Copper(II)-quenched oligonucleotide probes for fluorescent DNA sensing

Interaction of N-nitrosamines with binuclear copper complexes for luminescent detection

Cu(I) from tetrakis(acetonitrile)copper(I) hexafluorophosphate ([Cu(MeCN)₄]PF₆) was complexed with five structurally related phosphines containing N-heterocycles. The interactions between the resulting complexes and some N-nitrosamines were studied using X-ray crystallography as well as emission spectroscopy. Upon complexation, three phosphine ligands bridge two Cu(I) centers to give paddlewheel type structures that displayed a range of emission wavelengths spanning the visible region. N-Nitrosodimethylamine (NDMA) was shown to coordinate to one of the two copper centers in some of the paddlewheel complexes in the solid state and this interaction also quenches their emissions in solution. The influence of the weakly coordinating anion on crystal and spectroscopic properties of one of the paddlewheel complexes was also examined using tetrakis(acetonitrile)copper(I) perchlorate ([Cu(MeCN)₄]ClO₄) as an alternative Cu(I) source. Similarly, copper(II) perchlorate hexahydrate (Cu(ClO₄)₂·6H₂O) was used for complexation to observe the impact of metal oxidation state on the two aforementioned properties. Lastly, the spectroscopic properties of the complex between Ph₂P(1-Isoquinoline) and Cu(I) was shown to exhibit solvent dependence when the counterion is ClO₄^-. These Cu(I) complexes are bench stable solids and may be useful materials for developing a fluorescence based detection method for N-nitrosamines.

A Tetranuclear Copper(II)/Calcium(II) Complex as Dual Chemosensor for Colorimetric and Fluorescent Detection of Non-Steroidal Anti-Inflammatory Drugs

The tetranuclear Cu²⁺ /Ca²⁺ /Ca2⁺ /Cu²⁺ complex based on Malten ligand has been investigated as a platform for anion binding. Simple organic carboxylates and non-steroidal anti-inflammatory drugs (NSAIDs) have been tested, revealing the ability of the platform to bind them. The receiving platform hosts at least two guests in solution although a third anion can be bound, as suggested by X-ray diffraction analysis. The addition of the anions is accompanied by a color change of the solution, making the system a colorimetric sensor for carboxylates (LOD values comprised between 3.6 and 20.7 ppm). A fluorescent system consisting of the 2-(3-oxido-6-oxoxanthen-9-yl)benzoate (fluorescein anion) linked to the tetranuclear platform has been also prepared and used in a chemosensing ensemble approach to signal the presence of the selected anions (Log K between 2.6 and 5.6 for the addition of two guests). The latter also works in a paper strip test, offering the chemosensor a possible practical application.

Progress in the Development of Biosensors Based on Peptide-Copper Coordination Interaction

Copper ions, as the active centers of natural enzymes, play an important role in many physiological processes. Copper ion-based catalysts which mimic the activity of enzymes have been widely used in the field of industrial catalysis and sensing devices. As an important class of small biological molecules, peptides have the advantages of easy synthesis, excellent biocompatibility, low toxicity, and good water solubility. The peptide-copper complexes exhibit the characteristics of low molecular weight, high tenability, and unique catalytic and photophysical properties. Biosensors with peptide-copper complexes as the signal probes have promising application prospects in environmental monitoring and biomedical analysis and diagnosis. In this review, we discussed the design and application of fluorescent, colorimetric and electrochemical biosensors based on the peptide-copper coordination interaction.

Recent Advances in Peptides-Based Stimuli-Responsive Materials for Biomedical and Therapeutic Applications: A Review

Smart materials are engineered materials that have one or more properties that are introduced in a controlled fashion by surrounding stimuli. Engineering of biomacromolecules like proteins into a smart material call for meticulous artistry. Peptides have grabbed notable attention as a preferred source for smart materials in the medicinal field, promoted by their versatile chemical and biophysical attributes of biocompatibility, and biodegradability. Recent advances in the synthesis of multifunctional peptides have proliferated their application in diverse domains: agriculture, nanotechnology, medicines, biosensors, therapeutics, and soft robotics. Stimuli such as pH, temperature, light, metal ions, and enzymes have vitalized physicochemical properties of peptides by augmented sensitivity, stability, and selectivity. This review elucidates recent (2018-2021) advances in the design and synthesis of smart materials, from stimuli-responsive peptides followed by their biomedical and therapeutic applications.

