Nucleic acid-guided assembly of aromatic chromophores

Oligo-Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications

Oligo-adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter-triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A-motif duplex, A-cyanuric acid triplex, A-coralyne-A duplex, and T ⋅ A-T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli-responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA-derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli-responsiveness and conformational characteristics, advanced material development, such as pH-cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli-responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications.

Self-assembled π-conjugated chromophores: preparation of one- and two-dimensional nanostructures and their use in photocatalysis

Photocatalytic systems have attracted research interest as a clean approach to generate energy from abundant sunlight. In this context, developing efficient and robust photocatalytic structures is crucial. Recently, self-assembled organic chromophores have entered the stage as alternatives to both molecular systems and (in)organic semiconductors. Nanostructures made of self-assembled π-conjugated dyes offer, on the one hand, molecular customizability to tune their optoelectronic properties and activities and on the other hand, provide benefits from heterogeneous catalysis that include ease of separation, recyclability and improved photophysical properties. In this contribution, we present recent achievements in constructing supramolecular photocatalytic systems made of chromophores for applications in water splitting, H2O2 evolution, CO2 reduction, or environmental remediation. We discuss strategies that can be used to prepare ordered photocatalytic systems with an emphasis on the effect of packing between the dyes and the resulting photocatalytic activity. We further showcase supramolecular strategies that allow interfacing the organic nanostructures with co-catalysts, molecules, polymers, and (in)organic materials. The principles discussed here are the foundation for the utilization of these self-assembled materials in photocatalysis.

Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions

Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light harvesting. In a previous study, we found unexpectedly large excitonic interactions (quantified by the excitonic hopping parameter Jm,n) in DNA-templated aggregates of squaraine (SQ) dyes with hydrophilic-imparting sulfo and butylsulfo substituents. Here, we characterize DNA Holliday junction (DNA-HJ) templated aggregates of an expanded set of SQs and evaluate their optical properties in the context of structural heterogeneity. Specifically, we characterized the orientation of and Jm,n between dyes in dimer aggregates of non-chlorinated and chlorinated SQs. Three new chlorinated SQs that feature a varying number of butylsulfo substituents were synthesized and attached to a DNA-HJ via a covalent linker to form adjacent and transverse dimers. Various characteristics of the dye, including its hydrophilicity (in terms of log Po/w) and surface area, and of the substituents, including their local bulkiness and electron withdrawing capacity, were quantified computationally. The orientation of and Jm,n between the dyes were estimated using a model based on Kühn-Renger-May theory to fit the absorption and circular dichroism spectra. The results suggested that adjacent dimer aggregates of all the non-chlorinated and of the most hydrophilic chlorinated SQ dyes exhibit heterogeneity; that is, they form a mixture of dimers subpopulations. A key finding of this work is that dyes with a higher hydrophilicity (lower log Po/w) formed dimers with smaller Jm,n and large center-to-center dye distance (Rm,n). Also, the results revealed that the position of the dye in the DNA-HJ template, that is, adjacent or transverse, impacted Jm,n. Lastly, we found that Jm,n between symmetrically substituted dyes was reduced by increasing the local bulkiness of the substituent. This work provides insights into how to maintain strong excitonic coupling and identifies challenges associated with heterogeneity, which will help to improve control of these dye aggregates and move forward their potential application as quantum information systems.

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.

Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer

A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.

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.

Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies

Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.

Cascade Energy Transfer in Biopolymer-Templated Multi-Chromophoric Assemblies: Ratiometric Temperature Sensing

Natural light-harvesting complexes collect energy from sunlight and transfer it to the reaction center through a cascade of energy and electron transfer steps. Artificial light-harvesting systems functioning in aqueous media mimic natural photosynthetic systems. However, their design remains a challenging task as closely packed antenna chromophores often undergo severe self-quenching. Herein, we report luminescent co-assemblies between cationic pyrene-appended imidazolium amphiphiles and two anionic biopolymeric scaffolds, heparin and DNA in aqueous media. These co-assemblies served as excellent platforms for constructing artificial light-harvesting systems as upon co-embedding of multiple external dyes, highly efficient single-step and cascade energy transfer was observed from the pyrene donors to the acceptor dyes. Most notably, the efficiency of the energy transfer process was possible to modulate by employing multiple stimuli such as pH and temperature, and this resulted in the generation of multi-color luminescent materials in solution and film states, and they were also exploited in ratiometric temperature sensing. Their stimuli-responsive luminescence in the solid state was found to be advantageous for encryption studies.

