Luminescent probes for ultrasensitive detection of nucleic acids

Imaging Giant Vesicle Membrane Domains with a Luminescent Europium Tetracycline Complex

Microdomains in lipid bilayer membranes are routinely imaged using organic fluorophores that preferentially partition into one of the lipid phases, resulting in fluorescence contrast. Here, we show that membrane microdomains in giant unilamellar vesicles (GUVs) can be visualized with europium luminescence using a complex of europium III (Eu3+) and tetracycline (EuTc). EuTc is unlike typical organic lipid probes in that it is a coordination complex with a unique excitation/emission wavelength combination (396/617 nm), a very large Stokes shift (221 nm), and a very narrow emission bandwidth (8 nm). The probe preferentially interacts with liquid disordered domains in GUVs, which results in intensity contrast across the surface of phase-separated GUVs. Interestingly, EuTc also alters GM1 ganglioside partitioning. GM1 typically partitions into liquid ordered domains, but after labeling phase-separated GUVs with EuTc, cholera toxin B-subunit (CTxB), which binds GM1, labels liquid disordered domains. We also demonstrate that EuTc, but not free Eu3+ or Tc, significantly reduces lipid diffusion coefficients. Finally, we show that EuTc can be used to label cellular membranes similar to a traditional membrane probe. EuTc may find utility as a membrane imaging probe where its large Stokes shift and sharp emission band would enable multicolor imaging.

Circularly polarized lanthanide luminescence for advanced security inks

Authenticating products and documents with security inks is vital to global commerce, security and health. Lanthanide complexes are widely used in luminescent security inks owing to their unique and robust photophysical properties. Lanthanide complexes can also be engineered to undergo circularly polarized luminescence (CPL), which encodes chiral molecular fingerprints in luminescence spectra that cannot be decoded by conventional optical measurements. However, chiral CPL signals have not yet been exploited as an extra security layer in advanced security inks. This Review introduces CPL and related concepts that are necessary to appreciate the challenges and potential of lanthanide-based, CPL-active security inks. We describe recent advances in CPL analysis and read-out technologies that have expedited CPL-active security ink applications. Further, we provide a systematic meta-analysis of strongly CPL-active Euⁱⁱⁱ, Tbⁱⁱⁱ, Smⁱⁱⁱ, Ybⁱⁱⁱ, Cmⁱⁱⁱ, Dyⁱⁱⁱ and Crⁱⁱⁱ complexes, discussing the suitability of their photophysical properties and highlighting promising candidates. We conclude by providing key recommendations for the development and advancement of the field.

Quinolone Complexes with Lanthanide Ions: An Insight into their Analytical Applications and Biological Activity

Quinolones comprise a series of synthetic bactericidal agents with a broad spectrum of activity and good bioavailability. An important feature of these molecules is their capacity to bind metal ions in complexes with relevant biological and analytical applications. Interestingly, lanthanide ions possess extremely attractive properties that result from the behavior of the internal 4f electrons, behavior which is not lost upon ionization, nor after coordination. Subsequently, a more detailed discussion about metal complexes of quinolones with lanthanide ions in terms of chemical and biological properties is made. These complexes present a series of characteristics, such as narrow and highly structured emission bands; large gaps between absorption and emission wavelengths (Stokes shifts); and long excited-state lifetimes, which render them suitable for highly sensitive and selective analytical methods of quantitation. Moreover, quinolones have been widely prescribed in both human and animal treatments, which has led to an increase in their impact on the environment, and therefore to a growing interest in the development of new methods for their quantitative determination. Therefore, analytical applications for the quantitative determination of quinolones, lanthanide and miscellaneous ions and nucleic acids, along with other applications, are reviewed here.