Carbohydrate based biomarkers enable hybrid near infrared fluorescence and 64Cu based radio-guidance for improved surgical precision

Increasing numbers of lung tumors are identified at early disease stages by diagnostic imaging in screening programs, but difficulties in locating these during surgical intervention has prevented an improved treatment outcome. Surgical biomarkers that are visible on diagnostic images, and that provide the surgeon with real-time image guidance during the intervention are thus highly warranted to bridge diagnostic precision into enhanced therapeutic outcome. In this paper, a liquid soft tissue marker for near infrared fluorescence and radio-guidance is presented. The biocompatible marker is based on the carbohydrate ester, sucrose acetate isobutyrate, ethanol, and a multifunctional naphthalocyanine dye, which enable near infrared fluorescence image-guided resection at short, medium and long tissue depths. Naphthalocyanine dyes have high quantum yields and may further act as chelators of radionuclides. Upon injection of the liquid marker, a gel-like depot is formed in situ at the site of injection, wherein the fluorescent dye and radionuclide is retained. The radiolabeled markers were optimized for minimal fluorescence quenching and high retention of the positron emission tomography radionuclide ⁶⁴Cu. The performance of the radiolabeled marker was tested in vivo in mice, where it displayed high photostability over a period of 4 weeks, and high retention of ⁶⁴Cu for 48 hours. The retention and biodistribution of ⁶⁴Cu was quantified via PET/CT, and the fluorescence emission by an in vivo imaging system. The presented data demonstrate proof-of-concept for naphthalocyanine markers as multimodal imaging agents that can bridge the precision of diagnostic imaging into surgical interventions.

Solvent-Regulated Fluorimetric Differentiation of Al3+ and Zn2+ Using an AIE-Active Single Sensor

The absence of d-orbital electrons or presence of full-filled d-orbital electrons in metal ions is a well-known Achilles' heel problem for the detection of these metal ions by a simple UV-visible study. For this reason, detection of metal ions such as Al³⁺ with no d-orbital electrons or Zn²⁺ with filled d-orbital electrons is a challenging task. Herein, we report a 2-naphthol-based fluorescent probe [1-((E)-((E)-(5-bromo-2-hydroxybenzylidene)hydrazono)methyl)naphthalen-2-ol] (H₂L) that has been used to sense and discriminate Al³⁺ and Zn²⁺ via solvent regulation. The probe exhibits excellent selectivity and swift sensitivity toward Al³⁺ in MeOH-water (9:1, v/v) and toward Zn²⁺ in dimethyl sulfoxide (DMSO)-water (9:1, v/v) among various metal ions. The respective detection limit is found to be 9.78 and 3.65 μM. The sensing mechanism is attributed to multiple processes, viz., the inhibition of photo-induced electron transfer (PET) along with the introduction of chelation-enhanced emission (CHEF) and excited-state intramolecular proton transfer (ESIPT) inhibition, which are experimentally well verified by UV-vis absorption spectroscopy, emission spectroscopy, and NMR spectroscopy. The probe shows aggregation-induced emissive (AIE) response in ≥70% aqueous media as well as in the solid state. The experimental results are well corroborated by time-resolved photoluminescence (TRPL) and density functional theory (DFT) calculations. An advanced-level OR-AND-NOT logic gate has been constructed from a different chemical combinational input and emission output. The reversible recognition of both Al³⁺ in MeOH-water (9:1, v/v) and Zn²⁺ in DMSO-water (9:1, v/v) is also ascertained in the presence of Na₂EDTA, enabling the construction of a molecular memory device. The probe H₂L also detects intracellular Al³⁺/Zn²⁺ ions in Hela cells. Altogether, our fundamental findings will pave the way for designing and synthesis of unique chemosensors that could be used for cell imaging studies as well as constructing molecular logic gates.

