Cut and Paste for Cancer Treatment: A DNA Nanodevice that Cuts Out an RNA Marker Sequence to Activate a Therapeutic Function

DNA nanotechnology uses oligonucleotide strands to assemble molecular structures capable of performing useful operations. Here, we assembled a multifunctional prototype DNA nanodevice, DOCTR, that recognizes a single nucleotide mutation in a cancer marker RNA. The nanodevice then cuts out a signature sequence and uses it as an activator for a “therapeutic” function, namely, the cleavage of another RNA sequence. The proposed design is a prototype for a gene therapy DNA machine that cleaves a housekeeping gene only in the presence of a cancer-causing point mutation and suppresses cancer cells exclusively with minimal side effects to normal cells.     

Target‐Selective Fluorescence Imaging and Photocytotoxicity against H2O2 High‐Expressing Cancer Cells Using a Photoactivatable Theranostic Agent

A purpose‐designed and synthesized H₂O₂‐reactive and photoactivatable theranostic agent 1 consisting of 1) an arylboronic acid moiety, 2) pro‐fluorophore moiety, and 3) photoactivatable moiety (photosensitizer), selectively and effectively reacted with H₂O₂ while simultaneously releasing resorufin for fluorescence detection under neutral aqueous conditions. In addition, 1 was cell‐permeable, and exhibited effective photocytotoxicity against fluorescently visualized cells only upon photoirradiation. The results also showed that 1 produced a selective fluorescence response to H₂O₂, even in living cultured cells.     

Spectrometry: Spectrofluorimetric Study of Benzo[a]Quinolizidines as Potential Fluorescent Probes for DNA

Abstract

The interaction between DNA and several benzo[a]quinolizidines, including emetine and four synthetic benzo[a]quinolizidine derivatives, has been studied using spectrophotometric and spectrofluorimetric techniques. An appreciable decrease in molar absorptivity at the maxima at λ = 230 nm and λ = 280 nm is observed when increasing DNA concentrations (10 mg/ml-100 mg/ml) are added to aqueous buffered solutions (pH = 7) of the benzo[a]quinolizidine derivatives. These compounds exhibit native fluorescence at 315 nm (λex = 285 nm), which is quenched by increasing amounts of DNA. The interaction between DNA and benzo[a]quinolizidines was confirmed by viscosimetry. Increases between 1.9% and 10.8% in the reduced specific viscosity (n/no) of DNA solutions were observed due to the presence of the benzo[a]quinolizidines studied.     

Electron-Rich EDOT Linkers in Tetracationic bis-Triarylborane Chromophores: Influence on Water Stability,Biomacromolecule Sensing,and Photoinduced Cytotoxicity

Three novel tetracationic bis-triarylboranes with 3,4-ethylenedioxythiophene (EDOT) linkers, and their neutral precursors, showed significant red-shifted absorption and emission compared to their thiophene-containing analogues, with one of the EDOT-derivatives emitting in the NIR region. Only the EDOT-linked trixylylborane tetracation was stable in aqueous solution, indicating that direct attachment of a thiophene or even 3-methylthiophene to the boron atom is insufficient to provide hydrolytic stability in aqueous solution. Further comparative analysis of the EDOT-linked trixylylborane tetracation and its bis-thiophene analogue revealed efficient photo-induced singlet oxygen production, with the consequent biological implications. Thus, both analogues bind strongly to ds-DNA and BSA, very efficiently enter living human cells, accumulate in several different cytoplasmic organelles with no toxic effect but, under intense visible light irradiation, they exhibit almost instantaneous and very strong cytotoxic effects, presumably attributed to singlet oxygen production. Thus, both compounds are intriguing theranostic agents, whose intracellular and probably intra-tissue location can be monitored by strong fluorescence, allowing switching on of the strong bioactivity by well-focused visible light.     

Engineered rHDL Nanoparticles as a Suitable Platform for Theranostic Applications

