DNA-Decorated, Helically Twisted Nanoribbons: A Scaffold for the Fabrication of One-Dimensional, Chiral, Plasmonic Nanostructures

Article abstract of DOI:10.1002/anie.201813900

Crafting of chiral plasmonic nanostructures is extremely important and challenging. DNA-directed organization of nanoparticle on a chiral template is the most appealing strategy for this purpose. Herein, we report a supramolecular approach for the design of DNA-decorated, helically twisted nanoribbons through the amphiphilicity-driven self-assembly of a new class of amphiphiles derived from DNA and hexaphenylbenzene (HPB). The ribbons are self-assembled in a lamellar fashion through the hydrophobic interactions of HPB. The transfer of molecular chirality of ssDNA into the HPB core results in the bias of one of the chiral propeller conformations for HPB and induces a helical twist into the lamellar packing, and leads to the formation of DNA-wrapped nanoribbons with M-helicity. The potential of the ribbon to act as a reversible template for the 1D chiral organization of plasmonic nanomaterials through DNA hybridization is demonstrated.

Full text of DOI:10.1002/anie.201813900

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International Edition: DOI: 10.1002/anie.201813900
German Edition: DOI: 10.1002/ange.201813900
DNA Nanotechnology
DNA-Decorated, Helically Twisted Nanoribbon: A Scaffold for the
Fabrication of One-Dimensional, Chiral, Plasmonic Nanostructures
Murali Golla, Shine K. Albert, Siriki Atchimnaidu, Devanathan Perumal,
Nithiyanandan Krishnan, and Reji Varghese*
Abstract: Crafting of chiral plasmonic nanostructures is
extremely important and challenging. DNA-directed organ-
ization of nanoparticle on a chiral template is the most
appealing strategy for this purpose. Herein, we report a supra-
molecular approach for the design of DNA-decorated, heli-
cally twisted nanoribbons through the amphiphilicity-driven
self-assembly of a new class of amphiphiles derived from DNA
and hexaphenylbenzene (HPB). The ribbons are self-assem-
bled in a lamellar fashion through the hydrophobic interac-
tions of HPB. The transfer of molecular chirality of ssDNA
into the HPB core results in the bias of one of the chiral
propeller conformations for HPB and induces a helical twist
into the lamellar packing, and leads to the formation of DNA-
wrapped nanoribbons with M-helicity. The potential of the
ribbon to act as a reversible template for the 1D chiral
organization of plasmonic nanomaterials through DNA
hybridization is demonstrated.
Amphiphilicity-driven self-assembly is a bottom-up
supramolecular approach for the design of well-defined
nanostructures.[10] Recently, DNA-based amphiphiles have
emerged as a unique building block for the creation of DNA
nanostructures.[11] The most remarkable feature of the DNA
nanostructures obtained using this strategy is the dense
display of single-stranded DNA (ssDNA) on the surface of
the nanostructure, allowing them to act as a DNA-based
template for the organization of functional molecules through
DNA hybridization. Usually, DNA-based amphiphiles have
flexible chains as the hydrophobic part, which self-assemble
into micellar nanostructures.[12] We have shown that the
incorporation of a large p-surface as the hydrophobic domain
drives the assembly in a lamellar fashion, leading to the
formation of vesicles[13] and nanosheets.[14] However, the
design of chiral nanostructures via DNA-based amphiphile
self-assembly is not well explored.[15] We envisioned that the
incorporation of a hydrophobic p-surface that has a propeller
conformation (chiral geometry), such as hexaphenylbenzene
(HPB), could potentially induce a helical twist in the lamellar
organization and direct the assembly into a DNA-decorated,
chiral nanostructure, such as a helically twisted ribbon.
