Design, synthesis, and applications of DNA-macrocyclic host conjugates

Design and Synthesis of an Adamantane Phosphoramidite for Programmable and Automated Oligonucleotide-Functionalization

Solid-phase synthesis has revolutionized the programmable preparation of oligonucleotides (ONs), enabling precise gene expression modulation and expanding their applications in therapeutic and material sciences. To further enhance ON functionality, this study introduces a novel adamantane-based phosphoramidite for oligonucleotide modification. Adamantane, known for its hydrophobicity and stability, was incorporated into nucleic acid aptamers using automated synthesis. Two aptamers─Sgc8 and AS1411─were functionalized with one or two adamantane units, and the products were purified and validated using high-performance liquid chromatography and mass spectrometry. The incorporation of adamantane significantly altered the aptamers' polarity and facilitated their self-assembly with poly-β-cyclodextrin, forming stable supramolecular complexes, as demonstrated by polyacrylamide gel electrophoresis. Additionally, adamantane-modified AS1411 exhibited enhanced degradation of its target protein, nucleolin, in MCF-7 cells, suggesting potential utility in targeted protein regulation. These findings establish a versatile platform for functionalizing ONs, broadening their potential for biomedical and nanotechnological applications.

Vesicle-Encapsulated Chemosensing Ensembles Allow Monitoring of Transmembrane Uptake Coupled with Enzymatic Reactions

Compartmentalized models with coupled catalytic networks are considered as "protocells" in the context of research related to the origin of life. To model the kinetics of a simple cellular uptake-metabolism process, we use a compartmentalized protocell system that combines liposome-encapsulated intravesicular reporter pairs with co-encapsulated enzymes to monitor the membrane transport of a substrate (analyte uptake) and its subsequent enzymatic reaction inside the vesicles (metabolism to the product). The intravesicular chemosensing ensembles consist of the macrocycles cucurbit[7]uril or p-sulfonatocalix[4]arene and matching fluorescent dyes to set up suitable reporter pairs. When these macrocycle/dye reporter pairs are co-encapsulated with enzymes (trypsin, protein kinase A, or butyrylcholinesterase), it is possible to monitor first the transport of different substrates (polylysine, protamine, H-LRRWSLG-OH, or butyrylcholine) through added pores (outer membrane proteins F and C), with synthetic carriers (amphiphilic calixarenes), or by direct permeation (only for butyrylcholine). The subsequent enzymatic conversions of the substrates after they have entered the corresponding protocells can be monitored as consecutive reactions. The new type of in vitro assays can be applied to different enzymes and analytes, affording a comprehensive chemosensing system of high chemical complexity.

Metal Nanocluster-Based Biosensors for DNA Detection

The early detection of genetic diseases is a critical need in modern medicine, underscoring the importance of developing deoxyribonucleic acid (DNA) biosensors. In recent years, metal nanoclusters (MNCs) have demonstrated significant potential as biosensors for DNA detection due to their ultra-small size, excellent photostability, bright photoluminescence, low toxicity and other outstanding properties. This review firstly discusses the characteristics of MNCs, which are effective in the early diagnosis of DNA diseases. Subsequently, different synthesis methods of MNCs are introduced. In the following section, DNA sensors based on different types of MNCs and their respective detection mechanisms are discussed in detail. Finally, the opportunities and challenges faced by DNA sensors based on MNCs are analyzed.

Molecular vessels from preorganised natural building blocks

Supramolecular vessels emerged as tools to mimic and better understand compartmentalisation, a central aspect of living matter. However, many more applications that go beyond those initial goals have been documented in recent years, including new sensory systems, artificial transmembrane transporters, catalysis, and targeted drug or gene delivery. Peptides, carbohydrates, nucleobases, and steroids bear great potential as building blocks for the construction of supramolecular vessels, possessing complexity that is still difficult to attain with synthetic methods - they are rich in functional groups and well-defined stereogenic centers, ready for noncovalent interactions and further functions. One of the options to tame the functional and dynamic complexity of natural building blocks is to place them at spatially designed positions using synthetic scaffolds. In this review, we summarise the historical and recent advances in the construction of molecular-sized vessels by the strategy that couples synthetic predictability and durability of various scaffolds (cyclodextrins, porphyrins, crown ethers, calix[n]arenes, resorcin[n]arenes, pillar[n]arenes, cyclotriveratrylenes, coordination frameworks and multivalent high-symmetry molecules) with functionality originating from natural building blocks to obtain nanocontainers, cages, capsules, cavitands, carcerands or coordination cages by covalent chemistry, self-assembly, or dynamic covalent chemistry with the ultimate goal to apply them in sensing, transport, or catalysis.