Coordination of mycotoxins with lanthanides in luminescent complexes

The ability of several chelating mycotoxins to form coordination complexes with the lanthanide metals europium and terbium was explored. The mycotoxins examined included ochratoxin A, citrinin, cyclopiazonic acid (CPA), kojic acid, and tenuazonic acid (TeA). Of these compounds, TeA and CPA resulted in the greatest luminescence. Parameters influencing luminescence of TeA were investigated further. These included the type of lanthanide and its concentration, certain environmental factors, and the effect of competing metal cations. Of the two lanthanide metals, the terbium coordination complex (TeA-Tb³⁺) showed greater luminescence relative to the europium complex (TeA-Eu³⁺). The effects of solvent type, water content, and pH on the TeA-Tb³⁺ system suggested that optimal conditions for luminescence were in 90% methanol with 10% aqueous buffer at pH 3. In competitive assays, the luminescence of the TeA-Tb³⁺ complex decreased as the concentration of competing metal cations increased. Among the cations tested, Cu²⁺ was the best inhibitor followed by Al³⁺, Au³⁺, Fe³⁺, Co²⁺, Mn²⁺, Mg²⁺, and Ca²⁺. Two cations, Na⁺ and K⁺, showed no significant inhibition. This is the first report to describe the coordination of the metal-chelating mycotoxin TeA with lanthanides and the ability of TeA to serve as an "antenna" for the efficient transfer of energy to the lanthanide with resulting luminescence. Understanding the ability of mycotoxins such as TeA to chelate metals provides insight into how they exert their toxic effects.

Efficient route to pre-organized and linear polyaminopolycarboxylates: Cy-TTHA, Cy-DTPA and mono/di- reactive, tert-butyl protected TTHA/Cy-TTHA

Pre-organized polyaminopolycarboxylate chelators Cy-TTHA and Cy-DTPA were synthesized via modular five-step syntheses from commercially available starting materials in ~ 62% and 47% overall yields, respectively. Furthermore, strategies are reported for the efficient preparation of mono- and di-reactive, tert-butyl-protected TTHA/Cy-TTHA to selectively functionalize central chelators' carboxylic acids.

Brightly Luminescent and Kinetically Inert Lanthanide Bioprobes Based on Linear and Preorganized Chelators

The synthesis, photophysical properties, and kinetic stability of a series of water-soluble, highly emissive Tb(III) and Eu(III) complexes featuring triethylenetetraamine hexaacetic acid (TTHA) and cyclohexyl triethylenetetraamine hexaacetic acid (cyTTHA) chelator scaffolds and carbostyril sensitizers are reported. The unique and modular design of the chelators gives rise to striking quantum yields of emission in aqueous solutions (up to 54%) as well as the characteristic lanthanides' photophysical properties (long excited-state lifetimes, large effective Stokes shifts, and narrow emission peaks). Furthermore, the preorganized chelators (L3, L4, and L6) bind metal within minutes at ambient temperature yet exhibit substantial resistance to transchelation in the presence of a challenge solution (EDTA, 1 mM). Moreover, the Eu(III) complex of L4 remains stably luminescent in HeLa cells over hours, demonstrating the suitability of these compounds for live-cell imaging applications. Representative chelators suitable for derivatization and protein bioconjugation were also prepared that were functionalized with clickable azide and alkyne moieties, biotin, and trimethoprim (TMP). With exceptional long-wavelength brightness, enhanced kinetic inertness, and an adaptable synthetic route, the reported lanthanide complexes are promising probes and labels for time-gated bioanalysis, biosensing, and optical microscopy.

Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders

Fluorescence in situ hybridization coupled with flow cytometry (FISH-Flow) is a highly quantitative, high-throughput platform allowing precise quantification of total mRNA transcripts in single cells. In undiagnosed infections posing a significant health burden worldwide, such as latent tuberculosis or asymptomatic recurrent malaria, an important challenge is to develop accurate diagnostic tools. Antigen-specific T cells create a persistent memory to pathogens, making them useful for diagnosis of infection. Stimulation of memory response initiates T-cell transitions between functional states. Numerous studies have shown that changes in protein levels lag real-time T-cell transitions. However, analysis at the single-cell transcriptional level can determine the differences. FISH-Flow is a powerful tool with which to study the functional states of T-cell subsets and to identify the gene expression profiles of antigen-specific T cells during disease progression. Advances in instrumentation, fluorophores, and FISH methodologies will broaden and deepen the use of FISH-Flow, changing the immunological field by allowing determination of functional immune signatures at the mRNA level and the development of new diagnostic tools.