Derivatives of HPB have received great attention in recent
years due to the atropisomerism associated with the rotation
of C(sp2)–C(sp2) bonds connecting the radial benzene rings
with the core benzene ring.[16] Hence, HPB can adopt two
chiral propeller conformations, which include the conforma-
tion with all radial benzene rings tilted in clockwise direction
and the other conformation with an anticlockwise tilt
(Scheme 1). Moreover, one of the chiral propeller conforma-
tions can be favored in the self-assembled state by the
incorporation of a chiral moiety on HPB due to the chirality
transfer.[17] This has been explored for the design of chiral
nanostructures of HPB.[18] Herein, the design and synthesis of
DNA-based amphiphiles derived from the hybrid of HPB and
ssDNA is reported, and their self-assembly into helically
twisted ribbons is demonstrated. Transfer and long-range
expression of molecular chirality of ssDNA to the HPB core
in the self-assembled state bias one of the chiral propeller
conformations of HPB that resulted in the exclusive forma-
tion of twisted ribbon with left-handed (M) helicity. The
potential of DNA-decorated chiral nanoribbon as a reversible
template for the construction of 1D chiral plasmonic nano-
structures is also demonstrated (Scheme 1).
T
he creation of chiral plasmonic nanostructures is extremely
important due to their potential applications in areas ranging
from material science[1] to medicine[2] to nanotechnology.[3]
The bottom-up approach using directed self-assembly of
nanoparticles on a chiral template is the most appealing
strategy for this purpose.[4] Different nanostructures derived
from the self-assembly of DNA,[5] peptide,[6] and small
molecules[7] have been efficiently applied as templates for
the chiral organization of plasmonic nanomaterials, and
undoubtedly DNA-based templates are the most powerful
and viable among them. This is because DNA nanostructures
offer the unique opportunity of DNA-directed spatial
addressability, which permits the design of extremely complex
plasmonic nanostructures that are otherwise difficult to
achieve.[8] Nanostructures of DNA are typically designed
using the principles of DNA nanotechnology.[9] Though this
strategy allows the design of chiral templates of any geometry,
scalability and the complex design principles involved are two
major concerns. Hence, the development of a simple, yet
efficient, bottom-up strategy for the design of DNA-based
chiral templates is highly demanding.
[*] M. Golla, Dr. S. K. Albert, S. Atchimnaidu, D. Perumal, N. Krishnan,
Dr. R. Varghese
School of Chemistry, Indian Institute of Science Education and
Research (IISER) Thiruvananthapuram
Trivandrum-695551, Kerala (India)
Amphiphiles (DNA1 and DNA2) were synthesized using
phosphoramidite chemistry. Details of the synthesis of 2,[19]
DNA1, and DNA2 are provided in the Supporting Informa-
tion. Both DNA1 and DNA2 have the same hydrophobic
E-mail: reji@iisertvm.ac.in
Supporting information and the ORCID identification number(s) for
the author(s) of this article can be found under:
https://doi.org/10.1002/anie.201813900.
HPB segment conjugated to
a
9-mer DNA (5’-
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Figure 1. Temperature-dependent a) CD and b) emission spectra of
DNA1. Inset of emission spectrum shows the corresponding changes
in absorption spectrum. c) Zoomed-out and d) zoomed-in TEM,
e) AFM, and f) SEM images of DNA1.
Scheme 1. Synthesis of DNA-based amphiphiles through phosphorami-
dite chemistry. Conditions: a) CH2Cl2, diisopropylamine, 2-cyanoethyl
N,N-diisopropylchlorophosphoramidite, RT, 2 h, 80%. Schematic for
the self-assembly of DNA-based amphiphiles into DNA-decorated,
twisted nanoribbons with M-helicity. DNA-directed chiral organization
of AuNPs and AuNRs is also shown.
ature from 108C to 908C and its complete disappearance at
908C. Importantly, a CD signal observed at 908C matches the
inherent CD signal of the ssDNA segment of DNA1. These
observations suggest that the transfer of molecular chirality of
ssDNA into the HPB core results in a bias towards one of the
chiral propeller conformations of HPB[20] and leads to the
formation of optically active aggregates, which, upon an
increase temperature, disassemble into the corresponding
monomeric species. Similar chiroptical behaviors were
observed for DNA2 (Supporting Information, Figure S4b),
which implies that the sequence of DNA has no effect on the
self-assembly and chirality induction. Fluorescence spectra of
DNA1 and DNA2 show the characteristic emission of HPB at
334 nm with quantum yields of 0.17 and 0.19, respectively.