Amphiphilic α-Peptoid-deoxynojirimycin Conjugate-based Multivalent Glycosidase Inhibitor for Hypoglycemic Effect and Fluorescence Imaging

Multivalent glycosidase inhibitors based on 1-deoxynojirimycin derivatives against α-glucosidases have been rapidly developed. Nonetheless, the mechanism based on self-assembled multivalent glucosidase inhibitors in living systems needs to be further studied. It remains to be determined whether the self-assembly possesses sufficient stability to endure transit through the small intestine and subsequently bind to the glycosidases located therein. In this paper, two amphiphilic compounds, 1-deoxynojirimycin and α-peptoid conjugates (LP-4DNJ-3C and LP-4DNJ-6C), were designed. Their self-assembling behaviors, multivalent α-glucosidase inhibition effect, and fluorescence imaging on living organs were studied. LP-4DNJ-6C exhibited better multivalent α-glucosidase inhibition activities in vitro. Moreover, the self-assembly of LP-4DNJ-6C could effectively form a complex with Nile red. The complex showed fluorescence quenching effect upon binding with α-glucosidases and exhibited potent fluorescence imaging in the small intestine. This result suggests that a multivalent hypoglycemic effect achieved through self-assembly in the intestine is a viable approach, enabling the rational design of multivalent hypoglycemic drugs.

Cascade signal amplification strategy for the electrochemical aptasensing of nucleic acid: Combination of dual-output toehold-mediated DNA strand displacement, DNA walker and Exo III

BACKGROUND

Sensitive and selective analysis of low content nucleic acid sequences plays an important role in pathogen analysis, disease diagnosis and biomedicine. The electrochemical biosensor based on toehold-mediated strand displacement reaction (TMSD) is highly attractive in nucleic acid detection due to their improved sensitivity and rapid response. But the traditional TMSD carried out on the electrode always with low displacement efficiency and complicated electrode operation, resulting in compromised sensing performance. There is a great need to construct a novel TMSD based electrochemical detection strategy to overcome such challenges in nucleic acid detecting.

RESULT

Herein, a triple signal amplification electrochemical aptasensor was developed for ultrasensitive detection of CYFRA21-1 DNA. The dual-output toehold mediated strand displacement reaction (dTMSD) can convert one input to two strands output within one strand displacement cycle. So that it possesses a higher efficiency for improving the sensitivity in comparison with the single-output TMSD. And the fuel strand was configured with a tail to realize successive DNA circuits through self-propelling as a DNA walker. All the above processes were carried out on magnetic beads, which is conducive to achieving effective sample purification and minimizing the background signals. Besides, Exonuclease III was further amplified signal. As a result, through the cascade use of above three technologies, the proposed biosensing strategy realized sensitive detection of target DNA with a low detection limit of 0.35 fM (S/N = 3) and wide linear range (0.5 fM-500 pM).

SIGNIFICANCE

The proposed novel dTMSD combining multiple signal amplification strategies for electrochemical detection of CYFRA21-1 DNA with easy operation not only possesses excellent sensitivity and selectivity, but also has potential application value for monitoring DNA in serum. Meanwhile, the development of highly sensitive and specific CYFRA21-1 DNA detection methods is very important for the prevention and treatment of lung cancer.

High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures

The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host-guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m-1 , directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower-affinity β-cyclodextrin-adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high-affinity CB[7]-adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high-affinity CB[7]-guest recognition as an orthogonal axis to drive self-assembly in DNA nanotechnology.

