Fluorescent hybridization probes for nucleic acid detection

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.     

Fluorescent probes for detection and bioimaging of leucine aminopeptidase

Leucine aminopeptidase (LAP) is one of important proteolytic enzymes and closely related with pathogenesis of cancer and liver injury. Determination of LAP activity in serum is used clinically for liver disorder diagnosis. The level of expressed LAP is very low in normal cells, but overexpressed in tumors and liver diseases, especially drug-induced hepatitis. LAP has become a predictive biomarker for many cancers and diverse physiological processes. Therefore, in situ dynamic monitoring and identifying intracellular LAP is imperative for LAP-related disease diagnosis. This review focuses on LAP-specific fluorescence imaging probes for the detection and tracking of intracellular LAP actively in vitro and in vivo. The progress suggests that fluorescence imaging is a vital and rapidly growing technology for early diagnosis of tumors.     

Fluorescent chemodosimeter for selective detection of cyanide in water

A coumarin-based fluorescent chemodosimeter with a salicylaldehyde functionality as a binding site has been developed for selective detection of cyanide anions over other anions in water at biological pH.     

Fluorescent peptide sensor for the selective detection of Cu

A new fluorescent peptidyl chemosensor for Cu²⁺ ions with fluorescence resonance energy transfer (FRET) capabilities has been synthesized via Fmoc solid-phase peptide synthesis. The metal chelating unit, which is flanked by the fluorophores tryptophan (donor) and dansyl chloride (acceptor), consists of the amino acids glycine and aspartic acid (Gly-Gly-Asp-Gly-Gly-Asp-Gly-Gly-Asp-Gly-Gly-Asp-Gly-Gly). Coordination of the Cu²⁺ ions to the metal chelating unit results in fluorescent quenching of both the donor and acceptor fluorophores. Although it was determined that Cu²⁺ binding causes no change in FRET efficiency, emission and Cu²⁺-induced quenching of the acceptor dye can be used to monitor the concentration of the copper ions, with a detection limit of 32 μg L⁻¹. The sensor also demonstrated sensitivity, reversibility and selectivity towards Cu²⁺ in a transition metal matrix at pH 7.0.     

DNA detection method based on the two-dimensional aggregation and selective desorption of nanoparticle probes

A label-free two-dimensional colorimetric DNA sensor is reported. This sensor is based on the 2D aggregation of oligonucleotide-modified gold nanoparticle probes induced by the molecular hybridization of single-stranded oligonucleotide probes and their complementary single-stranded DNA targets. To detect the aggregation, we have developed a new detection method based on the selective desorption of nonaggregated nanoparticles. We will show here that this detection method is highly specific and allows the quantification of the DNA targets.     

Fluorescent and luminescent probes for detection of reactive oxygen and nitrogen species

Oxidative and nitrosative stress induced by ROS/RNS play crucial roles in a wide range of physiological processes and are also implicated in various diseases, including cancer and neurodegenerative disorders. Sensitive and selective methods for the detection of ROS/RNS based on fluorescent and luminescent probes are of great use in monitoring the in vivo production of these species and elucidating their biological functions. This critical review highlights recent advances that have been made in the development of fluorescent and luminescent probes employed to monitor various ROS/RNS (132 references).     

Fluorescent chemosensor based-on naphthol-quinoline for selective detection of aluminum ions

In this study, an assay to quantify the presence of aluminum ions with a receptor containing naphthol and quinoline moieties was developed using a turn-on fluorescence enhancement approach. Upon treatment with aluminum ions, the fluorescence of the receptor was enhanced at 510 nm due to the formation of a complex between the ligand and aluminum ions at room temperature. As the concentration of Al³⁺ was increased, the fluorescence gradually increased. Other metal ions, such as K⁺, Ag⁺, Ca²⁺, Mg²⁺, Zn²⁺, Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, Cd²⁺, Cr³⁺, Fe³⁺, In³⁺, had no significant effect on the fluorescence.     

