Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

Enhanced Sequence-Specific DNA Recognition Using Oligodeoxynucleotide-Benzimidazole Conjugates

Synthetic modification of oligodeoxynucleotides (ODNs) via conjugation to nucleic acid binding small molecules can improve hybridization and pharmacokinetic properties. In the present study, five Hoechst 33258 derived benzimidazoles were conjugated to T rich ODNs and their hybridization effectiveness was tested. Thermal denaturation studies revealed significant stabilization of complementary duplexes by ODN-benzimidazole conjugates, with the extent of stabilization being highly dependent on the length of the linker between DNA and benzimidazole. The increases in thermal stability were determined to be due to the binding of the benzimidazole moiety to the duplex. Circular dichroism and molecular modeling studies provided insights toward the influence of conjugation on duplex structure and how linker length impacts placement of the benzimidazole moiety in the minor groove. Furthermore, thermal denaturation studies with the complementary strand containing a single base mismatch or being RNA revealed that covalent conjugation of benzimidazoles to an ODN also enhances the sequence specificity. The fundamental studies reported herein provide a strategy to improve the stability and specificity properties of the ODN probes, which can be of use for targeting and diagnostics applications.

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.

Rapid sensitive fluorescence detection of cadmium (II) with pyrene excimer switching aptasensor

Heavy metal cadmium (II) contamination often occurs, causing great health risk to human due to high toxicity of cadmium (II). Rapid, sensitive and simple detection of cadmium (II) are of great importance in environmental monitoring. Taking advantage of aptamer in specific recognition, easy modification, and capability of binding-induced structure change, here we reported a simple fluorescent sensor with rapid and sensitive response for Cd²⁺ using aptamer pyrene excimer switch. The aptamer was labeled with dual pyrene molecules at two ends of the sequence. The binding of Cd²⁺ to this aptamer probe brought the pyrene labels into close proximity and enhanced formation of a pyrene excimer, which generated increased fluorescence at 485 nm. By measuring the fluorescence of pyrene excimer, we achieved detection of Cd²⁺ with this aptasensor. Under the optimum experimental conditions, the detection limit of Cd²⁺ reached nanomolar levels. This method was selective and allowed for the detection of Cd²⁺ in tap water. This fluorescence aptasensor is promising for rapid detection of Cd²⁺ in broad applications.

Dynamically stable and amplified circularly polarized excimer emission regulated by solvation of chiral co-assembly process

Chiral supramolecular assembly has been assigned to be one of the most favorable strategies for the development of excellent circularly polarized luminescent (CPL)-active materials. Herein, we report our study of an achiral boron-containing pyrene (Py)-based chromophore (PyBO) as a circularly polarized excimer emission (CPEE) dye induced by chiral co-assemblies containing chiral binaphthyl-based enantiomers (R/S-M). Chiral co-assembly R/S-M-(PyBO)4 fresh film spin-coated from toluene solution can exhibit orderly nanofibers and strong green CPEE (λem = 512 nm, gem = ±0.45, ΦFL = 51.2 %) resulting from an achiral PyBO excimer. In contrast, only a very weak blue CPL was observed (λem = 461 nm, gem = ±  0.0125, ΦFL = 19.0 %) after 187 h due to PyBO monomer emission as spherulite growth. Interestingly, this kind of chiral co-assembly R-M-(PyBO)4-T film from tetrahydrofuran (THF) solution retains uniform morphology and affords the most stable and strongest CPEE performance (λem = 512 nm, gem = + 0.62, ΦFL = 53.3 %) after 10 days.

Highly Fluorescent Dyes Containing Conformationally Restrained Pyrazolylpyrene (Pyrazoolympicene) Chromophore

The triflic-acid-promoted cyclization of 1-phenyl-3-(pyren-1-yl)-1H-pyrazole-4-carbaldehyde afforded a mixture of 9-phenyl-7,9-dihydropyreno (10,1-fg)indazole and 9-phenylpyreno(10,1-fg)indazole-7(9H)-one, readily separable by column chromatography. Both products contained a rigid six-ringed pyrazoolympicene backbone and exhibited bright fluorescence in chloroform solution and a weak fluorescence in the solid state. DFT and TD DFT calculations revealed that the lowest excited state (S1) of these compounds is populated via HOMO →LUMO π-π * transition. Furthermore, the synthesized compounds behaved as weak bases and their emission spectra showed substantial changes upon protonation. Therefore, they may be of interest for sensing of strongly acidic fluorophore environments.