Metal-organic frameworks for virus detection

Virus severely endangers human life and health, and the detection of viruses is essential for the prevention and treatment of associated diseases. Metal-organic framework (MOF), a novel hybrid porous material which is bridged by the metal clusters and organic linkers, has become a promising biosensor platform for virus detection due to its outstanding properties including high surface area, adjustable pore size, easy modification, etc. However, the MOF-based sensing platforms for virus detection are rarely summarized. This review systematically divided the detection platforms into nucleic acid and immunological (antigen and antibody) detection, and the underlying sensing mechanisms were interpreted. The nucleic acid sensing was discussed based on the properties of MOF (such as metal ion, functional group, geometry structure, size, porosity, stability, etc.), revealing the relationship between the sensing performance and properties of MOF. Moreover, antibodies sensing based on the fluorescence detection and antigens sensing based on molecular imprinting or electrochemical immunoassay were highlighted. Furthermore, the remaining challenges and future development of MOF for virus detection were further discussed and proposed. This review will provide valuable references for the construction of sophisticated sensing platform for the detection of viruses, especially the 2019 coronavirus.

A copper complex formed with neurokinin B: binding stoichiometry, redox properties, self-assembly and cytotoxicity

The tachykinin neuropeptide of neurokinin B (NKB) is a copper-binding amyloid peptide with important roles in the regulation of physiological functions and pathophysiological processes in the central and peripheral nervous systems. In this work, the formation of a NKB-Cu²⁺ complex in a 1 : 1 stoichiometry was confirmed by mass spectrometry. The self-assembly of NKB and its mutant species was investigated by Thioflavin T (ThT) fluorescence assay and atomic force microscopy (AFM), and at the same time, the effect of Cu²⁺ on the aggregation of NKB was studied. As evidenced by cyclic voltammetry, the redox potential of NKB-Cu²⁺ was determined to be 0.77 V (vs. Ag/AgCl). It has been demonstrated that NKB at low concentrations exerts its neuroprotective function by inhibiting Cu²⁺-mediated reactive oxygen species (ROS) production in the presence of ascorbic acid (AA). In comparison with equivalent Cu²⁺, the peptide-Cu²⁺ aggregates aggravated the viability of PC-12 cells more seriously in the absence of AA. These results should be extremely valuable for understanding the NKB/Cu²⁺ interactions and the toxicity mechanism of Cu²⁺ associated with neurodegenerative diseases.

An atom-economical design of PET tracer for imaging αvβ3 integrin via utilizing the three-in-one function of 64Copper

In this study, α_vβ₃ integrin in U87 tumor cells was imaged with a ⁶⁴Cu-peptidic probe, in which the linear peptide GHRGDHG is used as a pre-ligand, while ⁶⁴Cu bears three functional roles that include generation of the PET signal, coordination with two GH moieties of the pre-ligand, and cyclizing the linear pre-ligand into an active cyclic-RGD form (termed as ⁶⁴Cu-Cyclo-RGD) for α_vβ₃ integrin.

Synthesis of N-acetyl-l-cysteine capped Mn:doped CdS quantum dots for quantitative detection of copper ions

In this work, a new assembled copper ions sensor based on the Mn metal-enhanced fluorescence of N-acetyl-l-cysteine protected CdS quantum dots (NAC-Mn:CdS QDs) was developed. The NAC and Mn:CdS QDs nanoparticles were assembled into NAC-Mn:CdS QDs complexes through the formation of CdS and MnS bonds. As compared to NAC capped CdS QDs, higher fluorescence quantum yields of NAC-Mn:CdS QDs was observed, which is attributed to the surface plasmon resonance of Mn metal. In addition, the fluorescence intensity of as-formed complexes weakened in the presence of copper ions. The decrease in fluorescence intensity presented a linear relationship with copper ions concentration in the range from 0.16-3.36μM with a detection limit of 0.041μM . The characterization of as-formed QDs was analyzed by photoluminescence (PL), ultra violet-visible (UV-vis), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and energy dispersive spectroscopy (EDS) respectively. Furthermore, the recoveries and relative standard deviations of Cu²⁺ spiked in real water samples for the intra-day and inter-day analyses were 88.20-117.90, 95.20-109.90, 0.80-5.80 and 1.20-3.20%, respectively. Such a metal-enhanced QDs fluorescence system may have promising application in chemical and biological sensors.

Single-molecule porphyrin-metal ion interaction and sensing application

It remains a significant challenge to study the interactions between metal ions and porphyrin molecules at single ion level. Here, we constructed a nanopore-based sensing for label-free and real-time analysis of the interaction between Cu²⁺ and 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin (TPPS). The results demonstrate that emerging electronic signatures of the Cu²⁺-TPPS complex that is completely different form the original free TPPS were observed in the α-hemolysin (α-HL) nanopore. Based on the distinctive electronic signal patterns between TPPS and Cu²⁺-TPPS complex, the unique nanopore sensor can achieve a highly sensitive detection of Cu²⁺ in aqueous media. The frequency of signature events showed a linear response toward the concentration of Cu²⁺ in the range of 0.03 µM - 1.0 μM, with a detection limit of 16 nM (S/N = 3). The sensing system also exhibited high selectivity against other metal ions, and the feasibility of this approach for practical applications was demonstrated with the determination of Cu²⁺ in running water.