Fluorescent probes for cellular assays

A fluorescent probe is a fluorophore designed to localize within a specific region of a biological specimen or to respond to a specific stimulus. Fluorescent probes have been used for nearly a century to study cellular processes due to their exquisite sensitivity and selectivity. Fluorescent probes have also gained in popularity as safety and environmental concerns over the use of radioactive probes have grown. At the same time, cellular assays are being more widely used now than ever before. This review will give a broad overview of types of fluorescent probes, types of fluorescent assays, and their application in cellular assays for a number of pharmaceutically relevant target classes.     

Carbon dots-based fluorescent probes for sensitive and selective detection of iodide

We report on a simple method for the determination of iodide in aqueous solution by exploiting the fluorescence enhancement that is observed if the complex formed between carbon dots and mercury ion is exposed to iodide. Fluorescent carbon dots (C-dots) were treated with Hg(II) ion which causes quenching of the emission of the C-dots. On addition of iodide, the Hg(II) ions are removed from the complex due to the strong interaction between Hg(II) and iodide. This causes the fluorescence to be restored and enables iodide to be determined in the 0.5 to 20 μM concentration range and with a detection limit of ~430 nM. The test is highly selective for iodide (over common other anions) and was used for the determination of iodide in urine.

Fluorescent molecular probes for the detection of chemical warfare agents and their mimics

Owing to their direct toxic effects on human beings, animals, and plants, chemical warfare agents (CWAs) and their mimics have become widespread in chemical warfare and agriculture. The considerable concerns about their entry into biological systems and the residues in environment stimulate the development of rapid and sensitive methods for the detection and analysis of this family of compounds. In the progress of sensitive, selective, and fast responsive detection, fluorescent molecular probes have been widely used in the detection of CWAs in recent years. Here the recent reports on the design of fluorescent molecular probes and their advantages in the detection of CWAs were reviewed. Furthermore, the extensive interests accelerate the development of novel fluorescent molecular probes and detection techniques in this field.     

Fluorescent probes for recognition of ATP

Adenosine 5'-triphosphate (ATP) plays an important role in various physiological activities and pathological processes in living cells. Consequently, a large number of fl uorescent sensors for detecting ATP have developed in recent years. In this review, we summarized these fl uorescent sensors, where these sensors were divided into fi ve typed ones according to the structure of probes used.     

Fluorescent probes for the stabilization and detection of G-quadruplexes and their prospective applications

This review article discusses the non-covalent interaction of various probe molecules of different structural diversity with G-quadruplex forming Guanine rich DNA sequences, revealing remarkable stimuli responsive fluorescence changes which are appropriate for sensing and other technological applications. Tailor-made probes having quadruplex inducing/stabilizing attachments of well-known dye molecules and its derivatives such as, coumarins, cyanines, thiazole orange, pyrazines, thioflavin T, triphenylmethane, tetraphenylethene, dimethylindole red etc have been employed. These probes express their modulations due to the binding to the topologically distinct G-quadruplexes through structural rigidization, aggregation propensity, binding strengths, tunability and other competitive interactions and are viewed as remarkable changes particularly in their fluorescence features. Based on this concept, several studies have reported the development of label free fluorescence sensor for the selective detection of topology specific G-quadruplexes, therapeutic, early diagnostic of cancer, cation-sensing, trace level detection of an anti-cancer drugs etc. have been accomplished. In vivo imaging is also achieved using a cholesterol attached G-quadruplex forming oligonucleotide probe labelled with specific dyes. Since the fine details of the topological information and control mechanisms of G-quadruplex forming sequences are very much essential for targeting and tuning several important biological processes relevant to cancer proliferation and developing stimuli responsive sensors, it is sure that many more contributions in this field will emerge in the coming years.     

New sensitive fluorophores for selective DNA detection

4,7-Disubstituted benzothiadiazoles containing 1-arylethynyl and 4-methoxyphenyl groups are selective photoluminescent "light up" probes to duplex DNA with unprecedented sensibility in both spectrophotometric and spectrofluorimetric measurements.     

