Nucleic-Acid-Templated Synthesis of Smart Polymer Vectors for Gene Delivery

Nucleic acids are information-rich and readily available biomolecules, which can be used to template the polymerization of synthetic macromolecules. Here, we highlight the control over the size, composition, and sequence one can nowadays obtain by using this methodology. We also highlight how templated processes exploiting dynamic covalent polymerization can, in return, result in therapeutic nucleic acids fabricating their own dynamic delivery vector - a biomimicking concept that can provide original solutions for gene therapies.

Modulation of supramolecular chirality by stepwise axial coordination in a nano-size trizinc(ii)porphyrin trimer

Herein, we report a chiral guest's triggered spring-like contraction and extension motions coupled with unidirectional twisting in a novel flexible and 'nano-size' achiral trizinc(ii)porphyrin trimer host upon step-wise formation of 1 : 1, 1 : 2, and 1 : 4 host-guest supramolecular complexes based on the stoichiometry of the diamine guests for the first time. During these processes, porphyrin CD responses have been induced, inverted, and amplified, and reduced, respectively, in a single molecular framework due to the change in the interporphyrin interactions and helicity. Also, the sign of the CD couplets is just the opposite between R and S substrates which suggests that the chirality is dictated solely by the stereographic projection of the chiral center. Interestingly, the long-range electronic communications between the three porphyrin rings generate trisignate CD signals that provide further information about molecular structures.

Aggregation-induced emission by sequence-selective assembly of cyanolytated distyrylbenzene in supramolecular DNA architectures

The cyanolated distyrylbenzene conjugated to 2’-deoxyuridine is a new building block for supramolecular DNA architectures combining aggregation-induced emission and sequence-selective binding. A high number of binding sites at the DNA...

DNA-templated control of chirality and efficient energy transport in supramolecular DNA architectures with aggregation-induced emission

Two conjugates of tetraphenylethylene with d-2′-deoxyuridine (1d) and l-2′-deoxyuridine (1l) were synthesized to construct new supramolecular DNA-architectures by self-assembly. The non-templated assemblies of 1d and 1l show strong aggregation-induced emission and their chirality is exclusively controlled by the configuration of their sugar part. In contrast, the chirality of the DNA-templated assemblies is governed by the configuration of the DNA, and there is no configuration-selective binding of 1d to d-A₂₀ and 1l to l-A₂₀. The quantum yield of the assembly of 1d along the single-stranded DNA A₂₀ is 0.40; approximately every second available binding site on the DNA template is occupied by 1d. The strong aggregation-induced emission of these DNA architectures can be efficiently quenched and the excitation energy can be transported to Atto dyes at the 5′-terminus. A multistep energy transport “hopping” precedes the final energy transfer to the terminal acceptor. The building block 1d promotes this energy transport as stepping stones. This was elucidated by reference DNA double strands in which 1d was covalently incorporated at two distinct sites in the sequences, one near the Atto dye, and one farther away. This new type of completely self-assembled supramolecular DNA architecture is hierarchically ordered and the DNA template controls not only the binding but also the energy transport properties. The high intensity of the aggregation-induced emission and the excellent energy transport properties make these DNA-based materials promising candidates for optoelectronic applications.

DNA architectures with tetraphenylethylene are assembled in a non-covalent way. The strong aggregation-induced emission of the chromophores is quenched and the energy is transported to Atto dyes by a multistep energy “hopping”.

