Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base-Mismatch Detection

Recent Advances in Excimer-Based Fluorescence Probes for Biological Applications

The fluorescent probe is a powerful tool for biological sensing and optical imaging, which can directly display analytes at the molecular level. It provides not only direct visualization of biological structures and processes, but also the capability of drug delivery systems regarding the target therapy. Conventional fluorescent probes are mainly based on monomer emission which has two distinguishing shortcomings in practice: small Stokes shifts and short lifetimes. Compared with monomer-based emission, excimer-based fluorescent probes have large Stokes shifts and long lifetimes which benefit biological applications. Recent progress in excimer-based fluorescent sensors (organic small molecules only) for biological applications are highlighted in this review, including materials and mechanisms as well as their representative applications. The progress suggests that excimer-based fluorescent probes have advantages and potential for bioanalytical applications.

Improving structural stability and anticoagulant activity of a thrombin binding aptamer by aromatic modifications

The thrombin binding aptamer (TBA) is a 15-mer DNA oligonucleotide (5'-GGTTGGTGTGGTTGG-3'), that can form a stable intramolecular antiparallel chair-like G-quadruplex structure. This aptamer shows anticoagulant properties by interacting with one of the two anion binding sites of thrombin, namely the fibrinogen-recognition exosite. Here, we demonstrate that terminal modification of TBA with aromatic fragments such as coumarin, pyrene and perylene diimide (PDI), improves the G-quadruplex stability. The large aromatic surface of these dyes can π-π stack to the G-quadruplex or to each other, thereby stabilizing the aptamer. With respect to the original TBA, monoPDI-functionalized TBA exhibited the most remarkable improvement in melting temperature (ΔT m ≈ +18 °C) and displayed enhanced anticoagulant activity.

Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations

Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.

Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures

We report a new Förster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.

Ultrabright Red-Emitting Photostable Perylene Bisimide Dyes: New Indicators for Ratiometric Sensing of High pH or Carbon Dioxide

New pH-sensitive perylene bisimide indicator dyes were synthesized and used for fabrication of optical sensors. The highly photostable dyes show absorption/emission bands in the red/near-infrared (NIR) region of the electromagnetic spectrum, high molar absorption coefficients (up to 100 000 m-1  cm-1 ), and fluorescence quantum yields close to unity. The absorption and emission spectra show strong bathochromic shifts upon deprotonation of the imidazole nitrogen atom, which makes the dyes promising as ratiometric fluorescent indicators. Physical entrapment of the indicators into a polyurethane hydrogel enables pH determination at alkaline pH values. It is also shown that a plastic carbon dioxide solid-state sensor can be manufactured by immobilization of the pH indicator in a hydrophilic polymer, along with a quaternary ammonium base. The influences of the plasticizer, different lipophilic bases, and humidity on the sensitivity of the sensor material are systematically investigated. The disubstituted perylene, particularly, features two deprotonation equilibria, enabling sensing over a very broad pCO2 range of 0.5 to 1000 hPa.

NIR fluorescent organic nanoparticles for photoinduced nitric oxide delivery with self monitoring and real time reporting abilities

Nitric oxide photodonor (NOD) conjugated perylene tetracarboxylate ester (TPT) based fluorescent organic TPT(NOD)₄ nanoparticles (NPs) with aggregation induced NIR emission have shown photoinduced nitric oxide delivery along with a red to green emission transition.

Photoresponsive Electrodes Modified with DNA Duplexes Possessing a Porphyrin Dimer

This work describes the formation of a porphyrin (Por) dimer using a DNA duplex as a scaffold and photocurrent generation from electrodes modified with a monolayer of Por-DNA conjugates. The solid-phase click reaction between an azide-porphyrin and oligonucleotide labeled with an ethynyl group on CPG support was utilized to conjugate the Por to the DNA. UV/Vis absorption and circular dichroism (CD) spectral studies revealed that the Por dimer can be formed through DNA hybridization and that through-space electronic interactions, characterized from the exciton-coupled absorption and the bisignate CD, can occur between the two Por molecules. Photoelectrochemical experiments were performed for the electrodes functionalized with a monolayer composed of the Por-DNA conjugates. It was found that the Por dimer on the electrode, which was designed to resemble the special pair in natural photosynthesis, shows efficient photocurrent generation in the presence of electron-acceptor reagents compared with the Por monomer. These findings strongly support the idea that the DNA structures could be useful to construct Por arrays, which is essential for the design of photo- and bio-electronic devices.