Self-assembly of a metallo-peptide into a drug delivery system using a “switch on” displacement strategy

Two newly designed tripeptides and their corresponding Cu²⁺ conjugates self-assemble into nanometric structures of different morphologies. These self-assembled metallo-peptide networks can serve as a drug delivery platform using a fluorescent-based "Turn-On" displacement strategy.

Novel fluorescent anthracene–bodipy dyads displaying sensitivity to pH and turn-on behaviour towards Cu(ii) ions

The effect of the nature of the spacer in three new bichromophoric compounds showing intramolecular PET and EET processes has been studied.

Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex

DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.

Fluorophore ATCUN complexes: combining agent and probe for oxidative DNA cleavage

DNA can be oxidatively cleaved by copper complexes of the ATCUN peptide (amino terminal Cu(II)- and Ni(II)-binding motif). In order to investigate the fate of the metal ion throughout this process, we have exploited quenching/dequenching effects of conjugated fluorophores.

Analysis of Fluorescence Lifetime and Energy Transfer Efficiency in Single-Molecule Photon Trajectories of Fast-Folding Proteins

In single-molecule Förster resonance energy transfer (FRET) spectroscopy, the dynamics of molecular processes are usually determined by analyzing the fluorescence intensity of donor and acceptor dyes. Since FRET efficiency is related to fluorescence lifetimes, additional information can be extracted by analyzing fluorescence intensity and lifetime together. For fast processes where individual states are not well separated in a trajectory, it is not easy to obtain the lifetime information. Here, we present analysis methods to utilize fluorescence lifetime information from single-molecule FRET experiments, and apply these methods to three fast-folding, two-state proteins. By constructing 2D FRET efficiency-lifetime histograms, the correlation can be visualized between the FRET efficiency and fluorescence lifetimes in the presence of the submicrosecond to millisecond dynamics. We extend the previously developed method for analyzing delay times of donor photons to include acceptor delay times. To determine the kinetics and lifetime parameters accurately, we used a maximum likelihood method. We found that acceptor blinking can lead to inaccurate parameters in the donor delay time analysis. This problem can be solved by incorporating acceptor blinking into a model. While the analysis of acceptor delay times is not affected by acceptor blinking, it is more sensitive to the shape of the delay time distribution resulting from a broad conformational distribution in the unfolded state.

Novel core-shell structure microspheres based on lanthanide complexes for white-light emission and fluorescence sensing

A series of new core-shell structure materials based on lanthanide complexes [H2NMe2]3[Ln(dpa)3] (Ln = Eu, Tb, Sm, Dy, Nd, and Yb; [H2NMe2](+) = dimethylamino cation; dpa = 2-dipicolinate) and silica microspheres has been prepared under solvothermal conditions. Electron microscopy reveals that the nanosized materials SiO2@Ln-dpa are spherical with a narrow size distribution and a [H2NMe2]3[Ln(L)3] coating was generated on the surface of silica microspheres successfully. The core-shell structure materials exhibit excellent optical performance. The white-light-emitting material SiO2@(Dy:Eu)-dpa has a potential application in the development of a white-light device, as a result of the fact that its CIE chromaticity coordinate is very close to that of pure white. Then, we selected SiO2@Eu-dpa as a representative sample for sensing experiments. Eventually, we found that the core-shell structure sensors are highly selective and sensitive for acetone and Cu(2+) cations. The detection of Cu(2+) in the human body is an important issue. Interestingly, the core-shell structure materials display better selectivity and higher sensitivity than the pure lanthanide complexes in sensing Cu(2+) and the value of the quenching effect coefficient has increased by more than 20%.

Rationally designed molecular beacons for bioanalytical and biomedical applications

Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.