Reconstituted high-density lipoproteins (rHDLs) can transport and specifically release drugs and imaging agents, mediated by the Scavenger Receptor Type B1 (SR-B1) present in a wide variety of tumor cells, providing convenient platforms for developing theranostic systems. Usually, phospholipids or Apo-A1 lipoproteins on the particle surfaces are the motifs used to conjugate molecules for the multifunctional purposes of the rHDL nanoparticles. Cholesterol has been less addressed as a region to bind molecules or functional groups to the rHDL surface. To maximize the efficacy and improve the radiolabeling of rHDL theranostic systems, we synthesized compounds with bifunctional agents covalently linked to cholesterol. This strategy means that the radionuclide was bound to the surface, while the therapeutic agent was encapsulated in the lipophilic core. In this research, HYNIC-S-(CH₂)₃-S-Cholesterol and DOTA-benzene-p-SC-NH-(CH₂)₂-NH-Cholesterol derivatives were synthesized to prepare nanoparticles (NPs) of HYNIC-rHDL and DOTA-rHDL, which can subsequently be linked to radionuclides for SPECT/PET imaging or targeted radiotherapy. HYNIC is used to complexing ^99mTc and DOTA for labeling molecules with ^{111, 113m}In, ^{67, 68}Ga, ¹⁷⁷Lu, ¹⁶¹Tb, ²²⁵Ac, and ⁶⁴Cu, among others. In vitro studies showed that the NPs of HYNIC-rHDL and DOTA-rHDL maintain specific recognition by SR-B1 and the ability to internalize and release, in the cytosol of cancer cells, the molecules carried in their core. The biodistribution in mice showed a similar behavior between rHDL (without surface modification) and HYNIC-rHDL, while DOTA-rHDL exhibited a different biodistribution pattern due to the significant reduction in the lipophilicity of the modified cholesterol molecule. Both systems demonstrated characteristics for the development of suitable theranostic platforms for personalized cancer treatment.     

A Maltol-Containing Ruthenium Polypyridyl Complex as a Potential Anticancer Agent

Cancer is one of the main causes of death worldwide. Chemotherapy, despite its severe side effects, is to date one of the leading strategies against cancer. Metal-based drugs present several potential advantages when compared to organic compounds and they have gained trust from the scientific community after the approval on the market of the drug cisplatin. Recently, we reported the ruthenium complex ([Ru(DIP)₂(sq)](PF₆) (where DIP is 4,7-diphenyl-1,10-phenantroline and sq is semiquinonate) with a remarkable potential as chemotherapeutic agent against cancer, both in vitro and in vivo. In this work, we analyse a structurally similar compound, namely [Ru(DIP)₂(mal)](PF₆), carrying the flavour-enhancing agent approved by the FDA, maltol (mal). To possess an FDA approved ligand is crucial for a complex, whose mechanism of action might include ligand exchange. Herein, we describe the synthesis and characterisation of [Ru(DIP)₂(mal)](PF₆), its stability in solutions and under conditions that resemble the physiological ones, and its in-depth biological investigation. Cytotoxicity tests on different cell lines in 2D model and on HeLa MultiCellular Tumour Spheroids (MCTS) demonstrated that our compound has higher activity than cisplatin, inspiring further tests. [Ru(DIP)₂(mal)](PF₆) was efficiently internalised by HeLa cells through a passive transport mechanism and severely affected the mitochondrial metabolism.     

Asymmetric Distyrylpyridinium Dyes as Red‐Emitting Fluorescent Probes for Quadruplex DNA

The interactions of three cationic distyryl dyes, namely 2,4‐bis(4‐dimethylaminostyryl)‐1‐methylpyridinium ( 1 a ), its derivative with a quaternary aminoalkyl chain ( 1 b ), and the symmetric 2,6‐bis(4‐dimethylaminostyryl)‐1‐methylpyridinium ( 2 a ), with several quadruplex and duplex nucleic acids were studied with the aim to establish the influence of the geometry of the dyes on their DNA‐binding and DNA‐probing properties. The results from spectrofluorimetric titrations and thermal denaturation experiments provide evidence that asymmetric (2,4‐disubstituted) dyes 1 a and 1 b bind to quadruplex DNA structures with a near‐micromolar affinity and a fair selectivity with respect to double‐stranded (ds) DNA [K_a(G4)/K_a(ds)=2.5–8.4]. At the same time, the fluorescence of both dyes is selectively increased in the presence of quadruplex DNAs (more than 80–100‐fold in the case of human telomeric quadruplex), even in the presence of an excess of competing double‐stranded DNA. This optical selectivity allows these dyes to be used as quadruplex‐DNA‐selective probes in solution and stains in polyacrylamide gels. In contrast, the symmetric analogue 2 a displays a strong binding preference for double‐stranded DNA [K_a(ds)/K_a(G4)=40–100), presumably due to binding in the minor groove. In addition, 2 a is not able to discriminate between quadruplex and duplex DNA, as its fluorescence is increased equally well (20–50‐fold) in the presence of both structures. This study emphasizes and rationalizes the strong impact of subtle structural variations on both DNA‐recognition properties and fluorimetric response of organic dyes.     

