Molecular engineering of DNA: molecular beacons

Quencher-free molecular beacon: Enhancement of the signal-to-background ratio with graphene oxide

We report the highly improved version of quencher-free molecular beacon (QF-MB) system by using graphene oxide (GO) as an external quencher. This QF-MB/GO system provided a higher S/B ratio (31.0) relative to that (2.2) of the same system in the absence of GO, while retaining a high selectivity for fully matched over single-base-mismatched targets.

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.

Tailoring DNA structure to increase target hybridization kinetics on surfaces

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.

A universal platform for sensitive and selective colorimetric DNA detection based on Exo III assisted signal amplification

Rapid growth of available sequence data has made the detection of nucleic acids critical to the development of modern life sciences. Many amplification methods based on gold nanoparticles and endonuclease for sensitive DNA detection have been developed. However, these approaches require specific target sequence for endonuclease recognition, which cannot be fulfilled in all systems. Replacing the restriction enzyme with a nuclease that does not require any specific recognition sequence may offer a universally adaptable system. Here we have developed a novel homogeneous, colorimetric DNA detection method, which consists of Exo III, a linker DNA, and two DNA-modified gold nanoparticles. This system is simple, low-cost, sensitive and selective. By coupling cyclic enzymatic cleavage and gold nanoparticle for signal amplification, our system provides a colorimetric detection limit of 15 pM, which is 3 orders of magnitude more sensitive than that of a general three-component sandwich assay format. Due to the intrinsic property of Exo III, our method shows excellent detection selectivity for single-base discrimination. More importantly, superior to other methods based on nicking and FokI endonuclease, our target sequence-independent platform is generally applicable for DNA sensing. This new approach could be widely applied to sensitive nucleic acids detection.

Facile synthesis of advanced photodynamic molecular beacon architectures

Nucleic acid photodynamic molecular beacons (PMBs) are a class of activatable photosensitizers that increase singlet oxygen generation upon binding a specific target sequence. Normally, PMBs are functionalized with multiple solution-phase labeling and purification steps. Here, we make use of a flexible solid-phase approach for completely automated synthesis of PMBs. This enabled the creation of a new type of molecular beacon that uses a linear superquencher architecture. The 3' terminus was labeled with a photosensitizer by generating pyropheophorbide-labeled solid-phase support. The 5' terminus was labeled with up to three consecutive additions of a dark quencher phosphoramidite. These photosensitizing and quenching moieties were stable in the harsh DNA synthesis environment and their hydrophobicity facilitated PMB purification by HPLC. Linear superquenchers exhibited highly efficient quenching. This fully automated synthesis method simplifies not only the synthesis and purification of PMBs, but also the creation of new activatable photosensitizer designs.

Novel insights into the use of Glowing LNA as nucleic acid detection probes--influence of labeling density and nucleobases

Appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA (locked nucleic acid) display large increases in fluorescence intensity and remarkably high quantum yields upon hybridization with nucleic acid targets. Thermal denaturation and fluorescence spectroscopy studies on ONs modified with known thymine monomer X and novel 5-methylcytosine monomer Y provide new insights into the design principles and mechanism of these Glowing LNA nucleic acid detection probes.

Fast molecular beacon hybridization in organic solvents with improved target specificity

DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.

The ODN probes conjugating the Cu(II) complex enhance the luminol chemiluminescence by assembling on the DNA template

Potent peroxidase-like activity of the β-ketoenamine (1)-dicopper (II) complex (2) for the chemiluminescence (CL) of luminol either in the presence or absence of H(2)O(2) has been previously demonstrated by our group. In this study, the β-ketoenamine (1) as the ligand unit for copper(II) was incorporated into the oligonucleotide (ODN) probes. It has been shown that the catalytic activity of the ODN probes conjugating the ligand-Cu(II) complex is activated by hybridization with the target DNA with the complementary sequence. Thus, this study has successfully demonstrated the basic concept for the sensitive detection of nucleic acids by CL based on the template-inductive activation of the catalytic unit for CL.