Aqueous Three-Component Self-Assembly of a Pseudo[1]rotaxane Using Hydrazone Bonds

We present herein the synthesis of a new polycationic pseudo[1]rotaxane, self-assembled in excellent yield through hydrazone bonds in aqueous media of three different aldehyde and hydrazine building blocks. A thermodynamically controlled process has been studied sequentially by analyzing the [1 + 1] reaction of a bisaldehyde and a trishydrazine leading to the macrocyclic part of the system, the ability of this species to act as a molecular receptor, the conversion of a hydrazine-pending cyclophane into the pseudo[1]rotaxane and, lastly, the one-pot [1 + 1 + 1] condensation process. The latter was found to smoothly produce the target molecule through an integrative social self-sorting process, a species that was found to behave in water as a discrete self-inclusion complex below 2.5 mM concentration and to form supramolecular aggregates in the 2.5-70 mM range. Furthermore, we demonstrate how the abnormal kinetic stability of the hydrazone bonds on the macrocycle annulus can be advantageously used for the conversion of the obtained pseudo[1]rotaxane into other exo-functionalized macrocyclic species.

Fluorophore-based host-guest assembly complexes for imaging and therapy

Recently, supramolecular chemistry with its unique properties has received considerable attention in many fields. Supramolecular fluorescent systems constructed on the basis of macrocyclic hosts are not only effective in overcoming the limitations of imaging and diagnostic reagents, but also in enhancing their performances. This paper summarizes the recent advances in supramolecular fluorescent systems based on host-guest interactions and their application in bioimaging and therapy as well as the challenges and prospects in developing novel supramolecular fluorescent systems.

Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.

DNA Strand Displacement Driven by Host-Guest Interactions

Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.

The chaotropic effect of ions on the self-aggregating propensity of Whitlock's molecular tweezers

Molecular tweezers feature the first class of artificial receptors to pique the interest of researchers and emerge as an effective therapeutic candidate. The exceptional structure and exquisite binding specificity of tweezers establish this overall class of receptors as a promising tool, with abundant applications. However, their inclination to self-aggregate by mutual π-π stacking interactions of their aromatic arms diminishes their efficacy as a therapeutic candidate. Therefore, following up on sporadic studies, since the discovery of the Hofmeister series, on the ability of ions to either solvate (salting-in) or induce aggregation (salting-out) of hydrophobic solutes, the notions of ion-specificity effects are utilized on tweezer moieties. The impacts of three different aluminum salts bearing anions Cl^-, ClO₄^- and SCN^- on the self-association propensity of Whitlock's caffeine-pincered molecular tweezers are investigated, with a specific emphasis placed on elucidating the varied behavior of the ions on the hydration ability of tweezers. The comparative investigation is conducted employing a series of all-atom molecular dynamics simulations of five tweezer molecules in pure water and three salt solutions, at two different concentrations each, maintaining a temperature of 300 K and a pressure of 1 atm, respectively. Radial distribution functions, coordination numbers, and SASA calculations display a steady reduction in the aggregation proclivity of the receptor molecules with an increase in salt concentration, as progressed along the Hofmeister series. Orientational preferences between the tweezer arms reveal a disruptive effect in the regular π-π stacking interactions, in the presence of high concentrations of ClO₄^- and SCN^- ions, while preferential interactions and tetrahedral order parameters unveil the underlying mechanism, by which the anions alter the solubility of the hydrophobic molecules. Overall, it is observed that SCN^- exhibits the highest salting-in effect, followed by ClO₄^-, with both anions inhibiting tweezer aggregation through different mechanisms. ClO₄^- ions impart an effect by moderately interacting with the solute molecules as well as modifying the water structure of the bulk solution promoting solvation, whereas, SCN^- ions engage entirely in interaction with specific tweezer sites. Cl^- being the most charge-dense of the three anionic species experiences stronger hydration and therefore, imparts a very negligible salting-in effect.

Development of Novel Tetrapyrrole Structure Photosensitizers for Cancer Photodynamic Therapy

