DNA-organized artificial LHCs - testing the limits of chromophore segmentation

Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres

The self-assembly of highly functionalized phenanthrene-DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3'-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene-pyrene exciplex formation.

Heteromeric guanosine (G)-quadruplex derived antenna modules with directional energy transfer

A heteromeric guanosine (G)-quadruplex centered self-assembly approach is developed to prepare compact light-harvesting antenna modules featuring multiple donor dyes and a single toehold region. Due to the mix-and-match nature of our approach, the number and placement of donor dyes can be readily fine-tuned via quadruplex assembly. Moreover, hybridization of the toehold with an acceptor containing sequence results in directional energy transfer ensembles with effective absorption coefficients in the 105 M-1 cm-1 range. These compact antennas exhibit system efficiencies that are comparable to much larger and elaborate DNA architectures containing numerous DNA strands.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Supramolecular assembly of pyrene-DNA conjugates: influence of pyrene substitution pattern and implications for artificial LHCs

The supramolecular self-assembly of pyrene-DNA conjugates into nanostructures is presented. DNA functionalized with different types of pyrene isomers at the 3'-end self-assemble into nano-objects. The shape of the nanostructures is influenced by the type of pyrene isomer appended to the DNA. Multilamellar vesicles are observed with the 1,6- and 1,8-isomers, whereas conjugates of the 2,7-isomer exclusively assemble into spherical nanoparticles. Self-assembled nano-spheres obtained with the 2,7-dialkynyl pyrene isomer were used for the construction of an artificial light-harvesting complex (LHC) in combination with Cy3 as the energy acceptor.

Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs

Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by ultraviolet (UV) melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the center of a DNA duplex led to a decrease of the thermal stability (ΔTm - 6 °C), the addition of a second pair restored or even increased the stability. In contrast, the introduction of DAN:NDI pairs at the end of a duplex always induced a strong stabilization (ΔTm up to +20 °C). Finally, a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4 loop (ΔTm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.

Tetraphenylethylene-DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles

The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow monitoring the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology.

The supramolecular assembly of tetraphenylethylene (TPE)–DNA conjugates is presented. The length of the TPE sticky ends exerts a pronounced effect on the formation of aggregation-induced emission (AIE)-active vesicles.

Complex DNA Architectonics─Self-Assembly of Amphiphilic Oligonucleotides into Ribbons, Vesicles, and Asterosomes

The precise arrangement of structural subunits is a key factor for the proper shape and function of natural and artificial supramolecular assemblies. In DNA nanotechnology, the geometrically well-defined double-stranded DNA scaffold serves as an element of spatial control for the precise arrangement of functional groups. Here, we describe the supramolecular assembly of chemically modified DNA hybrids into diverse types of architectures. An amphiphilic DNA duplex serves as the sole structural building element of the nanosized supramolecular structures. The morphology of the assemblies is governed by a single subunit of the building block. The chemical nature of this subunit, i.e., polyethylene glycols of different chain length or a carbohydrate moiety, exerts a dramatic influence on the architecture of the assemblies. Cryo-electron microscopy revealed the arrangement of the individual DNA duplexes within the different constructs. Thus, the morphology changes from vesicles to ribbons with increasing length of a linear polyethylene glycol. Astoundingly, attachment of a N-acetylgalactosamine carbohydrate to the DNA duplex moiety produces an unprecedented type of star-shaped architecture. The novel DNA architectures presented herein imply an extension of the current concept of DNA materials and shed new light on the fast-growing field of DNA nanotechnology.