A photonic dual nano-hybrid assay for detection of cell-free circulating mitochondrial DNA

Circulating cell free mitochondrial DNA (ccf-mtDNA) has emerged as a potential marker for diagnosis and prognosis of different chronic and age associated non-communicable diseases. Therefore, owing to its biomarker potential, we herein assessed a novel nano-photonic dual hybrid assay system for rapid and specific detection of ccf-mtDNA. The assay comprised of two systems, i.e. a capture and screen facet containing aminopyrene tethered carbon quantum dots for effective screening of circulating cell free nucleic acids (ccf-NAs) and a quantum dot conjugated probe for precise detection of ccf-mtDNA in the screened ccf-NAs. Our observations suggested that the developed dual-assay system possesses high feasibility and selectivity in screening of ccf-NAs and estimation of ccfmtDNA in a given sample. It also offers high versatility of measurement in different analytical platforms, indicating the translational potential of the method for possible disease risk assessment in control and field settings.

c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry

Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (U^py) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with U^py and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.

Gated Photoreactivity of Pyrene Copolymers in Multiresponsive Cross-Linked starPEG-Hydrogels

The synthesis and manufacturing of multiresponsive polymer hydrogels using simple components is a notable challenge. Pyrene is an excimer-forming fluorophore mostly used as microenvironmental probe and for the localization of molecules in close proximity in artificial and biomaterials. Here we make use of the solvophobic preaggregation and photolysis properties of pyrene to construct multiresponsive hydrogels. We synthesize poly(ethylene glycol) (PEG) hydrogels from well-defined pyrene-substituted macro-cross-linkers and elucidate their intricate intra- and intermolecular excimer formation pathways. We find that controlling the water content of the hydrogels through the degree of swelling acts as a gating stimulus governing the photoinduced solvolysis of pyrenylmethyl esters from their poly(methacrylate) backbone. This allows the implementation of a simple transient photolithography process. We thus demonstrate that multiresponsive soft materials with complex optical and mechanical responses can be obtained with comparatively little synthetic effort.

Pyrene-Modified Guanine Cluster Probes Forming DNA/RNA Hybrid Three-Way Junctions for Imaging of Intracellular MicroRNAs

MicroRNAs (miRNAs) regulate gene expression in cells; high levels of expression are associated with various cancers. In this paper, we describe ^PyA-modified nucleic acid probes that can detect intracellular miRNAs by forming DNA/RNA hybrid three-way junction structures containing a fluorescent scaffold-a so-called G-cluster. This G-cluster featured two mismatched strands, four guanine residues, and one fluorescent adenine residue having a pyrene moiety covalently connected at the 8-position through an acetylene linker. The scaffold underwent a dramatic shift in its emission wavelength when two mismatched strands formed a duplex, similar to the behavior of an adenine pentad system (A-cluster). We applied the G-cluster scaffold in a three-way junction system to probe for miRNAs; its red-shifted fluorescence intensity and stability were greater than those reported previously for A-cluster three-way junction probes. Furthermore, confocal microscopy of cancer cell lines revealed bright fluorescence emissions in response to the miRNAs in the cells. Thus, this system can be applied intracellularly as a potential fluorescent probe for the detection of various biologically important nucleic acids.

Fluorescent Probes for Selective Recognition of Hypobromous Acid: Achievements and Future Perspectives

Reactive oxygen species (ROS) have been implicated in numerous pathological processes and their homeostasis facilitates the dynamic balance of intracellular redox states. Among ROS, hypobromous acid (HOBr) has a high similarity to hypochlorous acid (HOCl) in both chemical and physical properties, whereas it has received relatively little attention. Meanwhile, selective recognition of endogenous HOBr suffers great challenges due to the fact that the concentration of this molecule is much lower than that of HOCl. Fluorescence-based detection systems have emerged as very important tools to monitor biomolecules in living cells and organisms owing to distinct advantages, particularly the temporal and spatial sampling for in vivo imaging applications. To date, the development of HOBr-specific fluorescent probes is still proceeding quite slowly, and the research related to this area has not been systematically summarized. In this review, we are the first to review the progress made so far in fluorescent probes for selective recognition and detection of HOBr. The molecular structures, sensing mechanisms, and their successful applications of these probes as bioimaging agents are discussed here in detail. Importantly, we hope this review will call for more attention to this rising field, and that this could stimulate new future achievements.