Luminescent lanthanide nanomaterials: an emerging tool for theranostic applications

Lanthanide materials have been gaining popularity for use in various theranostic applications, primarily due to their unique optical properties such as narrow emission bands, multiple emission wavelengths, emission tunability, long fluorescence lifetime and large Stokes shift. Apart from these, some lanthanide materials also exhibit magnetic and light-up conversion properties. Such nanomaterials have been used for a wide range of applications ranging from detection of biomarkers, in vitro and in vivo imaging to therapeutic applications. Recently, combined modalities of lanthanide nanomaterials for simultaneous detection/imaging and delivery of therapeutic agents (termed ‘theranostics’) have been explored. The various advantages and disadvantages of using lanthanide nanomaterials as theranostic agents and potential areas for future development have been discussed in this review.

Nanoparticle-based signal generation and amplification in microfluidic devices for bioanalysis

Signal generation and amplification based on nanomaterials and microfluidic techniques have both attracted considerable attention separately due to the demands for ultrasensitive and high-throughput detection of biomolecules. This article reviews the latest development of signal amplification strategies based on nanoparticles for bioanalysis and their integration and applications in microfluidic systems. The applications of nanoparticles in bioanalysis were categorized based on the different approaches of signal amplification, and the microfluidic techniques were summarized based on cell analysis and biomolecule detection with a focus on the integration of nanoparticle-based amplification in microfluidic devices for ultrasensitive bioanalysis. The advantages and limitations of the combination of nanoparticles-based amplification with microfluidic techniques were evaluated, and the possible developments for future research were discussed.

Long-lived luminogenic probe for detection of RNA in a crude solution of living bacterial cells

A pre-type sensitizer for a lanthanide complex on an oligonucleotide was successfully converted to a perfect final structure in a target DNA/RNA-templated reaction, without any chemical reagent or enzyme, under neutral conditions. The final form of the lanthanide-oligonucleotide provided a long-lived luminescence signal, appropriate for time-gated luminescence analysis and signal amplification. Target DNA/RNA-assisted time-gated luminescence analysis is a powerful tool for elimination of autofluorescence and detection of target RNA in living bacterial cells.

Tb(3+)-tRNA for LRET studies of protein synthesis

When suitably labeled bulk tRNAs are transfected into cells they give rise to FRET (fluorescence resonance energy transfer) signals via binding to ribosomes that provide a measure of total protein synthesis. Application of this approach to monitoring rates of specific protein synthesis requires achieving a very high signal-to-noise ratio. Such high ratios may be attainable using LRET (luminescence resonance energy transfer) in place of FRET. Lanthanide complexes containing an antenna chromophore are excellent LRET donors. Here we describe the synthesis of a Phe-tRNA(Phe) labeled with a Tb(3+) complex, denoted Tb(3+)-Phe-tRNA(Phe) that, notwithstanding the bulkiness of the Tb(3+) complex, is active in protein synthesis.

New quinolone-based thiol-reactive lanthanide luminescent probes

Luminescent lanthanide ion complexes are distinguished by unique light emitting properties that enable both highly sensitive detection of lanthanide labels attached to biomolecules and contrast imaging of various micro objects (cells, nanoparticles, etc.). Previously, we synthesized amine-reactive cs124-based luminescent lanthanide chelates with improved brightness and metal retention. Here we report the synthesis of new thiol-reactive derivatives of the same compounds including bromoacetamido-, and maleimido- forms of cs124 and cs124CF₃ fluorophores. Maleimido-compounds displayed exceptional reactivity instantaneously coupling to thiols at physiological conditions at micromolar probes concentrations. Surprisingly, they displayed strong quenching by adjacent maleimido-group, which was completely eliminated after reaction with thiols, thereby enabling their simple detection by monitoring the light emission of the reaction mixture. This reaction can be used for hyper-sensitive determination of biologically important sulphydryl compounds (e.g. glutathione, co-enzyme A, etc.) in time-resolved mode.