Highly effective heterogeneous chemosensors of luminescent silica@coordination polymer core-shell micro-structures for metal ion sensing

Heterogeneous solid sensors are regarded as promising next-generation sensor due to their excellent chemical stability, low contamination, and excellent recyclability, despite their low sensitivity and weak signal. The dispersity and signals specifically from the exterior of solid sensors are critical aspects which define the sensing sensitivity and selectivity. A novel strategy for the preparation of ideal heterogeneous sensors based upon luminescent lanthanide coordination polymers (LnCP) has been demonstrated. Ideal heterogeneous sensors are systematically achieved by producing the sensors in small, uniform, and thin core-shell particles (silica@LnCP, Ln = Eu, Tb). Eventually, we found that the extremely small amount of well-structured silica@LnCP microsphere, less than ca. 1/400 compared to the amount of several known coordination polymer-based sensors, was sufficient to achieve a reliable Cu²⁺ sensing with even much greater sensitivity (ca. 550% improvement).

Metal-organic framework MIL-101 as a low background signal platform for label-free DNA detection

A label-free and sensitive fluorescence method for recognition of sequence-specific DNA using DNA-intercalating dye and metal-organic frameworks (MOFs) is developed. Here, MIL-101 (Cr3F(H2O)2O[(O2C)-C6H4-(CO2)]3·nH2O) is introduced as a quenching platform to decrease the high background fluorescence of SYBR Green I (SG)/probe DNA complex. Mechanism investigations show that MIL-101 can strongly adsorb the SG/probe DNA complex through π-π stacking and electrostatic interactions, and as a consequence, the fluorescence of the SG dye is greatly quenched. While in the presence of target DNA, the as-formed rigid double-stranded (ds) structure of DNA will be far away from the surface of MIL-101; meanwhile, the SG dye can be bound with the dsDNA in the mode of intercalation and minor groove binding, resulting in enhancement of the SG dye fluorescence. The increased signal-to-background ratio has a linear relationship with the concentration of target DNA in the range of 0.1-14 nM. It is confirmed that the detection limit is 73 pM (3σ), which is much lower than that based on the carbon nanotubes and graphene oxide platform. Moreover, one-base-mismatched target DNA can be discriminated effectively. With the introduction of MIL-101, the signal-to-background ratio has been improved ∼8-fold, demonstrating that MIL-101 is an efficient low-background signal platform.

Activatable probes based on distance-dependent luminescence associated with Cerenkov radiation

Let me get my nanoruler: Activatable probes based on radionuclide and quantum dots (QDs) were constructed using DNA as a linker. Cerenkov radiation from (64)Cu was used to excite the QDs in a distance-dependent manner. The luminescence was lowest nearest to the QD and increased with distance.

Genetically encoded copper(I) reporters with improved response for use in imaging

Copper represents one of the most important biological metal ions due to its role as a catalytic cofactor in a multitude of proteins. However, an excess of copper is highly toxic. Thus, copper is heavily regulated, and copper homeostasis is controlled by many metalloregulatory proteins in various organisms. Here we report a genetically encoded copper(I) probe capable of monitoring copper fluctuations inside living cells. We insert the copper regulatory protein Ace1 into a yellow fluorescent protein, which selectively binds copper(I) and generates improved copper(I) probes.

A thymidine-terminated molecular beacon for selective Hg2+ or sequence-specific DNA assay

A new molecular beacon (MB) in which fluorescein (FAM) attached to its 3' end acts as a fluorophore and a bridged thymidine-Hg-thymidine (T-Hg-T) complex acts as a quencher is designed. The fluorescence resonance energy transfer (FRET) between the fluorophore and the quencher results in annihilation of the FAM fluorescence. Experimental conditions that govern the fluorescence quenching, such as number of thymidine bases, pH value, and salt concentration, have been optimized. The MB was found to be highly selective for Hg(2+) among a number of metal ions investigated. In the presence of single-stranded (ss-) target oligonucleotides (ODNs) with bases complementary to those in the loop of MB, the FAM fluorescence can be largely restored due to DNA duplex formation. The present method for DNA assay is also sequence-specific and can determine target ODN concentration at a nanomolar level. The substitution of the quencher group in a conventional MB molecule with simple thymidine bases affords an inexpensive ODN that retains the unique property of the MB molecule.

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.