Fluorescent carbohydrate probes for cell lectins

Fluorescein labeled carbohydrate (Glyc) probes were synthesized as analytical tools for the study of cellular lectins, i.e. SiaLe(x)-PAA-flu, Sia2-PAA-flu, GlcNAc2-PAA-flu, LacNAc-PAA-flu and a number of similar ones, with PAA a soluble polyacrylamide carrier. The binding of SiaLe(x)-PAA-flu was assessed using CHO cells transfected with E-selectin, and the binding of Sia2-PAA-flu was assessed by COS cells transfected with siglec-9. In flow cytometry assays, the fluorescein probes demonstrated a specific binding to the lectin-transfected cells that was inhibited by unlabeled carbohydrate ligands. The intense binding of SiaLe(x)-PAA-3H to the E-selectin transfected cells and the lack of binding to both native and permeabilized control cells lead to the conclusion that the polyacrylamide carrier itself and the spacer arm connecting the carbohydrate moiety with PAA did not contribute anymore to the binding. Tumors were obtained from nude mice by injection of CHO E-selectin or mock transfected cells. The fluorescent SiaLe(x)-PAA-flu probe could bind to the tumor sections from E-selectin positive CHO cells, but not from the control ones. Thus, these probes can be used to reveal specifically the carbohydrate binding sites on cells in culture as well as cells in tissue sections. The use of the confocal spectral imaging technique with Glyc-PAA-flu probes offered the unique possibility to detect lectins in different cells, even when the level of lectin expression was rather low. The confocal mode of spectrum recording provided an analysis of the probe localization with 3D submicron resolution. The spectral analysis (as a constituent part of the confocal spectral imaging technique) enabled interfering signals of the probe and intrinsic cellular fluorescence to be accurately separated, the distribution of the probe to be revealed and its local concentration to be measured.     

Fluorescent small organic probes for biosensing

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems. With this perspective we highlight sensing mechanisms including Förster resonance energy transfer (FRET), intramolecular charge transfer (ICT), photoinduced electron transfer (PeT), excited state intramolecular proton transfer (ESIPT), aggregation induced emission (AIE) and multiple modality fluorescence approaches including dual/triple sensing mechanisms (DSM or TSM). Throughout the perspective we highlight the remaining challenges and suggest potential directions for development towards improved small-molecule fluorescent probes suitable for biosensing.

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems.     

Molecular beacon probes for the detection of cisplatin-induced DNA damage

Cisplatin (cis-diamminedichloroplatinum(II)) causes crosslinking of DNA at AG and GG sites in cellular DNA, inhibiting replication, and making it a useful anti-cancer drug. Several techniques have been used previously to detect nucleic acid damage but most of these tools are labour-intensive, time-consuming, and/or expensive. Here, we describe a sensitive, robust, and quantitative tool for detecting cisplatin-induced DNA damage by using fluorescent molecular beacon probes (MB). Our results show a decrease of fluorescence in the presence of cisplatin-induced DNA damage, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The decrease in fluorescence upon damage scales with the number of AG and GG sites, indicating the ability of MB to quantitatively detect DNA damage by cisplatin.     

Polymer-DNA hybrids as electrochemical probes for the detection of DNA

The syntheses of several norbornene block copolymers containing oligonucleotide and ferrocenyl side chains and their use in the electrochemical detection of DNA are described. Two kinds of DNA-containing block copolymers with either ferrocenyl or dibromoferrocenyl groups were prepared via ring-opening metathesis polymerization (ROMP). Based on these two distinct ferrocene derivatives, a triblock copolymer labeling strategy was developed. With this strategy, the identity of DNA target can be determined by the E1/2s of the ferrocenyl moieties and the ratio of peak currents. These polymers exhibit predictable and tailorable electrochemical properties, high DNA duplex stability, and unusually sharp melting transitions, which are highly desirable characteristics for DNA detection applications. Significantly, single-base mismatches could be easily detected using two distinct block copolymers as dual-channel detection probes in an electrochemical DNA detection format.