Interestingly, a gradual decrease in emission intensity was
observed for DNA1 (Figure 1b) and DNA2 (Supporting
Information, Figure S5) upon increasing the temperature
from 208C to 908C, due to the disassembly of the aggregates.
These results indicate that the enhanced emission for the
aggregates of DNA1 and DNA2, compared to the corre-
sponding monomeric species, is due to the restricted rotation
of intramolecular C(sp2)–C(sp2) bonds of HPB in the
aggregated state.[21] It is also important to note that no shift
was observed in the absorption and emission maxima of HPB
in the aggregated state when compared with the correspond-
ing monomeric species, suggesting that the chiral tilt con-
TCGCACCCA-3’ for DNA1 and 5’-TCTACATTA-3’ for
DNA2) and the only structural difference between them is
the difference in the sequence of DNA (Scheme 1). Self-
assembly was achieved by annealing the amphiphile (1 mm) in
Tris-HCl buffer (50 mm, pH 7.4) containing NaCl (1 mm) at
908C for 5 min and allowing to cool to room temperature.
Denaturing PAGE (20%) analyses of DNA1 and DNA2
show no migration, suggesting the spontaneous formation of
DNA nanostructures with a dense display of ssDNA on their
surface (Supporting Information, Figure S3). The UV/Vis
spectra of DNA1 (Figure 1b inset) and DNA2 (Supporting
Information, Figure S4a) at 208C show the characteristic
absorption of DNA at 260 nm and HPB at 275 nm. Interest-
ingly, no significant change in absorption was observed upon
increasing the temperature from 208C to 708C, suggesting
that the monomeric species formed at high temperature have
a similar electronic behavior as the aggregated state.
At 108C, DNA1 aggregates showed an induced circular
dichroism (ICD) signal in the absorption region correspond-
ing to HPB. An ICD couplet with a first positive Cotton effect
at 284 nm, followed by a negative Cotton effect at 230 nm
with zero crossing at 267 nm was observed (Figure 1a).
Temperature-dependent CD studies showed a gradual dis-
appearance of the ICD signal upon increasing the temper-
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formation of HPB is retained and no planarization takes place
in the aggregated state.
Transmission electron (TEM), atomic force (AFM), and
scanning electron (SEM) microscopic analyses of DNA1
(Figure 1c–f) and DNA2 (Supporting Information, Figures S8
and S9) revealed the formation of helically twisted nano-
ribbons, and most importantly the ribbons have M-helicity.
However, at very few places flat ribbons were also observed,
which could be attributed to the loss of helical twist under the
experimental conditions of microscopic analyses.[22] Ribbons
of DNA1 were several hundred nanometers to few micro-
meters in length. The average helical pitch of the ribbon was
500 nm. The breadth of the ribbons was in the range of 50–
100 nm. The thickness of the ribbons was found to be
approximately 11 nm, which is approximately twice the
molecular length (bilayer distance) of DNA1 (approximately
12 nm). In the case of DNA2, the length of the ribbon was also
in the range of several hundred nanometers to few micro-
meters. The average helical pitch of the DNA2 ribbon was
450 nm. The breadth and thickness of the DNA2 ribbons were
50–100 nm and approximately 11 nm, respectively. Based on
optical, chiroptical, and microscopic data, a plausible molec-
ular model for the assembly of the amphiphiles is proposed in
Scheme 1.