Molecular Chromophore-DNA Architectures With Fullerenes: Optical Properties and Solar Cells

Supramolecular chemistry allows the construction of complex molecular architectures and the design of collective photophysical properties. DNA is an attractive template to build such supramolecular architectures due to its helical structure, the defined distances between the bases and the canonical base pairing that results in precise control of the chromophore position. The tailored properties of DNA-templated supramolecules eventually allow their implementation into optoelectronic applications. For the generation of free charge carriers from photo-generated excitons, fullerenes can be utilized. We synthesized two fullerene derivates, one of which binds by electrostatic interactions to single-stranded DNA, while the other contains two 2'-deoxyuridine moieties and assembles specifically along oligo-2'-deoxyadenosines (dA20) as DNA template. The DNA-directed assembly of both fullerenes in aqueous solution was investigated by UV/Vis absorbance and circular dichroism (CD) spectroscopy. The specific interactions with DNA make fullerenes with the 2'-deoxyuridine moieties a significantly better component for supramolecular DNA architectures. We studied the fluorescence quenching of both fullerenes with a DNA chromophore assembly. To investigate one of the key properties for optoelectronic applications, that is the supramolecular structure of the DNA-based assemblies in the solid phase, we characterized the CD of supramolecular chromophore-DNA architectures in thin films. Remarkably, the helical chirality of the chromophore assemblies that is induced by the DNA template is conserved even in the solid state. Upon implementation into organic solar cells, the external quantum efficiency measurements showed charge carrier generation on all three chromophore components of the DNA assemblies. The fullerenes with the 2'-deoxyuridine moieties enhance the quantum efficiency of the conversion process significantly, demonstrating the potential of DNA as structural element for ordering chromophores into functional π-systems, which may be employed in future organic solar cells.

Control of Energy Transfer Between Pyrene- and Perylene-Nucleosides by the Sequence of DNA-Templated Supramolecular Assemblies

DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2'-desoxy-2-aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2'-desoxyuridine that is complementary to 2'-desoxyadenosine (A). This donor-acceptor pair was assembled along single-stranded DNA templates of different A-T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A10T10 over (AATT)5 to (AT)10, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence-controlled supramolecular chemistry represents the key element for future functional π-systems in materials for light harvesting of solar energy.

Influences of Linker and Nucleoside for the Helical Self-Assembly of Perylene Along DNA Templates

Six different conjugates of perylene with 2'-deoxyuridine and with 2-amino-2'-deoxyadenosine were synthesized and applied for DNA-templated assembly in aqueous buffer solutions. They differ by the linkers ethynylene, phenylene, and phenylene-ethynylene between nucleoside and chromophore. The nucleosides were investigated as monomers in CHCl₃ and dimethyl sulfoxide by optical spectroscopy. The properties of the four phenylene-linked conjugates are similar to that of perylene as reference because these linkers separate both aromatic parts. The ethynylene linker electronically couples the chromophore with the respective nucleoside and thus red shifts the absorbance. The DNA-templated assembly properties were elucidated by mixing the templates in aqueous buffer with the perylene-nucleoside conjugates from a dimethyl sulfoxide stock solution. Specific binding of the nucleosides was probed by comparing the results with dA₂₀ and T₂₀ as single-stranded DNA templates. Our studies reveal the structural parameters that are important for the DNA-templated assembly of perylenes. First, perylene-2'-deoxyuridine conjugates do not form DNA-templated helical assemblies, regardless of the choice of linker. Second, the ethynylene linker is crucial for successful DNA-templated chromophore assemblies of perylene-2-amino-2'-deoxyadenosine conjugates. Third, in contrast, the phenylene linker inhibits self-assembly along single-stranded DNA templates. In conclusion, the 2-amino-2'-deoxyadenosin in combination with the ethynylene linker provides the best structural feature for specific and helical DNA-templated assembly of perylenes. This result is important for the design of future DNA-based supramolecular architectures with chromophores, in particular DNA-based light-harvesting systems and DNA systems for emitting or sensing circularly polarized luminescence.

Control of helical chirality in supramolecular chromophore-DNA architectures

Four different d- and l-configured chromophore-2'-deoxyuridine conjugates were applied to elucidate the helical chirality of their non-covalent assemblies along the d- and l-configured DNA templates by optical spectroscopy. There is no configuration-selective recognition between these nucleosides and the DNA templates. The helicity of the DNA assemblies is either controlled by the configuration of the DNA template or by the nucleoside configuration.

Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences

The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.

Fullerene Cluster Assisted Self-Assembly of Short DNA Strands into Semiconducting Nanowires

Programmable, hierarchical assembly of DNA nanostructures with precise organisation of functional components have been demonstrated previously with tiled assembly and DNA origami. However, building organised nanostructures with random oligonucleotide strands remains as an elusive problem. Herein, a simple and general strategy, in which nanoclusters of a fullerene derivative act as stapler motifs in bringing ordered nanoscale assembly of short oligonucleotide duplexes into micrometre-sized nanowires, is described. In this approach, the fullerene derivative, by virtue of its amphiphilic structure and unique hydrophobic-hydrophilic balance, pre-assembles to form 3-5 nm sized clusters in a mixture of DMSO-phosphate buffer, which further assists the assembly of DNA strands. The optimum cluster size, availability of DNA anchoring motifs and the nature of the DNA strands controls the structure of these nanomaterials. Furthermore, horizontal conductivity measurements through conductive AFM confirmed the charge transport properties of these nanowires. The current strategy could be employed to organise random DNA duplexes and tiles into functional nanostructures, and hence, open up new avenues in DNA nanotechnology.

Nanoarchitectonics with Porphyrin Functionalized DNA

DNA is well-known as bearer of the genetic code. Since its structure elucidation nearly seven decades ago by Watson, Crick, Wilkins, and Franklin, much has been learned about its detailed structure, function, and genetic coding. The development of automated solid-phase synthesis, and with it the availability of synthetic DNA with any desired sequence in lengths of up to hundreds of bases in the best case, has contributed much to the advancement of the field of DNA research. In addition, classic organic synthesis has allowed introduction of a very large number of modifications in the DNA in a sequence specific manner, which have initially been targeted at altering the biological function of DNA. However, in recent years DNA has become a very attractive scaffold in supramolecular chemistry, where DNA is taken out of its biological role and serves as both stick and glue molecule to assemble novel functional structures with nanometer precision. The attachment of functionalities to DNA has led to the creation of supramolecular systems with applications in light harvesting, energy and electron transfer, sensing, and catalysis. Functional DNA is clearly having a significant impact in the field of bioinspired nanosystems.

Of particular interest is the use of porphyrins in supramolecular chemistry and bionanotechnology, because they are excellent functional groups due to their electronic properties that can be tailored through chemical modifications of the aromatic core or through insertion of almost any metal of the periodic table into the central cavity. The porphyrins can be attached either to the nucleobase, to the phosphate group, or to the ribose moiety. Additionally, noncovalent templating through Watson–Crick base pairing forms an alternative and attractive approach. With this, the combination of two seemingly simple molecules gives rise to a highly complex system with unprecedented possibilities for modulation of function, and with it applications, particularly when combined with other functional groups. Here, an overview is given on the developments of using porphyrin modified DNA for the construction of functional assemblies. Strategies for the synthesis and characterization are presented alongside selected applications where the porphyrin modification has proven to be particularly useful and superior to other modifiers but also has revealed its limitations. We also discuss implications on properties and behavior of the porphyrin–DNA, where similar issues could arise when using other hydrophobic and bulky substituents on DNA. This includes particularly problems regarding synthesis of the building blocks, DNA synthesis, yields, solubility, and intermolecular interactions.

Control of porphyrin interactions via structural changes of a peptoid scaffold

A template to control porphyrin interactions is constructed by displaying porphyrins at defined positions on a helical peptoid.

Hierarchical coassembly of DNA-triptycene hybrid molecular building blocks and zinc protoporphyrin IX

Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)-DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA-organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5'-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA-TPA molecular building blocks as well as a model guest molecule within the DNA-TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA-TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA-DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA-TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.

A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies

DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes

A novel π-extended Ni^II-porphyrin shows a high selectivity towards human telomeric G-quadruplexes.