The effectiveness of photodynamic therapy (PDT) is based on the triad effects of photosensitizer (PS), molecular oxygen and visible light on malignant tumors. Such complex induces a multifactorial manner including reactive-oxygen-species-mediated damage and the killing of cells, vasculature damage of the tumor, and activation of the organism immunity. The effectiveness of PDT depends on the properties of photosensitizing drugs, their selectivity, enhanced photoproduction of reactive particles, absorption in the near infrared spectrum, and drug delivery strategies. Photosensitizers of the tetrapyrrole structure (porphyrins) are widely used in PDT because of their unique diagnostic and therapeutic functions. Nevertheless, the clinical use of the first-generation PS (sodium porfimer and hematoporphyrins) revealed difficulties, such as long-term skin photosensitivity, insufficient penetration into deep-seated tumors and incorrect localization to it. The second generation is based on different approaches of the synthesis and conjugation of porphyrin PS with biomolecules, which made it possible to approach the targeted PDT of tumors. Despite the fact that the development of the second-generation PS started about 30 years ago, these technologies are still in demand and are in intensive development, especially in the direction of improving the process of optimization split linkers responsive to input. Bioconjugation and encapsulation by targeting molecules are among the main strategies for developing of the PS synthesis. A targeted drug delivery system with the effect of increased permeability and retention by tumor cells is one of the ultimate goals of the synthesis of second-generation PS. This review presents porphyrin PS of various generations, discusses factors affecting cellular biodistribution and uptake, and indicates their role as diagnostic and therapeutic (theranostic) agents. New complexes based on porphyrin PS for photoimmunotherapy are presented, where specific antibodies are used that are chemically bound to PS, absorbing light from the near infrared part of the spectrum. Additionally, a two-photon photodynamic approach using third-generation photosensitizers for the treatment of tumors is discussed, which indicates the prospects for the further development of a promising method antitumor PDT.

Synthesis and Applications of Porphyrin-Biomacromolecule Conjugates

With potential applications in materials and especially in light-responsive biomedicine that targets cancer tissue selectively, much research has focused on developing covalent conjugation techniques to tether porphyrinoid units to various biomacromolecules. This review details the key synthetic approaches that have been employed in the recent decades to conjugate porphyrinoids with oligonucleotides and peptides/proteins. In addition, we provide succinct discussions on the subsequent applications of such hybrid systems and also give a brief overview of the rapidly progressing field of porphyrin-antibody conjugates. Since nucleic acid and peptide systems vary in structure, connectivity, functional group availability and placement, as well as stability and solubility, tailored synthetic approaches are needed for conjugating to each of these biomacromolecule types. In terms of tethering to ONs, porphyrins are typically attached by employing bioorthogonal chemistry (e.g., using phosphoramidites) that drive solid-phase ON synthesis or by conducting post-synthesis modifications and subsequent reactions (such as amide couplings, hydrazide-carbonyl reactions, and click chemistry). In contrast, peptides and proteins are typically conjugated to porphyrinoids using their native functional groups, especially the thiol and amine side chains. However, bioorthogonal reactions (e.g., Staudinger ligations, and copper or strain promoted alkyne-azide cycloadditions) that utilize de novo introduced functional groups onto peptides/proteins have seen vigorous development, especially for site-specific peptide-porphyrin tethering. While the ON-porphyrin conjugates have largely been explored for programmed nanostructure self-assembly and artificial light-harvesting applications, there are some reports of ON-porphyrin systems targeting clinically translational applications (e.g., antimicrobial biomaterials and site-specific nucleic acid cleavage). Conjugates of porphyrins with proteinaceous moieties, on the other hand, have been predominantly used for therapeutic and diagnostic applications (especially in photodynamic therapy, photodynamic antimicrobial chemotherapy, and photothermal therapy). The advancement of the field of porphyrinoid-bioconjugation chemistry from basic academic research to more clinically targeted applications require continuous fine-tuning in terms of synthetic strategies and hence there will continue to be much exciting work on porphyrinoid-biomacromolecule conjugation.

Functional DNA-Polymer Conjugates

DNA nanotechnology has seen large developments over the last 30 years through the combination of solid phase synthesis and the discovery of DNA nanostructures. Solid phase synthesis has facilitated the availability of short DNA sequences and the expansion of the DNA toolbox to increase the chemical functionalities afforded on DNA, which in turn enabled the conception and synthesis of sophisticated and complex 2D and 3D nanostructures. In parallel, polymer science has developed several polymerization approaches to build di- and triblock copolymers bearing hydrophilic, hydrophobic, and amphiphilic properties. By bringing together these two emerging technologies, complementary properties of both materials have been explored; for example, the synthesis of amphiphilic DNA-polymer conjugates has enabled the production of several nanostructures, such as spherical and rod-like micelles. Through both the DNA and polymer parts, stimuli-responsiveness can be instilled. Nanostructures have consequently been developed with responsive structural changes to physical properties, such as pH and temperature, as well as short DNA through competitive complementary binding. These responsive changes have enabled the application of DNA-polymer conjugates in biomedical applications including drug delivery. This review discusses the progress of DNA-polymer conjugates, exploring the synthetic routes and state-of-the-art applications afforded through the combination of nucleic acids and synthetic polymers.

