Sigma-Aldrich Handels GmbH (Vienna,
Austria) unless noted otherwise. Epoxy-functionalized NEXTERION glass
coverslips (24 mm × 50 mm, 175 ± 20 μm thickness)
were from Schott, Technical Glass Solution GmbH (Jena, Germany). Positive
photoresist G2 S1818 and developer ma-D 331S were from microresist
technology GmbH (Berlin, Germany). MeO-PEG-(CH2)3-Si(OMe)3 with a MW of 460–590 D was bought from
ABCR (No. SIM6492.7, Karlsruhe, Germany). Bovine serum albumin (BSA)
was obtained from SERVA Electrophoresis GmbH (Heidelberg, Germany).
Streptavidin-Cy5 (434316) was purchased from Life Technologies (Vienna,
Austria), and Atto550-strepavidin (96404) was obtained from Sigma-Aldrich.
DNA oligonucleotides were manufactured by Integrated DNA Technologies
(Leuven, Belgium). GelRed Nucleic Acid Gel Stain (41003) was supplied
by VWR International and Agarose NEEO ultraquality (2267.2) was purchased
by Carl Roth GmbH (Karlsruhe, Germany).
Preparation of Micropatterned
Surfaces Using Photolithography
To prepare micropatterned
streptavidin surfaces, a previously published
protocol was used.[37] Briefly, PEG was grafted
onto epoxy-functionalized glass coverslips by incubation of Jeffamine
ED 600. Subsequently the residual epoxy groups were blocked with ethanolamine
followed by biotinylation of terminal amine groups on the tethered
PEG chains with biotin NHS-ester. Free amine and hydroxyl groups were
blocked by acetylation using acetic anhydride and 4-(dimethylamino)pyridine
dissolved in acetonitrile. Biotin-PEG micropatterns were generated
via photolithography using positive photoresist G2 S1818 and an EVG
620 mask alignment system (EV group, Austria). After plasma etching
of the microstructured slides, PEG (2-[methoxy(polyethyleneoxy)propyl]
trimethoxysilane) was regrafted in the developed areas where biotin-PEG
had been removed. Biotin-PEG micropatterns were incubated with streptavidin
(100 μg/mL in PBS buffer containing 0.05% Tween) for 1
h at room temperature (rt), followed by washing in PBST and ddH2O, and drying in an argon stream followed by storage at 4
°C until use.
Analysis of Micropatterned Surfaces Using
Atomic Force Microscopy
AFM measurements of micropatterned
PEG substrates were conducted
with a commercial atomic force microscope (Agilent Picoplus 5500,
Agilent Technologies, Santa Clara, CA) equipped with a 90 μm
closed loop scanner. AFM topographical images of substrates with the
micropatterned biotin-PEG/PEG surface (not loaded with streptavidin)
were acquired in PBS buffer at rt using MSNL-10 cantilever in contact
mode. The nominal spring constant of the cantilever was 0.07 N/m.
Images were analyzed using Gwyddion 2.45 (Czech Metrology Institute,
Czech Republic).
Probing DNA-Mediated Cargo Release in Solution
with Streptavidin–DNA
Conjugates
To probe DNA-mediated release of cargo in solution,
conjugates of oligonucleotides and streptavidin were prepared. Cy5-labeled
streptavidin (16 μM in TE buffer: 40 mM Tris, 1 mM EDTA, pH
8) was incubated with biotinylated anchor oligonucleotide A-DNA (1
μM, 10 μL, in TE buffer supplemented with 30
mM NaCl). The sequence of A-DNA is 5′-ACA CGC ATA CAC CCA T-TEG-biotin-3′
for which TEG is a tetra(ethylene glycol) linker. To achieve hybridization,
A-DNA-streptavidin conjugate (1 μM, 20 μL) was incubated
with Cy3-labeled capture oligonucleotide C-DNA (1 μM, 10 μL)
with the sequence 5′-ATG GGT GTA TGC GTG TTT AAA GAC CCT AAG
CT-Cy3–3′ for 45 min at rt in the dark to avoid bleaching
of the fluorophore. The hybridization was carried out in TE buffer
supplemented with 30 mM NaCl. For DNA-mediated release, the hybridized
DNA–streptavidin conjugate was incubated with release oligonucleotide
R-DNA (10 μM, TE buffer; 5′-AGC TTA GGG TCT TTA
AAC ACG CAT ACA CCC AT-3′) for 90 min at rt. The sequences
of the three oligonucleotides were from ref (30). The results of the hybridization
and dehybridization were analyzed by electrophoresis using 1.5% agarose
gels and fluorescence scanning.