Photogeneration of Spin Quintet Triplet-Triplet Excitations in DNA-Assembled Pentacene Stacks

Singlet fission (SF), an exciton-doubling process observed in certain molecular semiconductors where two triplet excitons are generated from one singlet exciton, requires correctly tuned intermolecular coupling to allow separation of the two triplets to different molecular units. We explore this using DNA-encoded assembly of SF-capable pentacenes into discrete π-stacked constructs of defined size and geometry. Precise structural control is achieved via a combination of the DNA duplex formation between complementary single-stranded DNA and the local molecular geometry that directs the SF chromophores into a stable and predictable slip-stacked configuration, as confirmed by molecular dynamics (MD) modeling. Transient electron spin resonance spectroscopy revealed that within these DNA-assembled pentacene stacks, SF evolves via a bound triplet pair quintet state, which subsequently converts into free triplets. SF evolution via a long-lived quintet state sets specific requirements on intermolecular coupling, rendering the quintet spectrum and its zero-field-splitting parameters highly sensitive to intermolecular geometry. We have found that the experimental spectra and zero-field-splitting parameters are consistent with a slight systematic strain relative to the MD-optimized geometry. Thus, the transient electron spin resonance analysis is a powerful tool to test and refine the MD-derived structure models. DNA-encoded assembly of coupled semiconductor molecules allows controlled construction of electronically functional structures, but brings with it significant dynamic and polar disorders. Our findings here of efficient SF through quintet states demonstrate that these conditions still allow efficient and controlled semiconductor operation and point toward future opportunities for constructing functional optoelectronic systems.

Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction

While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.

Non-radiative deactivation of excited cytosine: probing of different DFT functionals and basis sets in solvents with different polarity

The vertical excitation and emission energies of the cytosine oxo-amino form were calculated at the TD DFT level of theory with several functionals, basis sets, and solvents with different polarity (PCM). They were compared with the experimental UV absorption and fluorescence maxima, revealing that the minimal deviation of the vertical excitation energies from the of UV absorption maxima can be achieved when the hybrid functional B3LYP is applied within the calculations. Regular correlations like curves with saturation between the vertical excitation/emission energies and the dielectric constants were registered. The relaxation of the ¹ππ^* excited state through an ethylene-like conical intersection S₀/S₁ should occur through decrease of the decay rate (commented qualitatively here) with the rise of the solvent polarity.

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye-dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.

Peptide Backbone Directed Self-Assembly of Merocyanine Oligomers into Duplex Structures

The pseudopeptide backbone provided by N-(2-aminoethyl)-glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N-(2-aminoethyl)-glycine backbone were prepared through peptide synthesis. Our concentration-, temperature- and solvent-dependent UV/Vis absorption studies show that under the control of dipole-dipole interactions, smaller-sized oligomers consisting of one, two or three dyes self-assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation-induced emission enhancement is observed.

Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.

Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides

Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of π-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular π wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.

Luminescence property switching in 1D supramolecular polymerization of organic donor–π-acceptor chromophores

The naphthalene monoimide building block endows with amide functionality undergoes supramolecular polymerization in a J type fashion in a particular co-solvent composition. This leads to luminescent property switching as a result of PET effect.

Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates

Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.

Ultrasound-Induced Amino Acid-Based Hydrogels With Superior Mechanical Strength for Controllable Long-Term Release of Anti-Cercariae Drug

Stimulus-responsive hydrogels are significantly programmable materials that show potential applications in the field of biomedicine and the environment. Ultrasound as a stimulus can induce the formation of hydrogels, which exhibit the superior performance of different structures. In this study, we reported an ultrasound-induced supramolecular hydrogel based on aspartic acid derivative N,N'-diaspartate-3,4,9,10-perylene tetracarboxylic acid imide, showing superior performance in drug release. The results show that the driving force of this ultrasonic induced hydrogel could be attributed to hydrogen bonding and π-π interaction. The rheological and cytotoxicity test illustrate excellent mechanical properties and biocompatibility of the hydrogel. The anti-Schistosoma japonicum cercariae (CC) drug release results show large drug loadings (500 mg/ml) and long-term release (15 days) of this hydrogel. This study demonstrates that this hydrogel may serve as a slow-release platform for anti-CC.

Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties

7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. K_Taut values calculated from H₂O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H₂O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.