Selective Identification of Phenylalanine Using Cucurbit[7,8]uril-Based Fluorescent Probes

The interactions of two host–guest inclusion complexes comprised of cucurbit[7]uril (Q[7]) and cucurbit[8]uril (Q[8]) with a derivative of toluidine blue O (TB) have been investigated using 1H NMR and fluorescence spectroscopy. The experimental results revealed that the Q[7] host interacts with a TB molecule to form a 1:1 inclusion complex and the Q[8] host interacts with two TB guest molecules to form a 1:2 inclusion complex. The inclusion of the TB guest molecule within the Q[7] host gave rise to significant fluorescence enhancement, whereas the inclusion of the TB guest molecule within the Q[8] host resulted in significant fluorescence quenching. Further recognition experiments involving a series of l-α-amino acids revealed that the TB@Q[7] inclusion fluorescence probe exhibits high selectivity for the recognition of phenylalanine via significant fluorescence quenching in an aqueous solution, whereas the TB@Q[8] inclusion fluorescence probe also exhibited high selectivity for phenylalanine recognition via fluorescence enhancement in an aqueous solution.

Cucurbiturils in nucleic acids research

During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.

Histidine-Based Reduction-Sensitive Star-Polymer Inclusion Complex as a Potential DNA Carrier: Biophysical Studies Using Time-Resolved Fluorescence as an Important Tool

An ideal DNA carrier is one that is capable of effectively condensing DNA into complexes of optimum size and shape, preventing premature decomplexation in the bloodstream and efficiently releasing the DNA into affected cells. In this context, we have developed a novel β-cyclodextrin (β-CD)-based four-arm star-shaped polymer inclusion complex (IC) with arms made of a poly(l-histidine)-based cationic polymer. The polymer was well characterized by gel permeation chromatography, NMR, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. We have also investigated its DNA complexation and release properties. Bisadamantane containing a disulfide bond was synthesized that linked two such poly(l-histidine)-containing β-CD units via guest-host interactions to prepare the presented IC. Besides using the conventional steady-state fluorescence spectroscopy, the ability of this IC to condense DNA to form polyplexes and their release behavior have been established by using the time-resolved fluorescence spectroscopy technique. Thiazole orange (TO) was used for the first time as a DNA-intercalating dye in the time-resolved fluorescence spectroscopic study. The superior DNA-condensing ability of the IC as compared to that of the precursor two-arm β-CD and linear poly(l-histidine) of a comparable molecular weight, as confirmed by dynamic light scattering, zeta potential, atomic force microscopy, and gel electrophoresis studies, could be attributed to a higher charge density. The IC-DNA polyplexes were found to be stable in a medium similar to an extracellular fluid but could efficiently release DNA in the presence of 10 mM glutathione, a concentration prevalent in the intracellular fluid of cancer cells. Hence, here, we have successfully demonstrated the synthesis of a novel biocompatible star-shaped IC with the potential to carry and release DNA in cancer cells and also established the feasibility of using the time-resolved fluorescence spectroscopic technique to study the complexation behavior of the polycation and DNA using TO as a DNA-intercalating dye.

Efficient Capturing of Polycyclic Aromatic Micropollutants From Water Using Physically Crosslinked DNA Nanoparticles

Design and synthesis of physically (non-covalently) cross-linked nanoparticles through host-guest interaction between β-CD and adamantane is reported. Specific molecular recognition between β-CD functionalized branched DNA nanostructures (host) and a star-shaped adamantyl-terminated 8-arm poly(ethylene glycol) polymer (guest) is explored for the design of the nanoparticles. The most remarkable structural features of DNA nanoparticles include their excellent biocompatibility and the possibility of various non-covalent interactions with both hydrophobic and hydrophilic organic molecules. Potential of DNA nanoparticles for the rapid and efficient capture of various micropollutants typically present in water including carcinogens (hydrophobic micropollutants), organic dyes (hydrophilic), and pharmaceutical molecules (hydrophilic) is also demonstrated. The capture of micropollutants by DNA nanoparticles is attributed to the various non-covalent interactions between DNA nanoparticles and the micropollutants. Our results clearly suggest that DNA based nanomaterials would be an ideal candidate for the capturing and removal of both hydrophilic and hydrophobic micropollutants typically present in water.