5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches

Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.

Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides

Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets for therapeutic intervention. Ligands based on polyaromatic moieties are especially suitable for targeting G-quadruplexes utilizing their size complementarity to interact with the large exposed surface area of four guanine bases. A predictable way of (de)stabilizing specific G-quadruplex structures through efficient base stacking of polyaromatic functional groups could become a valuable tool in our therapeutic arsenal. We have investigated the effect of pyrene-modified uridine nucleotides incorporated at several positions of the thrombin binding aptamer (TBA) as a model system. Characterization using spectroscopic and biophysical methods provided important insights into modes of interaction between pyrene groups and the G-quadruplex core as well as (de)stabilization by enthalpic and entropic contributions. NMR data demonstrated that incorporation of pyrene group into G-rich oligonucleotide such as TBA may result in significant changes in 3D structure such as formation of novel dimeric topology. Site specific structural changes induced by stacking of the pyrene moiety on nearby nucleobases corelate with distinct thrombin binding affinities and increased resistance against nuclease degradation.

Diagnostic and Therapeutic Value of Aptamers in Envenomation Cases

It is now more than a century since Albert Calmette from the Institut Pasteur changed the world of envenomation by demonstrating that antibodies raised against animal venoms have the ability to treat human victims of previously fatal bites or stings. Moreover, the research initiated at that time effectively launched the discipline of toxicology, first leading to the search for toxic venom components, followed by the demonstration of venoms that also contained compounds of therapeutic value. Interest from pharmaceutical companies to treat envenomation is, however, declining, mainly for economic reasons, and hence, the World Health Organization has reclassified this public health issue to be a highest priority concern. While the production, storage, and safety of antivenom sera suffer from major inconveniences, alternative chemical and technological approaches to the problem of envenomation need to be considered that bypass the use of antibodies for toxin neutralization. Herein, we review an emerging strategy that relies on the use of aptamers and discuss how close—or otherwise—we are to finding a viable alternative to the use of antibodies for the therapy of human envenomation.

Ab initio study on the excited states of pyrene and its derivatives using multi-reference perturbation theory methods

Low-lying singlet excited states of pyrene derivatives originated from the 1La and 1Lb states of pyrene have decisive influences on their absorption and fluorescence emission behaviors. Calculation of these excited states with quantitative accuracy is required for the theoretical design of pyrene derivatives tailored to target applications; this has been a long-standing challenge for ab initio quantum chemical calculations. In this study, we explore an adequate computational scheme through calculations of pyrene and its phenyl-substituted derivatives using multi-reference perturbation theory (MRPT) methods. All valence π orbitals on the pyrene moiety were assigned to the active orbitals. Computational load was reduced by restricting the electron excitations within the active orbitals in the preparation of reference configuration space. A generalized multi-configuration quasi-degenerate perturbation theory (GMCQDPT) was adopted to treat the reference space other than the complete active space. The calculated 1La and 1Lb excitation energies of pyrene are in good agreement with the experimental values. Calculations of 1,3,6,8-tetraphenyl pyrene suggest that the energetic ordering of 1La and 1Lb is inverted through tetraphenyl substitution and its lowest singlet excited state is the 1La parentage of pyrene, which is consistent with the experimentally deduced scheme. These results are not readily obtained by MRPT calculations with a limited number of active orbitals and single-reference theory calculations. Diphenyl pyrenes (DPPy) were also calculated at the same level of theory to investigate the dependence on the substitution positions of phenyl groups.

Solid-Phase Hybridization Assay for Detection of Mutated Cancer DNA by Fluorescence

We report a straightforward protocol for the detection of mutated DNA extracted from cancer cells. The assay combines a step-wise solid-phase hybridization and a readout by fluorescence emission. We detect a single-nucleotide polymorphism in two human oncogenes, BRAF and EGFR, and reach a limit of the detection of 300 pM by conventional fluorometry. The protocol described herein may be used as a foundation for development of automatic optimized assays capable for detection of mutant DNA and RNA in vitro and in cells.

A self-delivery DNA nanoprobe for reliable microRNA imaging in live cells by aggregation induced red-shift-emission

A Y-shape and pyrene-modified DNA self-assembly is developed to sensitively and specifically detect microRNA through a pyrene excimer–monomer switch.

Diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide: Isolation and properties

Recently, a new type of nucleic acid analogues with modified phosphate group, namely, phosphoryl guanidine oligonucleotides, has been described. In the present work, we assess the difference between diastereomers of a mono-substituted phosphoryl guanidine oligonucleotide and analyze their resistance to nuclease digestion. Individual diastereomers ('fast' and 'slow') of a trideoxynucleotide d (TpCp*A) were isolated by reverse-phase HPLC. Snake venom phosphodiesterase digestion showed that the native trideoxynucleotide was fully degraded after 30 min, whereas both 'fast' and 'slow' diastereomers of d (TpCp*A) were not completely digested even after 7 days. UV and CD spectra revealed similarities in the structure of the diastereomers. Structural analysis by 1D and 2D NMR spectroscopy also uncovered significant similarity in the properties of Rp and Sp diastereomers. Structural analysis of nuclear Overhauser effect spectroscopy (NOESY) data and restrained molecular dynamics methods showed very flexible single-stranded oligonucleotide structures. Detailed computational analysis of restraint penalty energies via restrained molecular dynamics simulations with the 2D NMR interproton distance data allowed us to conclude that most likely, the 'fast' isomer is the Sp diastereomer, and the 'slow' isomer is the Rp diastereomer.

Interaction between 1-pyrenesulfonic acid and albumin: Moving inside the protein

Due to the high sensitivity to alterations in microenvironment polarity of macromolecules, pyrene and its derivatives have long been applied in biosciences. Human serum albumin (HSA), besides its numerous physiological functions, is the main responsible by transport of endogenous and exogenous compounds in the circulatory system. Here, a comprehensive study was carry out to understand the interaction between HSA and the pyrene derivative 1-pyrenesulfonic acid (PMS), which showed a singular behaviour when bound to this protein. The complexation of PMS with HSA was studied by steady state, time-resolved and anisotropy fluorescence, induction of circular dichroism (ICD) and molecular docking. The fluorescence quenching of PMS by HSA was abnormal, being stronger at lower concentration of the quencher. Similar behaviour was obtained by measuring the ICD signal and fluorescence lifetime of PMS complexed in HSA. The displacement of PMS by site-specific drugs showed that this probe occupied both sites, but with higher affinity for site II. The movement of PMS between these main binding sites was responsible by the abnormal effect. Using the holo (PDB: ID 1A06) and apo (PDB: ID 1E7A) HSA structures, the experimental results were corroborated by molecular docking simulation. The abnormal spectroscopic behaviour of PMS is related to its binding in different regions in the protein. The movement of PMS into the protein can be traced by alteration in the spectroscopic signals. These findings bring a new point of view about the use of fluorescence quenching to characterize the interaction between albumin and ligands.

Preparation and characterization of pyrene modified uridine derivatives as potential electron donors in RNA

Charge transfer across double stranded DNA was observed for the first time about 20 years ago, and ever since it has been the subject of a large number of studies. RNA has been hardly investigated in this regard, which not least is due to the lack of suitably functionalized ribonucleotide building blocks to serve as electron sources upon incorporation into oligoribonucleotides. We have synthesized two uridine derivatives carrying pyrene or dimethylaminopyrene linked to C5 of the nucleobase. The key to successful synthesis was the adaptation of Suzuki-Miyaura conditions to the coupling of the pyrene moiety with the ribonucleoside. Final decoration of the pyrenylated nucleosides with standard 5'-O- and 2'-O-protecting groups and subsequent 3'-O-phosphitylation delivered the building blocks for incorporation into RNA. Spectroscopic analysis of the two pyrenylated uridines and of the accordingly modified oligonucleotides showed that in particular the dimethyaminopyrene functionalized nucleoside is a promising candidate as an electron source for RNA charge transport studies.

Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine

Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic building block and then self-assemble into nanomaterials. Of particular note, a recent state-of-the-art research has turned our attention to the amphiphilic DNA organic hybrids including small molecule modified DNA (lipid-DNA, fluorescent molecule-DNA, etc.), DNA block copolymers, and DNA-dendron hybrids. This review focuses mainly on the development of their self-assembly behavior and their potential application in nanomaterial and biomedicine. The potential challenges regarding of the amphiphilic DNA organic hybrids are also briefly discussed, aiming to advance their practical applications in nanoscience and biomedicine.

Single-Labeled Oligonucleotides Showing Fluorescence Changes Upon Hybridization with Target Nucleic Acids

Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.