Aging induced Ag nanoparticle rearrangement under ambient atmosphere and consequences for nanoparticle-enhanced DNA biosensing

Localized surface plasmons of metallic nanoparticles can strongly amplify the magnitude of the surrounding electric field. This in turn enhances fluorescence from nearby fluorophores. However, little is known regarding how time-dependent changes in nanoparticle structure due to exposure to the ambient environment affect their behavior in plasmonic devices. Here, we report the interesting finding that the aging of a nanostructured Ag substrate in ambient atmosphere markedly improves the fluorescence signal of a plasmonic-based DNA detection system. The effect can be observed with an exposure time as short as two days, and a nearly 17-fold signal enhancement can be achieved with 30 days of aging. Analysis of substrate surface topography by atomic force microscopy (AFM) reveals a substantial change in nanoparticle morphology as the substrates age despite being covalently attached to a solid dry substrate. Nanoparticle morphological changes also manifest in extinction spectra. This process can be further accelerated by light. Together, our findings address the important question of Ag nanoparticle stability over time and its potential ramifications for plasmon-enabled sensors. They also imply that nanoparticle aging may be used strategically to tune nanoparticle size and geometry and plasmon spectrum, which may be beneficial for studies on plasmonics as well as sensor optimization.

Dual sensing of hairpin and quadruplex DNA structures using multicolored peptide nucleic acid fluorescent probes

Synthesis of water-soluble 5-mer peptide nucleic acids (PNAs) functionalized at their 5'- and 3'-ends with two original precursors of pentamethine cyanine dye synthesis is reported. The successful use of these PNA probes for sensing DNA hairpin structures in vitro was also demonstrated where specific hairpin formation was associated with the appearance of a characteristic fluorescence signal at 660 nm. A comparative study between three different strategies where PNAs were targeting either the stem or the loop of the hairpin was carried out. Best sensitivity was obtained using PNA sequences complementary to the loop sequence and directing both functional moieties toward the base of loop. Unprecedented proof-of-concept for the simultaneous sensing of hairpin and quadruplex DNAs with a nonoverlapping two-color system (C3 and C5) is also demonstrated.

Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells

Graphene has shown fascinating applications in bionanotechnology, including DNA sensing, protein assays, and drug delivery. However, exploration of graphene with intracellular monitoring and in situ molecular probing is still at an early stage. In this regard, we have designed an aptamer-carboxyfluorescein (FAM)/graphene oxide nanosheet (GO-nS) nanocomplex to investigate its ability for molecular probing in living cells. Results demonstrate that uptake of aptamer-FAM/GO-nS nanocomplex and cellular target monitoring were realized successfully. The dramatic delivery, protection, and sensing capabilities of GO-nS in living cells indicate that graphene oxide could be a robust candidate for many biological fields, such as DNA and protein analysis, gene and drug delivering, and intracellular tracking.

Optimisation of a multivalent Strep tag for protein detection

The Strep tag is a peptide sequence that is able to mimic biotin's ability to bind to streptavidin. Sequences of Strep tags from 0 to 5 have been appended to the N-terminus of a model protein, the Stefin A Quadruple Mutant (SQM) peptide aptamer scaffold, and the recombinant fusion proteins expressed. The affinities of the proteins for streptavidin have been assessed as a function of the number of tags inserted using a variety of labelled and label-free bioanalytical and surface based methods (Western blots, microarray assays and surface plasmon resonance spectroscopy). The binding affinity increases with the number of tags across all assays, reaching nanomolar levels with 5 inserts, an observation assigned to a progressive increase in the probability of a binding interaction occurring. In addition a novel interfacial FRET based assay has been developed for generic Strep tag interactions, which utilises a conventional microarray scanner and bypasses the requirement for expensive lifetime imaging equipment. By labelling both the tagged StrepX-SQM(2) and streptavidin targets, the conjugate is primed for label-free FRET based displacement assays.

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.

DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes

Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.

Aptamers embedded in polyacrylamide nanoparticles: a tool for in vivo metabolite sensing

We describe a new type of aptamer-based optical nanosensor which uses the embedding of target responsive oligonucleotides in porous polyacrylamide nanoparticles to eliminate nuclease instability. The latter is a common problem in the use of aptamer sensors in biological environments. These aptamers embedded in nanoparticles (AptaNPs) are proposed as a tool in real-time metabolite measurements in living cells. The AptaNPs comprise 30 nm polyacrylamide nanoparticles, prepared by inverse microemulsion polymerization, which contain water-soluble aptamer switch probes (ASPs) trapped in the porous matrix of the nanoparticles. The matrix acts as a molecular fence allowing rapid diffusion of small metabolites into the particles to interact with the aptamer molecules, but at the same time it retains the larger aptamer molecules inside the nanoparticles providing protection against intracellular degradation. We tested the ability of the AptaNPs to measure the adenine-nucleotide content in yeast cells. Our results successfully demonstrate the potential for monitoring any metabolite of interest in living cells by selecting specific aptamers and embedding them in nanoparticles.