Figure 2. TEM images of DNA1–AuNPs assembly of a) approximately
30 nm and b) approximately 10 nm AuNPs. c) CD spectra of DNA1–
AuNP (approximately 10 nm) assembly at 208C and 608C. d) Compar-
ison of absorption spectrum of AuNPs (approximately 10 nm) alone
and after their assembly onto a DNA1 ribbon. Inset shows the
corresponding changes in emission spectrum at different temper-
atures.
The potential of the ribbon to act as a chiral template for
the organization of plasmonic nanomaterials through DNA
hybridization was explored. Ribbons of DNA1 were used as
the representative template. For this purpose, gold nano-
particles (AuNPs) with average diameters of approximately
30 nm and approximately 10 nm were synthesized and their
surface was modified with ssDNA of sequence 5’-
TGGGTGCGAA-3’, complementary to the DNA on the
surface of the ribbon.[8c] The assembly of AuNPs on DNA1
ribbons was achieved by annealing a 1:1 molar solution of
AuNPs (1 mm) and DNA1 ribbons (1 mm) from 358C to 48C in
0.5 ꢀ Tris/Borate/EDTA (TBE) buffer containing 50 mm
NaCl. TEM images clearly show the 1D assembly of
approximately 30 nm (Figure 2a) and approximately 10 nm
(Figure 2b) AuNPs along the template. Furthermore, AuNPs
are organized on either faces of the ribbon in a left-handed
helical manner, which demonstrates the DNA-directed
assembly of AuNPs. In accordance with this, CD studies
show an ICD signal in the surface plasmon frequency of
AuNPs (approximately 10 nm) at 520 nm (Figure 2c). How-
ever, the non-bisignated nature of the ICD signal suggests
that no interparticle surface plasmon coupling occur in the
AuNP assembly. In support of this, no shift was observed in
the electronic absorption maximum for the chiral AuNP
assembly when compared with the absorption maximum of
the corresponding non-assembled AuNPs (Figure 2d). Nota-
bly, significant quenching (76%) of fluorescence was
observed for DNA1 after the formation of the DNA1–
AuNP assembly (Figure 2d, inset). This could be due to the
electronic interaction between the AuNPs and the HPB
stacks.[13] Another unique feature of the chiral template is its
thermo-responsive nature. Temperature-dependent CD stud-
ies show a gradual decrease in the ICD signal at 520 nm and
its complete disappearance at 608C (Figure 2c). Accordingly,
the fluorescence of the DNA1 ribbon was almost restored
(90%) to the emission intensity of DNA1 at 608C (Figure 2d,
inset). These results reveal that the dissociation of the AuNPs
from the template with increasing temperature is due to the
melting of the duplex DNA between the template and AuNPs,
as well as the disassembly of the template itself.
To establish the universal nature of the template, we have
also demonstrated the potential of the ribbon for the chiral
assembly of gold nanorods (AuNRs). To this end, AuNRs
with an average length of 40 nm and average width of 8 nm
were prepared[23] and the surface was functionalized with
ssDNA complementary to the ssDNA on the surface of the
ribbon.[24] Self-assembly of AuNRs and DNA1 ribbons was
achieved using the same protocol described for AuNP
assembly. Interestingly, TEM images display the formation
1D organization of the AuNRs (end-to-end) preferably along
the longitudinal direction of the ribbon (Figure 3a). Assem-
bly of the rods across the longitudinal axis of the ribbon (side-
by-side) is rarely seen (Figure 3b). Unlike DNA1–AuNPs, no
clear helical organization is seen for the DNA1–AuNR
assembly. This might be due to the partial straightening of
the helical ribbon upon AuNR binding due to the long length
of AuNRs compared to AuNPs. Accordingly, the UV/Vis
absorption spectrum of the assembly shows a decrease in
intensity and broadening of the longitudinal surface plasmon
band of AuNR centered at 752 nm, indicating the coupling of
longitudinal plasmon oscillation (Supporting Information,
Figure S16a). Whereas the transverse plasmon absorption
band at 521 nm remains nearly unaffected. This is a character-
istic absorption behavior for the end-to-end assembly of
AuNRs.[25] As in the case of AuNPs, a significant quenching of
fluorescence (72%) of DNA1 was observed after the
assembly of the AuNRs on the ribbon due to the DNA-
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applications in the fields of chiral sensing, enantioselective
synthesis, and photonic materials. Moreover, this approach
permits the easy integration of functional domains of interest
as hydrophobic segments into the DNA nanostructures. To
our knowledge, this is the first report demonstrating the
design of a helically twisted ribbon with one handedness from
the self-assembly of a DNA-based amphiphile that can act as
a universal template for the fabrication of 1D chiral
plasmonic nanomaterials.