DNA-Targeting RuII-Polypyridyl Complex with a Long-Lived Intraligand Excited State as a Potential Photodynamic Therapy Agent

Subtle ligand modifications on Ru^II-polypyridyl complexes may result in different excited-state characteristics, which provides the opportunity to tune their photo-physicochemical properties and subsequently change their biological functions. Here, a DNA-targeting Ru^II-polypyridyl complex (named Ru1 ) with highly photosensitizing ³IL (intraligand) excited state was designed based on a classical DNA-intercalator [Ru(bpy)₂(dppz)] ⋅ 2 PF₆ by incorporation of the dppz (dipyrido[3,2-a:2′,3′-c]phenazine) ligand tethered with a pyrenyl group, which has four orders of magnitude higher potency than the model complex [Ru(bpy)₂(dppz)] ⋅ 2 PF₆ upon light irradiation. This study provides a facile strategy for the design of organelle-targeting Ru^II-polypyridyl complexes with dramatically improved photobiological activity.     

Conjugated Polyelectrolytes as New Platforms for Drug Screening

In recent years, conjugated polyelectrolytes (CPEs) have attracted increasing attention for their applications in highly sensitive biosensors by taking advantage of their unique optical amplification properties. In comparison to previous applications tailored for highly sensitive biomacromolecule detection, this Focus Review highlights recent research efforts in the development of water‐soluble CPEs as a new class of optical platforms for the screening of potential drugs. Three types of biological targets for the search of small‐molecule active drugs are described: nucleic acids, enzymes, and RNA–protein complexes. Future research directions for drug screening based on CPEs are also presented.     

Twin probes as a novel tool for the detection of single-nucleotide polymorphisms

Single-nucleotide polymorphisms (SNPs) are the most common form of DNA sequence variation. There is a strong interest from both academy and industry to develop rapid, sensitive and cost effective methods for SNP detection. Here we report a novel structural concept for DNA detection based on fluorescence dequenching upon hybridization. The so-called "twin probe" consists of a central fluorene derivative as fluorophore to which two identical oligonucleotides are covalently attached. This probe architecture is applied in homogeneous hybridization assays with subsequent fluorescence spectroscopic analysis. The bioorganic hybrid structure is well suited for sequence specific DNA detection and even SNPs are identified with high efficiency. Additionally, the photophysical properties of the twin probe were investigated. The covalent attachment of two single stranded oligonucleotides leads to strong quenching of the central fluorescence dye induced by the nucleobases. The twin probe is characterized by supramolecular aggregate formation accompanied by red-shifted emission and broad fluorescence spectra.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

A 1,3‐Indandione‐Functionalized Tetraphenylethene: Aggregation‐Induced Emission,Solvatochromism, Mechanochromism,and Potential Application as a Multiresponsive Fluorescent Probe

A tetraphenylethene (TPE) derivative substituted with the electron‐acceptor 1,3‐indandione (IND) group was designed and prepared. The targeted IND‐TPE reserves the intrinsic aggregation‐induced emission (AIE) property of the TPE moiety. Meanwhile, owing to the decorated IND moiety, IND‐TPE demonstrates intramolecular charge‐transfer process and pronounced solvatochromic behavior. When the solvent is changed from apolar toluene to highly polar acetonitrile, the emission peak redshifts from 543 to 597 nm. IND‐TPE solid samples show an evident mechanochromic process. Grinding of the as‐prepared powder sample induces a redshift of emission from green (peak at 515 nm) to orange (peak at 570 nm). The mechanochromic process is reversible in multiple grinding–thermal annealing and grinding–solvent‐fuming cycles, and the emission of the solid sample switches between orange (ground) and yellow (thermal/solvent‐fuming‐treated) colors. The mechanochromism is ascribed to the phase transition between amorphous and crystalline states. IND‐TPE undergoes a hydrolysis reaction in basic aqueous solution, thus the red‐orange emission can be quenched by OH^? or other species that can induce the generation of sufficient OH^?. Accordingly, IND‐TPE has been used to discriminatively detect arginine and lysine from other amino acids, due to their basic nature. The experimental data are satisfactory. Moreover, the hydrolyzation product of IND‐TPE is weakly emissive in the resultant mixture but becomes highly blue‐emissive after the illumination for a period by UV light. Thus IND‐TPE can be used as a dual‐responsive fluorescent probe, which may extend the application of TPE‐based molecular probes in chemical and biological categories.     

Deciphering the Chemical Basis of Fluorescence of a Selenium-Labeled Uracil Probe when Bound at the Bacterial Ribosomal A-Site

We unveil in this work the main factors that govern the turn-on/off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. Whereas the constraint into an “in-plane” conformation of the two rings of the fluorophore is the main driver for the observed turn-on fluorescence emission in the presence of the antibiotic paromomycin, the electrostatics of the environment plays a minor role during the emission process. Our computational strategy clearly indicates that, in the absence of paromomycin, the probe prefers conformations that show a dark S₁ electronic state with participation of nπ* electronic transition contributions between the selenium atom and the π-system of the uracil moiety.