A single molecular beacon probe is sufficient for the analysis of multiple nucleic acid sequences

Molecular beacon (MB) probes are dual-labeled hairpin-shaped oligodeoxyribonucleotides that are extensively used for real-time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real-time assays and improve the accuracy of single-nucleotide polymorphism genotyping.

In vitro selection of structure-switching, self-reporting aptamers

We describe an innovative selection approach to generate self-reporting aptamers (SRAs) capable of converting target-binding events into fluorescence readout without requiring additional modification, optimization, or the use of DNA helper strands. These aptamers contain a DNAzyme moiety that is initially maintained in an inactive conformation. Upon binding to their target, the aptamers undergo a structural switch that activates the DNAzyme, such that the binding event can be reported through significantly enhanced fluorescence produced by a specific stacking interaction between the active-conformation DNAzyme and a small molecule dye, N-methylmesoporphyrin IX. We demonstrate a purely in vitro selection-based approach for obtaining SRAs that function in both buffer and complex mixtures such as blood serum; after 15 rounds of selection with a structured DNA library, we were able to isolate SRAs that possess low nanomolar affinity and strong specificity for thrombin. Given ongoing progress in the engineering and characterization of functional DNA/RNA molecules, strategies such as ours have the potential to enable rapid, efficient, and economical isolation of nucleic acid molecules with diverse functionalities.

Increasing the sensitivity and single-base mismatch selectivity of the molecular beacon using graphene oxide as the "nanoquencher"

Here, we report a novel, highly sensitive, selective and economical molecular beacon using graphene oxide as the "nanoquencher". This novel molecular beacon system contains a hairpin-structured fluorophore-labeled oligonucleotide and a graphene oxide sheet. The strong interaction between hairpin-structured oligonucleotide and graphene oxide keep them in close proximity, facilitating the fluorescence quenching of the fluorophore by graphene oxide. In the presence of a complementary target DNA, the binding between hairpin-structured oligonucleotide and target DNA will disturb the interaction between hairpin-structured oligonucleotide and graphene oxide, and release the oligonucleotide from graphene oxide, resulting in restoration of fluorophore fluorescence. In the present study, we show that this novel graphene oxide quenched molecular beacon can be used to detect target DNA with higher sensitivity and single-base mismatch selectivity compared to the conventional molecular beacon.

The Polyvalent Gold Nanoparticle Conjugate-Materials Synthesis, Biodiagnostics, and Intracellular Gene Regulation

Advances in nanoscale directed assembly strategies have enabled researchers to analogize atomic assembly via chemical reactions and nanoparticle assembly, creating a new nanoscale "periodic table." We are just beginning to realize the nanoparticle equivalents of molecules and extended materials and are currently developing the ground rules for creating programmable nanometer-scale coordination environments. The ability to create a diverse set of nanoscale architectures from one class of nanoparticle building blocks would allow for the synthesis of designer materials, wherein the physical properties of a material could be predicted and controlled a priori. Our group has taken the first steps toward this goal and developed a means of creating tailorable assembly environments using DNA-nanoparticle conjugates. These nanobioconjugates combine the discrete plasmon resonances of gold nanoparticles with the synthetically controllable and highly selective recognition properties of DNA. Herein, we elucidate the beneficial properties of these materials in diagnostic, therapeutic, and detection capabilities and project their potential use as nanoscale assembly agents to realize complex three-dimensional nanostructures.

Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity

The catalytic beacon has emerged as a general platform for sensing metal ions and organic molecules. However, few reports have taken advantage of the true potential of catalytic beacons in signal amplification through multiple enzymatic turnovers, as existing designs require either equal concentrations of substrate and DNAzyme or an excess of DNAzyme in order to maintain efficient quenching, eliminating the excess of substrate necessary for multiple turnovers. On the basis of the large difference in the melting temperatures between the intramolecular molecular beacon stem and intermolecular products of identical sequences, we here report a general strategy of catalytic and molecular beacon (CAMB) that combines the advantages of the molecular beacon for highly efficient quenching with the catalytic beacon for amplified sensing through enzymatic turnovers. Such a CAMB design allows detection of metal ions such as Pb(2+) with a high sensitivity (LOD = 600 pM). Furthermore, the aptamer sequence has been introduced into DNAzyme to use the modified CAMB for amplified sensing of adenosine with similar high sensitivity. These results together demonstrate that CAMB provides a general platform for amplified detection of a wide range of targets.