A dumbbell molecular beacon for the specific recognition of nucleic acids

A dumbbell molecular beacon (DMB) was designed and synthesized with the attachment of a fluorophore and a quencher at two ends. This DMB probe can be used to detect single mismatch of a 20mer oligodeoxynucleotide in two different buffers and discrimination factors were as high as 60 at 37°C. Statistics of single substitutions of analytes showed that both substituted positions and substituted nucleotides have important contributions for this probe to efficiently distinguish the true analyte from mismatched ones. Hybridization kinetics of DMB with the target oligonucleotide was also studied.

Distinguishing between protein dynamics and dye photophysics in single-molecule FRET experiments

Förster resonance energy transfer (FRET) efficiency distributions in single-molecule experiments contain both structural and dynamical information. Extraction of this information from these distributions requires a careful analysis of contributions from dye photophysics. To investigate how mechanisms other than FRET affect the distributions obtained by counting donor and acceptor photons, we have measured single-molecule fluorescence trajectories of a small alpha/beta protein, i.e., protein GB1, undergoing two-state, folding/unfolding transitions. Alexa 488 donor and Alexa 594 acceptor dyes were attached to cysteines at positions 10 and 57 to yield two isomers-donor(10)/acceptor(57) and donor(57)/acceptor(10)-which could not be separated in the purification. The protein was immobilized via binding of a histidine tag added to a linker sequence at the N-terminus to cupric ions embedded in a polyethylene-glycol-coated glass surface. The distribution of FRET efficiencies assembled from the trajectories is complex with widths for the individual peaks in large excess of that caused by shot noise. Most of this complexity can be explained by two interfering photophysical effects-a photoinduced red shift of the donor dye and differences in the quantum yield of the acceptor dye for the two isomers resulting from differences in quenching rate by the cupric ion. Measurements of steady-state polarization, calculation of the donor-acceptor cross-correlation function from photon trajectories, and comparison of the single molecule and ensemble kinetics all indicate that conformational distributions and dynamics do not contribute to the complexity.

Fluorescent probes and delivery methods for single-molecule experiments

The recent explosion in papers utilising single-molecule experiments pushes the envelope further for increased spatial and temporal resolution. In order to achieve this, a combination of novel fluorescent probes and spectroscopy techniques are required. Herein, we provide an overview on our contribution to developments in the field of fluorescent probes along with a palette of alternative delivery methods for introducing the probes into living cells. We discuss probe requirements arising from the use of single-molecule spectroscopy methods and the customisation of probes that depends on the target molecule, the chemical state of the molecule as well as the distance and the type of interaction between sensor and ligand. We explain how Förster resonance energy transfer (FRET) and photon-induced electron transfer (PET) can increase the probe customisation. We also discuss additional requirements that arise when performing experiments in living cells like toxicity and cell permeability. Regarding the latter, we devote a special paragraph on the different ways to introduce the desired probe into the cell and how the different properties of each probe and cell type may require different delivery methods. We offer insights based on our experience working with a variety of single-molecule methods, fluorescent probes and delivery systems. Overall, we encompass the latest developments on probe design and delivery and illustrate that the wealth of information provided by single-molecule studies goes along with increased complexity.

Analysis of single-molecule fluorescence spectroscopic data with a Markov-modulated Poisson process

We present a photon-by-photon analysis framework for the evaluation of data from single-molecule fluorescence spectroscopy (SMFS) experiments using a Markov-modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu2+ ions with the bidentate ligand 2,2'-bipyridine-4,4'dicarboxylic acid in aqueous media. The process of association and dissociation of Cu2+ ions is monitored with SMFS. The dcbpy-DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon-by-photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon-by-photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short-lived.

Label-free dual assay of DNA sequences and potassium ions using an aptamer probe and a molecular light switch complex

A homogeneous assay is reported using Ru(phen)(2)(dppz)(2+) and a K(+)-binding aptamer for the selective and sensitive detection of a target oligonucleotide and potassium ions, based on reduction in fluorescence emission according to the formation of the G-quadruplex structure from the aptamer in the presence of K(+).

Metal ion CHElate-aSSisted LIGAtion (CHESS LIGA) for SNP detection on microarrays

We developed a metal ion chelate-assisted ligation for SNP detection by microarray. An oligonucleotide probe was separated into two 9-10-mers bearing iminodiacetic residues at the gap point. Duplex formation with the DNA target was possible only if nickel ions were added, but a nucleotide substitution opposite the gap point prevented duplex formation. Here we demonstrate the application of this approach for SNP detection (A1298C) within the 5,10-methylenetetrahydrofolate reductase gene on a microarray.