Free Charge Carriers in Homo-Sorted π-Stacks of Donor-Acceptor Conjugates

Inspired by the high photoconversion efficiency observed in natural light-harvesting systems, the hierarchical organization of molecular building blocks has gained impetus in the past few decades. Particularly, the molecular arrangement and packing in the active layer of organic solar cells (OSCs) have garnered significant attention due to the decisive role of the nature of donor/acceptor (D/A) heterojunctions in charge carrier generation and ultimately the power conversion efficiency. This review focuses on the recent developments in emergent optoelectronic properties exhibited by self-sorted donor-on-donor/acceptor-on-acceptor arrangement of covalently linked D-A systems, highlighting the ultrafast excited state dynamics of charge transfer and transport. Segregated organization of donors and acceptors promotes the delocalization of photoinduced charges among the stacks, engendering an enhanced charge separation lifetime and percolation pathways with ambipolar conductivity and charge carrier yield. Covalently linking donors and acceptors ensure a sufficient D-A interface and interchromophoric electronic coupling as required for faster charge separation while providing better control over their supramolecular assemblies. The design strategies to attain D-A conjugate assemblies with optimal charge carrier generation efficiency, the scope of their application compared to state-of-the-art OSCs, current challenges, and future opportunities are discussed in the review. An integrated overview of rational design approaches derived from the comprehension of underlying photoinduced processes can pave the way toward superior optoelectronic devices and bring in new possibilities to the avenue of functional supramolecular architectures.

Highly sensitive and ratiometric luminescence sensing of heparin through templated cyanostilbene assemblies

The assembly of organic dyes on bio-molecular templates is an attractive strategy for the creation of bio-materials with intriguing optical properties. This principle is exploited here for the detection of polyanion heparin, a known anticoagulant, by employing di-cationic cyanostilbene derivatives with inherent aggregation induced emission (AIE) features. The cyanostilbene derivatives exhibited weak cyan-blue monomeric emissions in solutions but upon electrostatic co-assembly with heparin, formed highly luminescent clusters on the polyanion surface. The cyanostilbene chromophores in the clusters exhibited greenish-yellow excimer emissions with remarkably longer life-times (up to 70-fold) and higher quantum yields (up to 85-fold) compared to their aqueous solutions. This led to heparin detection in aqueous buffer in low nanomolar concentrations. Additionally, and more importantly, a ratiometric detection of heparin was achieved in highly competitive media such as 50% human serum and 60% human plasma in medically relevant concentrations.

Modulation of Aggregation-Induced Emission by Excitation Energy Transfer: Design and Application

Excitation energy transfer (EET) as a fundamental photophysical process is well-explored for developing functional materials with tunable photophysical properties. Compared to traditional fluorophores, aggregation-induced emission luminogens (AIEgens) exhibit unique advantages for building EET systems, especially serving as energy donors, due to their outstanding photophysical properties such as bright fluorescence in aggregation state, broad absorption and emission spectra, large Stokes shift, and high photobleaching resistance. In addition, the photophysical properties of AIEgens can be modulated by energy transfer for improved luminescence performance. Therefore, a variety of EET systems based on AIEgens have been constructed and their applications in different areas have been explored. In this review, we summarize recent progress in the design strategy of AIE-based energy transfer systems for light-harvesting, fluorescent probes and theranostic systems, with an emphasis on design strategies to achieve desirable properties. The limitations, challenges and future opportunities of AIE-EET systems are briefly outlined. Design strategies and applications (light-harvesting, fluorescent probe and theranostics) of AIEgen-based excitation energy systems are discussed in this review.

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations-transverse dimer, adjacent dimer, and tetramer-were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.

N,N-dicarboxymethyl Perylene-diimide modified CeCoO3: Enhanced peroxidase activity, synergetic catalytic mechanism and glutathione colorimetric sensing