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.

Core-Substituted Naphthalenediimides: LUMO Levels Revisited, in Comparison with Preylenediimides with Sulfur Redox Switches in the Core

Core‐substituted naphthalenediimides (NDIs) attract increasing attention to bind, transport, and transform electrons, anions, anionic intermediates, and anionic transition states, and to shine as most colorful rainbow fluorophores. The energy level of their lowest unoccupied molecular orbital (LUMO) is decisive for many of these applications. Here, differential pulse voltammetry (DPV) measurements for a consistent series of NDIs are reported to extract exact LUMO levels under identical conditions. The influence of primary and secondary substituents in the core and on the primary imides is compared with general trends for the reliable prediction of LUMO levels in functional systems. Emphasis is on sulfur redox switches in the NDI core because of their frequent use as isostructural probes for π acidity. The same sulfur redox chemistry is expanded to perylenediimides (PDIs), and LUMO engineering is discussed in a broader context, including also fullerenes, aminonaphthalimides (ANIs), and aminoperyleneimides (APIs). The result is a comprehensive reference table that graphically maps out the LUMO space covered by the leading families of electronaccepting aromatics. This graphical summary of general trends in the π‐acidic space is expected to be both inspiring and quite useful in practice.

Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling

Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.

Mesityl phenanthroline-modified 2'-deoxyuridine for heteroleptic complexes in metal ion-mediated assembly of DNA

The synthesis of a new DNA building block that bears the metal ion ligand 2,9-bis-mesityl-3-ethynyl-phenanthroline attached to the 5-position of 2'-deoxyuridine is presented. In the presence of Zn(2+), Cu(2+), Fe(2+) and Ni(2+) the complex formation of an accordingly modified DNA double strand with a second DNA duplex bearing the 2,2':6',2''-terpyridine ligand was studied by optical spectroscopy. The selective formation of heteroleptic assemblies between the two different DNA pieces was evidenced by denaturing polyacrylamide gel electrophoresis.

The donor–acceptor complexes of quantum dots and ionic perylene diimides for ratiometric detection of double-stranded DNA

We developed a FRET ratiometric system based on quantum dots and perylene diimides for detection of double-stranded DNAs.

Interdependence of pyrene interactions and tetramolecular G4-DNA assembly

Our results demonstrate the expanded capabilities of G-quadruplex DNAs for directed chromophore arrangements and show new perspectives in the design of G-quadruplexes governed by non-guanine moieties.

Surface architectures built around perylenediimide stacks

Simple stacks of perylenediimides (PDIs) grown directly on solid surfaces are an intriguing starting point for the construction of multicomponent architectures because their intrinsic activity is already very high. The ability of PDI stacks to efficiently generate photocurrent originates from the strong absorption of visible light and the efficient transport of both electrons and holes after generation with light. The objective of this study was to explore whether or not the excellent performance of these remarkably simple single-channel photosystems could be further improved in more sophisticated multicomponent architectures. We report that the directional construction of strings of anions or cations along the PDI stacks does not significantly improve their activity; that is, the intrinsic activity of PDI stacks is too high to yield ion-gated photosystems. The directional construction of electron- and hole-transporting stacks of naphthalenediimides (NDIs) and oligothiophenes along the central PDI stack did not improve photocurrent generation under standard conditions either. However, the activity of double-channel photosystems increased with increasing thickness, whereas increasing charge recombination with single-channel PDI stacks resulted in decreasing activity with increasing length. Most efficient long-distance charge transport was found with double-channel photosystems composed of PDIs and NDIs. This finding suggests that over long distances, PDI stacks transport holes better than electrons, at least under the present conditions. Triple-channel photosystems built around PDI stacks with oligothiophenes and triphenylamines were less active, presumably because hole mobility in the added channels was inferior to that in the original PDI stacks, thus promoting charge recombination.