Acknowledgements
Financial supports from KSCSTE and DBT are gratefully
acknowledged. We thank UGC and CSIR for research
fellowships. The help of Rafeeque Poolamuri Pottammel
with the drawings is acknowledged.
Conflict of interest
Figure 3. a and b) TEM images of DNA1–AuNR assembly. c) CD
spectra of DNA1–AuNR assembly at 208C and 608C. d) TEM image of
DNA1 ribbon after the assembly with AuNR-modified noncomplemen-
tary DNA.
The authors declare no conflict of interest.
Keywords: amphiphiles · chirality · DNA nanostructures ·
plasmonic nanomaterials · supramolecular chemistry
mediated electronic interaction of AuNRs and HPB (Sup-
porting Information, Figure S16b). Furthermore, the emission
was almost restored (79%) to the emission intensity of DNA1
at 608C upon increasing the temperature of the DNA1–
AuNR assembly to 608C. CD analysis of the DNA1–AuNR
assembly shows a bisignated CD couplet at the longitudinal
surface plasmon resonance position of AuNR (Figure 3c). A
negative Cotton effect at 790 nm, followed by a positive
Cotton effect at 665 nm with a zero crossing at 740 nm was
observed. As observed with the DNA1–AuNP assembly, the
intensity of the CD signal gradually decreased with the rise in
temperature and completely disappeared at 608C. It is to be
noted that the DNA1–AuNR assembly exhibits plasmon
coupled CD signal, whereas the DNA1–AuNP assembly
shows an ICD signal without interparticle plasmon coupling.
This difference in chiroptical behavior can be attributed to the
strong dipolar coupling of AuNRs compared to AuNPs.[2] In
order to further confirm that the assembly of the AuNRs is
indeed due to sequence-specific DNA hybridization, control
experiments were carried out with AuNRs functionalized
with ssDNA (5’-TCTACATTA-3’), which is noncomplemen-
tary to the ssDNA on the surface of the ribbon. As expected,
no assembly of AuNRs on the ribbon was observed (Fig-
ure 3d).
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Manuscript received: December 6, 2018
Accepted manuscript online: January 28, 2019
Version of record online: && &&, &&&&
Angew. Chem. Int. Ed. 2019, 58, 1 – 6
ꢀ 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
5
These are not the final page numbers!

Angewandte
Communications
Chemie
Communications
DNA Nanotechnology
M. Golla, S. K. Albert, S. Atchimnaidu,
D. Perumal, N. Krishnan,
R. Varghese*
&&&& — &&&&
DNA-Decorated, Helically Twisted
Nanoribbon: A Scaffold for the
Fabrication of One-Dimensional, Chiral,
Plasmonic Nanostructures
Scarlet ribbons: This work reports the
amphiphilicity-driven self-assembly of
DNA–hexaphenylbenzene conjugates
into DNA-decorated, helically twisted
nanoribbons, which can act as a universal
template for the fabrication of 1D chiral
plasmonic nanomaterials.
6
www.angewandte.org
ꢀ 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2019, 58, 1 – 6
These are not the final page numbers!