N,N-dicarboxymethyl Perylene-diimide (PDI) modified CeCoO₃ nanocomposites were prepared by a two-step method. After modification with PDI molecules, the obtained PDI-CeCoO₃ nanocomposites were demonstrated to possess the heightened peroxidase-like activity, compared with that of pure CeCoO₃ nanoparticles. In the presence of H₂O₂, the heightened peroxidase-like behaviors of PDI-CeCoO₃ were evaluated by the oxidation of the colorless substrate 3,3,5,5-tetramethylbenzidine (TMB) into blue oxTMB, which was detected visually only in 4 min. Importantly, a systematic study of catalytic activity of PDI-CeCoO₃ by different means, including fluorescent probe, electrochemical data, diffuse reflection spectra together with free radical scavenger is executed, verifying that the catalytic activity were from O₂^- and electron holes (h⁺). And, the transfer of photogenerated carriers in the PDI-CeCoO₃ was the Z-scheme heterojuntion mechanism. Furthermore, the peroxidase-like activity of PDI-CeCoO₃ was significantly inhibited by Glutathione (GSH), resulting in fading of blue oxTMB. Based on this, a colorimetric assay for GSH biosensing has been developed. And, the liner range for GSH detection is from 1 to 10 μM with a detection limit of 0.658 μM. The recovery of GSH with different concentrations from 90.0% to 105.9% and the relative standard deviation (RSD) from 1.9% to 5.1%. This colorimetric sensor can be used to detect GSH in real samples.

Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties

Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.

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

DNA-organized multi-chromophoric systems containing phenanthrene and pyrene derivatives exhibit a highly efficient excitation energy transfer from phenanthrene (donor) to pyrene (acceptor). The energy transfer also occurs if the phenanthrene antenna is interrupted by intervening DNA base pairs. Artificial light-harvesting complexes composed of up to five phenanthrene-DNA alternations with fluorescence quantum yields as high as 68% are described.

From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.

The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases

Unnatural base pairs (UBPs) greatly increase the diversity of DNA and RNA, furthering their broad range of molecular biological and biotechnological approaches. Different candidates have been developed whereby alternative hydrogen-bonding patterns and hydrophobic and packing interactions have turned out to be the most promising base-pairing concepts to date. The key in many applications is the highly efficient and selective acceptance of artificial base pairs by DNA polymerases, which enables amplification of the modified DNA. In this Review, computational as well as experimental studies that were performed to characterize the pairing behavior of UBPs in free duplex DNA or bound to the active site of KlenTaq DNA polymerase are highlighted. The structural studies, on the one hand, elucidate how base pairs lacking hydrogen bonds are accepted by these enzymes and, on the other hand, highlight the influence of one or several consecutive UBPs on the structure of a DNA double helix. Understanding these concepts facilitates optimization of future UBPs for the manifold fields of applications.

A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution

DNA-based molecular rulers enable scientists to determine important parameters across biology, from the measurement of protein binding interactions, to the study of membrane dynamics in cells. However, existing rulers can suffer from poor nanometre resolution due to the flexible nature of linkers used to tether to the DNA framework. We aimed to overcome this problem using zinc and free-base porphyrin chromophores attached via short and rigid acetylene linkers. This connectivity enables the distance and angle between the porphyrins to be fine-tuned along the DNA scaffold. The porphyrins undergo favorable energy transfer and chiral exciton coupling interactions to act as highly sensitive molecular ruler probes. To validate the system, we monitored the detection of small changes in DNA structure upon intercalation of ethidium bromide. CD spectroscopy showed the porphyrins undergo highly sensitive changes in excitation coupling to facilitate base pair resolution of the novel system.

Nanosheets and 2D-nanonetworks by mutually assisted self-assembly of fullerene clusters and DNA three-way junctions

Programmable construction of two dimensional (2D) nanoarchitectures using short DNA strands is of utmost interest in the context of DNA nanotechnology. Previously, we have demonstrated fullerene-cluster assisted self-assembly of short oligonucleotide duplexes into micrometer long, semiconducting nanowires. This report demonstrates the construction of micrometer-sized nanosheets and 2D-nanonetworks from the mutual self-assembly of fullerene nanoclusters with three way junction DNA (3WJ-DNA) and 3WJ-DNA with a 12-mer overhang (3WJ-OH), respectively. The interaction of unique sized fullerene clusters prepared from an aniline appended fullerene derivative, F-An, with two 3WJ-DNAs, namely, 3WJ-20 and 3WJ-30, having 20 and 30 nucleobases, respectively at each strand was characterized using UV-visible absorption, circular dichroism and fluorescence techniques. The morphological characterization of nanosheets embedded with F-An clusters was performed via AFM, TEM and DLS analyses. The programmability and structural tunability of the resultant nanostructures were further demonstrated using 3WJ-OH containing a cytosine rich, single stranded DNA 12-mer overhang, which forms entangled 2D-nanonetwork structures instead of nanosheets due to the differential interaction of F-An nanoclusters with single and duplex strands of 3WJ-OH. Moreover, the selective modification of the cytosine rich sequence present in 3WJ-OH with silver nanoclusters (AgNCs) resulted in significant enhancement in silver nanocluster fluorescence (∼40%) compared to 3WJ-OH/AgNCs owing to the additional stability of AgNCs embedded in 2D nanostructures. This unique strategy of constructing DNA based 2D nanomaterials and their utilization in the integration of functional motifs could find application in the area of DNA nanotechnology and bio-molecular sensing.