De novo design of functional oligonucleotides with acyclic scaffolds

In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.

Bifunctional DNA architectonics: three-way junctions with sticky perylene bisimide caps and a central metal lock

A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris-bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe(3+), Ni(2+) and Zn(2+) by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5'-terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady-state fluorescence. The PDI-mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal-ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher-ordered structures as the result of DNA assemblies mediated by the PDI interactions.

Differential self-assembly and tunable emission of aromatic peptide bola-amphiphiles containing perylene bisimide in polar solvents including water

We demonstrate the self-assembly of bola-amphiphile-type conjugates of dipeptides and perylene bisimide (PBI) in water and other polar solvents. Depending on the nature of the peptide used (glycine-tyrosine, GY, or glycine-aspartic acid, GD), the balance between H-bonding and aromatic stacking can be tailored. In aqueous buffer, PBI-[GY]2 forms chiral nanofibers, resulting in the formation of a hydrogel, while for PBI-[GD]2 achiral spherical aggregates are formed, demonstrating that the peptide sequence has a profound effect on the structure formed. In water and a range of other polar solvents, self-assembly of these two PBI-peptides conjugates results in different nanostructures with highly tunable fluorescence performance depending on the peptide sequence employed, e.g., fluorescent emission and quantum yield. Organogels are formed for the PBI-[GD]2 derivative in DMF and DMSO while PBI-[GY]2 gels in DMF. To the best of our knowledge, this is the first successful strategy for using short peptides, specifically, their sequence/structure relationships, to manipulate the PBI nanostructure and consequent optical properties. The combination of controlled self-assembly, varied optical properties, and formation of aqueous and organic gel-phase materials may facilitate the design of devices for various applications related to light harvesting and sensing.

The base discriminating potential of pyrrolidinyl PNA demonstrated by magnetic Fe(x)O(y) particles

Pyrrolidinyl PNA was immobilized on Fe(x)O(y) magnetic particles and was able to capture and thereby discriminate single base alterations in DNA counterstrands better than DNA. The selectivities of matched vs. mismatched oligonucleotides measured by the absorption differences were up to 10-12 which are remarkable values for linear probes.

EPR based distance measurement in Cu-porphyrin–DNA

Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.

Ground and excited state electronic spectra of perylenediimide dimers with flexible and rigid geometries in DNA conjugates

Ground and excited state spectra of co-facial PDI dimers embedded in DNA constructs depend on the geometry imposed by the construct.

Bis-thioether-substituted perylene diimides: structural, electrochemical, and spectroelectrochemical properties

The synthesis and separation of the 1,6- and 1,7- isomers of N,N'-bis(alkyl)diadamantylthio-3,4,9,10-perylenetetracarboxylic acid diimide are reported. Investigations of the structural, electrochemical, spectroscopic, and spectroelectrochemical properties of the isomers reveal a sequence of electrochemically and chemically reversible reduction processes for both isomers. Three X-ray crystal structures are reported including a pair of 1,6- and 1,7-isomers demonstrating the twist of the perylene core in the solid state. Our studies thoroughly characterize the mono- and direduced states of the two isomers allowing unequivocal characterization of the reduced species by UV-vis and IR spectroscopic measurements. EPR studies also allow direct identification of the monoreduced PTCDI species and spectroscopic measurements confirm the delocalization of electronic density around the carbonyl moieties of the reduced species.

Reversed assembly of dyes in an RNA duplex compared with those in DNA

We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4'-methylthioazobenzene, and thiazole orange) on D-threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3'-side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5'-side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H-aggregates) even on an A-type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA-thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA-dye conjugates are potentially useful probes for real-time monitoring of RNA interference (RNAi) mechanisms.