Release Experiments on
Micropatterns Generated Using Photolithography
For release
experiments, substrates were covered with round incubation
chambers with a volume of 20 μL and covered by on the top side
with a transparent lid featuring two holes for pipetting. The streptavidin
micropatterned surfaces were incubated for 30 min at rt with biotinylated
anchor strand A-DNA (1 μM, in TE buffer supplemented
with 30 mM NaCl). The surfaces were then washed with TE buffer (500 μL),
and incubated with Cy3-tagged C-DNA (1 μM) for 30 min at rt
in the dark. After drying with air stream, the surfaces were analyzed
with fluorescence microscopy (Figure ). Furthermore, A-DNA coated micropatterns were incubated
with a conjugate of Atto550-labeled streptavidin and biotinylated
C-DNA at a molar ratio of 1:4 or 1:10 for streptavidin to DNA subjected
to agarose gel electrophoresis (Figure S6). The incubation duration was 30 min at rt. After washing and drying,
C-DNA-streptavidin coated surfaces were analyzed with fluorescence
microscopy (Figure and Figure S7). For toehold-mediated
DNA strand displacement, R-DNA (10 μM) was added to Cy3-tagged
C-DNA or C-DNA-streptavidin-conjugates hybridized to tethered A-DNA
about 2 h after binding them onto the surface. The incubation was
performed for 2 h at rt. Subsequent DNA strands were rehybridized
onto the same micropatterned surface.
Preparation of Micropatterned
DNA Surfaces Using Microcontact
Printing
Microstructured surfaces were made following an
adapted protocol.[1] Briefly, polymer stamps
with a total surface area of 0.25 cm2 bearing circular
features with a diameter of 1 μm and a spacing of 3 μm
were incubated with 50 μg/mL streptavidin in PBS for 15 min,
rinsed with PBS and ddH2O, and dried with N2. Immediately after drying, the stamp was placed onto an epoxy-coated
coverslip (Schott) and incubated for 30 min at rt. After removal of
the stamp, a 50 μL Secure-Seal hybridization chamber (Grace
Biolabs, Bend, OR) was placed onto the coverslip, and a 1%
BSA solution was added and incubated for 30 min to passivate
those surface areas not printed with streptavidin.
Release
Experiments on DNA Patterns Generated with Microcontact
Printing
For toehold-mediated DNA strand displacement, biotinylated
anchor oligonucleotide A′-DNA (5′-biotin-TEG-AGC TTA
GGG TCT TTA AGT GGA CTA GCC TAA TG-3′), fluorescently labeled
cargo oligonucleotide C′-DNA (5′-atto488-TTT TAC ATT
AGG CTA GTC CAC-3′), and release strand R′-DNA (5′-CAT
TAG GCT AGT CCA CTT AAA GAC CCT AAG CT-3′) were dissolved in
TE buffer containing 30 mM NaCl. Streptavidin patterns were incubated
with biotinylated A′-DNA (1 μM) for 30 min at rt. After
washing with TE buffer (1 mL), the functionalized surfaces were incubated
with 1 mM fluorescently labeled oligonucleotide C′-DNA for
30 min at rt followed by another washing step with TE buffer (1 mL),
and drying with air stream. After fluorescence microscopic imaging,
the surfaces were incubated for 75 min with release strand R′-DNA
(10 mM) to release fluorescently labeled oligonucleotide C′-DNA.
Patterns were washed again with TE buffer (1 mL) before imaging. The
release step was performed 2 h after binding C′-DNA to the
surface.
Fluorescence Microscopy
Fluorescence imaging was performed
using an Axiovert 200 microscope equipped with a mercury lamp 80 HBO100
(both Zeiss, Jena, Germany) and appropriate filter sets (AHF Analysentechnik,
Tübingen, Germany). Fluorescence emission was collected via
a 40× Neofluar objective (Zeiss) and detected using a CCD camera
(Photometrics, Tucson, USA). Image processing and analysis were performed
using ImageJ (NIH, Bethesda, USA).
Authors: Amit Singhai; Devin L Wakefield; Kirsten L Bryant; Stephen R Hammes; David Holowka; Barbara Baird Journal: Biophys J Date: 2014-12-02 Impact factor: 4.033
Authors: Robert R F Machinek; Thomas E Ouldridge; Natalie E C Haley; Jonathan Bath; Andrew J Turberfield Journal: Nat Commun Date: 2014-11-10 Impact factor: 14.919
Authors: Michaela Schwarzenbacher; Martin Kaltenbrunner; Mario Brameshuber; Clemens Hesch; Wolfgang Paster; Julian Weghuber; Bettina Heise; Alois Sonnleitner; Hannes Stockinger; Gerhard J Schütz Journal: Nat Methods Date: 2008-11-09 Impact factor: 28.547