Evaluation of triazole-chelated lanthanides as chemically stabile bioimaging agents

Europium (Eu), dysprosium (Dy), samarium (Sm), and terbium (Tb) complexes were prepared using the neutral tridentate chelator 2,6-bis(1-benzyl-1,2,3-triazol-4-yl)pyridine and one equivalent of each lanthanide salt. The physicochemical, aerodynamic, and in vitro cellular properties of each lanthanide metal complex were studied to determine their viability as cell surface fluorescent probes. Each compound was characterized by electrospray ionization mass spectroscopy (ESI-MS), ultraperformance liquid chromatography (UPLC), differential scanning calorimetry (DSC), and thermogravimetic analysis (TGA). Upon excitation at 320 nm each complex displayed characteristic lanthanide-based fluorescence emission in the visible wavelength range with stokes shifts greater than 200 nm. Each complex was found to be chemically stable when exposed to pH range of 1-11 for 72 h and resistant to photobleaching. To simulate pulmonary administration of these fluorophores, the aerodynamic properties of the Eu and Tb complexes were determined using a next generation impactor (NGI). This measurement confirmed that the complexes retain their fluorescence emission properties after nebulization. Cellular cytotoxicity was determined on A-549 lung cancer cell line using methylthiazol tetrazolium (MTT) cytotoxicity assay at 24, 48, and 72 h postexposure to the complexes. The complexes showed a dose and time-dependent effect on the percent viability of the cells.

Simple no-chromatography procedure for amine-reactive Eu3+ luminescent chelates optimal for bioconjugation

Lanthanide ions luminescence has long life time enabling highly sensitive detection in time-gated mode. The synthesis of reactive lanthanide probes for covalent labeling of the objects of interest is cumbersome task due to the large size of the probes, complex multi-step procedures and the presence of sensitive groups, which often prevents introduction of reactive cross-linking functions optimal for conjugation. We suggest simple synthetic protocol for luminescent europium chelates based on serendipitous reaction yielding acylating compounds, whose reactivity is comparable to that of commonly used N-hydroxysuccinimide (NHS) esters. The probes react with proteins at pH 7.0 within several minutes at ambient temperature displaying high coupling efficiency. The resulting conjugates survive electrophoretic separation under denaturing conditions, which makes the labels useful in proteomic studies that rely on high detection sensitivity.

An elegant biosensor molecular beacon probe: challenges and recent solutions

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

Highly bright avidin-based affinity probes carrying multiple lanthanide chelates

Lanthanide ion luminescence has a long lifetime enabling highly sensitive detection in time-gated mode. The sensitivity can be further increased by using multiple luminescent labels attached to a carrier molecule, which can be conjugated to an object of interest. We found that up to 30 lanthanide chelates can be attached to avidin creating highly bright constructs. These constructs with Eu(3+) chelates display synergistic effect that enhance the brightness of heavily modified samples, while the opposite effect was observed for Tb(3+) chelates thereby significantly reducing their light emission. This undesirable quenching of Tb(3+) luminophores was completely suppressed by the introduction of an aromatic spacer between the chelate and the protein attachment site. The estimated detection limit for the conjugates is in the 10(-14)-10(-15) M range. We demonstrated a high sensitivity for the new probes by using them to label living cells of bacterial and mammalian origin.

New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling

A variety of contemporary analytical platforms, utilized in technical and biological applications, take advantage of labeling the objects of interest with fluorescent tracers-compounds that can be easily and sensitively detected. Here we describe the synthesis of new fluorescent quinoline and quinolone compounds, whose light emission can be conveniently tuned by simple structural modifications. Some of these compounds can be used as sensitizers for lanthanide emission in design of highly sensitive luminescent probes. In addition, we also describe simple efficient derivatization reactions that allow introduction of amine- or click-reactive cross-linking groups into the fluorophores. The reactivity of synthesized compounds was confirmed in reactions with low molecular weight nucleophiles, or alkynes, as well as with click-reactive DNA-oligonucleotide containing synthetically introduced alkyne groups. These reactive derivatives can be used for covalent attachment of the fluorophores to various biomolecules of interest including nucleic acids, proteins, living cells and small cellular metabolites. Obtained compounds are characterized using NMR, steady-state fluorescence spectroscopy as well as UV absorption spectroscopy.