Manipulating Enzymes Properties with DNA Nanostructures

Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.

Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns

The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.

Protein-protein interaction modulators: advances, successes and remaining challenges

Modulating disease-relevant protein-protein interactions (PPIs) using small-molecule inhibitors is a quite indispensable diagnostic and therapeutic strategy in averting pathophysiological cues and disease progression. Over the years, targeting intracellular PPIs as drug design targets has been a challenging task owing to their highly dynamic and expansive interfacial areas (flat, featureless and relatively large). However, advances in PPI-focused drug discovery technology have been reported and a few drugs are already on the market, with some potential drug-like candidates already in clinical trials. In this article, we review the advances, successes and remaining challenges in the application of small molecules as valuable PPI modulators in disease diagnosis and therapeutics.

DNA-supramolecule conjugates in theranostics

The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to develop various molecular probes, drug delivery carriers and theranostic systems for cancer diagnosis and therapy. In addition, supramolecular chemistry, also termed "chemistry beyond the molecule", is a promising research field that aims to develop functional chemical systems by bringing discrete molecular components together in a manner that invokes noncovalent intermolecular forces, such as hydrophobic interaction, hydrogen bonding, metal coordination, and shape or size matching. Thus, DNA-supramolecule conjugates (DSCs) combine accurate recognition, programmability and addressability of DNA with the greater toolbox of supramolecular chemistry. This review discusses the applications of DSCs in sensing, protein activity regulation, cell behavior manipulation, and biomedicine.

Supramolecular nanotheranostics based on pillarenes

With the rapid development of supramolecular chemistry and nanomaterials, supramolecular nanotheranostics has attracted remarkable attention owing to the advantages compared with conventional medicine. Supramolecular architectures relying on non-covalent interactions possess reversible and stimuli-responsive features; endowing supramolecular nanotheranostics based on supramolecular assemblies great potentials for the fabrication of integrated novel nanomedicines and controlled drug delivery systems. In particular, pillarenes, as a relatively new class of synthetic macrocycles, are important candidates in the construction of supramolecular therapeutic systems due to their excellent features such as rigid and symmetric structures, facile substitution, and unique host-guest properties. This review summarizes the development of pillarene-based supramolecular nanotheranostics for applications in biological mimicking, virus inhibition, cancer therapy, and diagnosis, which contains the following two major parts: (a) pillarene-based hybrid supramolecular nanotheranostics upon hybridizing with porous materials such as mesoporous silica nanoparticles, metal-organic frameworks, metal nanoparticles, and other inorganic materials; (b) pillarene-based organic supramolecular therapeutic systems that include supramolecular amphiphilic systems, artificial channels, and prodrugs based on host-guest complexes. Finally, perspectives on how pillarene-based supramolecular nanotheranostics will advance the field of pharmaceuticals and therapeutics are given.

Pharmaceutical Applications of Molecular Tweezers, Clefts and Clips

Synthetic acyclic receptors, composed of two arms connected with a spacer enabling molecular recognition, have been intensively explored in host-guest chemistry in the past decades. They fall into the categories of molecular tweezers, clefts and clips, depending on the geometry allowing the recognition of various guests. The advances in synthesis and mechanistic studies have pushed them forward to pharmaceutical applications, such as neurodegenerative disorders, infectious diseases, cancer, cardiovascular disease, diabetes, etc. In this review, we provide a summary of the synthetic molecular tweezers, clefts and clips that have been reported for pharmaceutical applications. Their structures, mechanism of action as well as in vitro and in vivo results are described. Such receptors were found to selectively bind biological guests, namely, nucleic acids, sugars, amino acids and proteins enabling their use as biosensors or therapeutics. Particularly interesting are dynamic molecular tweezers which are capable of controlled motion in response to an external stimulus. They proved their utility as imaging agents or in the design of controlled release systems. Despite some issues, such as stability, cytotoxicity or biocompatibility that still need to be addressed, it is obvious that molecular tweezers, clefts and clips are promising candidates for several incurable diseases as therapeutic agents, diagnostic or delivery tools.

Trehalose-based Siamese twin amphiphiles with tunable self-assembling, DNA nanocomplexing and gene delivery properties

Trehalose Siamese twin vectors, encompassing gemini and facial amphiphilicity, promote pDNA compaction into core–shell nanocomplexes and selective delivery in the lungs.