Chiral self-assembly of fullerene clusters on CT-DNA templates

Herein we discuss the differential interaction of three monosubstituted fullerene derivatives possessing pyridinium, aniline or phenothiazine end groups (F-Py, F-An and F-PTz, respectively) with calf thymus DNA (CT-DNA), probed via spectroscopic and imaging techniques. The pyridinium derivative, F-Py becomes molecularly dissolved in 10% DMSO-PBS and interacts with CT-DNA via groove binding and electrostatic interactions, leading to the initial condensation of CT-DNA into micrometer sized aggregates and subsequent precipitation. On the other hand, the aniline derivative F-An, which is reported to form nanoclusters of 3-5 nm size, interacts with DNA through ordered, chiral assemblies on the CT-DNA template, thus perturbing the highly networked structure of CT-DNA to form nanonetworks, which eventually transform into condensed aggregates. The binding interactions between CT-DNA and F-An nanoclusters were established via UV-Vis, AFM and TEM analysis, and the chiral nature of the fullerene nanocluster assemblies on CT-DNA was confirmed by the presence of induced circular dichroism that was exhibited around the 250-370 nm region, corresponding to F-An nanocluster absorption. In contrast, the phenothiazine derivative F-PTz, which forms larger nanoclusters of ∼70 nm size in 10% DMSO-PBS, exhibited only weak interactions with CT-DNA without affecting its network structure. These results demonstrate the role of the hydrophobic-hydrophilic balance in the design of DNA interacting fullerene derivatives by controlling their cluster size and interactions with CT-DNA, and are significant in applications such as DNA condensation, gene delivery and dimension controlled nanomaterial fabrication.

Dynamic Nanostructures from DNA-Coupled Molecules, Polymers, and Nanoparticles

Dynamic and reconfigurable systems that can sense and react to physical and chemical signals are ubiquitous in nature and are of great interest in diverse areas of science and technology. DNA is a powerful tool for fabricating such smart materials and devices due to its programmable and responsive molecular recognition properties. For the past couple of decades, DNA-based self-assembly is actively explored to fabricate various DNA-organic and DNA-inorganic hybrid nanostructures with high-precision structural control. Building upon past development, researchers have recently begun to design and assemble dynamic nanostructures that can undergo an on-demand transformation in the structure, properties, and motion in response to various external stimuli. In this Review, recent advances in dynamic DNA nanostructures, focusing on hybrid structures fabricated from DNA-conjugated molecules, polymers, and nanoparticles, are introduced, and their potential applications and future perspectives are discussed.

Directed Energy Transfer through DNA-Templated J-Aggregates

Strongly coupled molecular dye aggregates have unique optoelectronic properties that often resemble those of light harvesting complexes found in Nature. The exciton dynamics in coupled dye aggregates could enhance the long-range transfer of optical excitation energy with high efficiency. In principle, dye aggregates could serve as important components in molecular-scale photonic devices; however, rational design of these coupled dye aggregates with precise control over their organization, interactions, and dynamics remains a challenge. DNA nanotechnology has recently been used to build an excitonic circuit by organizing pseudoisocyanine (PIC) dyes forming J-aggregates on the templates of poly(dA)-poly(dT) DNA duplexes. Here, the excitonic properties of the PIC J-aggregates on DNA are characterized spectroscopically in detail using poly(dA)-poly(dT) tract lengths of 24 and 48 base pairs. The excitonic properties of these DNA templated dye assemblies depend on the length and sequence of the DNA template. The incorporation of a gap of two GC base pairs between two segments of poly(dA)-poly(dT) DNA markedly reduces the delocalization of excitation in the J-aggregates. With a quantum dot (QD) as the light absorber and energy donor and using Alexa Fluor 647 (AF647) as the energy acceptor, with a DNA-templated J-aggregate in between, significant energy transfer from QD to AF647 is observed over a distance far longer than possible without the aggregate bridge. By comparing the efficiency of energy transfer through a continuous J-aggregate with the efficiency when the aggregate has a discontinuity in the middle, the effects of energy transfer within the aggregate bridge between the donor and acceptor are evaluated.