Recent trends in molecular beacon design and applications

A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.

Luminescent trimethoprim-polyaminocarboxylate lanthanide complex conjugates for selective protein labeling and time-resolved bioassays

Labeling proteins with long-lifetime emitting lanthanide (III) chelate reporters enables sensitive, time-resolved luminescence bioaffinity assays. Heterodimers of trimethoprim (TMP) covalently linked to various cs124-sensitized, polyaminocarboxylate chelates stably retain lanthanide ions and exhibit quantum yields of europium emission up to 20% in water. A time-resolved, luminescence resonance energy transfer (LRET) assay showed that TMP-polyaminocarboxylates bind to Escherichia coli dihydrofolate reductase (eDHFR) fusion proteins with nanomolar affinity in purified solutions and in bacterial lysates. The ability to selectively impart terbium or europium luminescence to fusion proteins in complex physiological mixtures bypasses the need for specific antibodies and simplifies sample preparation.

Nucleic acid-based fluorescent probes and their analytical potential

It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.

Design of a room-temperature phosphorescence-based molecular beacon for highly sensitive detection of nucleic acids in biological fluids

Ultrasensitive fluorescent analysis or monitoring of significant molecules in complex samples is important for many biological studies, clinical diagnosis, and forensic investigations, the major obstacle for which is the background signals from ubiquitous endogenous fluorescent components of the environments. Herein, a room-temperature phosphorescence (RTP)-based molecular beacon (MB), employing a Eu(3+) complex of chlorosulfonylated tetradentate β-diketone (L) and the quencher BHQ-2, was engineered for highly sensitive detection of DNA sequences in biological fluids. Complexation of Eu(3+) with the ligand L formed a strongly luminescent complex EuL(2). But when EuL(2) and BHQ-2 were labeled to two ends of a DNA molecule with hairpin structure, the luminescence of EuL(2) was quenched by BHQ-2 due to the stem-closed conformation of the beacon. Due to very low background luminescence from the probe molecule, >200-fold signal enhancement was achieved when nanomolar target sequence was introduced. This sensitivity is about 20-fold higher than the level achieved with conventional fluorescence-based molecular beacons. Furthermore, because the Eu(3+) complex has a much longer luminescence lifetime (≈0.8 ms) than that of the background (<10 ns), RTP measurements were used to directly detect as low as 500 pM DNA in cell media quantitatively without any sample pretreatment.

New strategy for label-free and time-resolved luminescent assay of protein: conjugate Eu3+ complex and aptamer-wrapped carbon nanotubes

We report here a carbon nanotube-based approach for label-free and time-resolved luminescent assay of lysozyme (LYS) by engineering an antilysozyme aptamer and luminescent europium(III) (Eu(3+)) complex. The sensing mechanism of the approach is based on the exceptional quenching capability of carbon nanotubes for the proximate luminescent Eu(3+) complex and different propensities of single-stranded DNA and the DNA/protein complex to adsorb on carbon nanotubes. The luminescence of a mixture of chlorosulfonylated tetradentate β-diketone-Eu(3+) and the antilysozyme aptamer was efficiently quenched by single-walled carbon nanotubes (SWNTs) unless the aptamer interacted with LYS. Due to the highly specific recognition ability of the aptamer for the target and the powerful quenching property of SWNTs for luminescence regents, this proposed approach has a good selectivity and high sensitivity for LYS. In the optimum conditions described, >700-fold signal enhancement was achieved for micromolar LYS, and a limit of detection as low as 0.9 nM was obtained, which is about 60-fold lower than those of commonly used fluorescent aptamer sensors. Moreover, due to the much longer lifetime of the Eu(3+) luminescence than those of the ubiquitous endogenous fluorescent components, the time-resolved luminescence technique could be conveniently used for application in complicated biological samples. LYS concentrations in human urine were thus detected using time-resolved luminescence measurement with satisfactory recoveries of 95-98%.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.