A graphene-enhanced molecular beacon for homogeneous DNA detection

In this work, we report the design of a novel graphene-based molecular beacon (MB) that could sensitively and selectively detect specific DNA sequences. The ability of water-soluble graphene oxide (GO) to differentiated hairpin and dsDNA offered a new approach to detect DNA. We found that the background fluorescence of MB was significantly suppressed in the presence of GO, which increased the signal-to-background ratio, hence the sensitivity. Moreover, the single-mismatch differentiation ability of hairpin DNA was maintained, leading to high selectivity of this new method.

Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for real-time, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.

Orientation difference of chemically immobilized and physically adsorbed biological molecules on polymers detected at the solid/liquid interfaces in situ

A surface sensitive second order nonlinear optical technique, sum frequency generation vibrational spectroscopy, was applied to study peptide orientation on polymer surfaces, supplemented by a linear vibrational spectroscopy, attenuated total reflectance Fourier transform infrared spectroscopy. Using the antimicrobial peptide Cecropin P1 as a model system, we have quantitatively demonstrated that chemically immobilized peptides on polymers adopt a more ordered orientation than less tightly bound physically adsorbed peptides. These differences were also observed in different chemical environments, for example, air versus water. Although numerous studies have reported a direct correlation between the choice of immobilization method and the performance of an attached biological molecule, the lack of direct biomolecular structure and orientation data has made it difficult to elucidate the relationship between structure, orientation, and function at a surface. In this work, we directly studied the effect of chemical immobilization method on biomolecular orientation/ordering, an important step for future studies of biomolecular activity. The methods for orientation analysis described within are also of relevance to understanding biosensors, biocompatibility, marine-antifouling, membrane protein functions, and antimicrobial peptide activities.

Recent developments in oligonucleotide conjugation

Synthetic oligonucleotides (ONs) are being investigated for various therapeutic and diagnostic applications. The interest in ONs arises because of their capability to cause selective inhibition of gene expression by binding to the target DNA/RNA sequences through mechanisms such as antigene, antisense, and RNA interference. ONs with catalytic activity (ribozymes and DNAzymes) against the target sequences, and ability to bind to the target molecules (aptamers), ranging from small molecules to proteins, are also known. Therefore ONs are considered potentially useful for the treatment of viral diseases and cancer. ONs also find use in the design of DNA microchips (a powerful bio-analytical tool) and novel materials in nanotechnology. However, the clinical success achieved so far with ONs has not been satisfactory, and the major impediments have been recognised as their instability against nucleases, lack of target specificity, and poor uptake and targeted delivery. Tremendous efforts have been made to improve the ON properties by either incorporating chemical modifications in the ON structure or covalently linking (conjugation) reporter groups, with biologically relevant properties, to ONs. Conjugation is of great interest because it can be used not only to improve the existing ON properties but also to impart entirely new properties. This tutorial review focuses on the recent developments in ON conjugation, and describes the key challenges in efficient ON conjugation and major synthetic approaches available for successful ON conjugate syntheses. In addition, an overview on major classes of ON conjugates along with their use in therapeutics, diagnostics and nanotechnology is provided.

RNA-cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection

Along with biocompatibility, chemical stability, and simplicity of structural prediction and modification, deoxyribozyme-based molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357, 748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring in homogeneous solution. The LOD of the sensor was found to be approximately 1.6 x 10(-10) M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenic substrates was derived and experimentally verified. According to the equation, "catalytically perfect" enzymes can serve as scaffolds for the design of sensors with the LOD not lower than approximately 2 x 10(-15) M after 3 h of incubation. A new value termed the detection efficiency (DE) is suggested as a time-independent characteristic of a sensor's sensitivity. The expressions for the theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms.

Using graphene to protect DNA from cleavage during cellular delivery

We have proved that functionalized nanoscale graphene oxide can protect oligonucleotides from enzymatic cleavage and efficiently deliver oligonucleotides into cells.

Synthetic incorporation of Nile Blue into DNA using 2'-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

The Nile Blue chromophore was incorporated into oligonucleotides using "click" chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV-vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.

Reduction-triggered fluorescence probe for peptide-templated reactions

We developed a new nucleic acid-based fluorescence probe for protein detection. The method is based on the scission of an aptamer into two probes, which are then attached with a chemically reactive fluorogenic compound. The protein-dependent association of the two probes accelerates a reduction-triggered fluorogenic reaction and indicates the presence of the target protein, which is detected using a fluorescence readout. The fluorescence signal is generated via the deprotection of the azidomethyl group of fluorescein. The arginine-rich motif peptide of the human immunodeficiency virus-1 Rev protein was targeted by this type of probe. Emission was detected at 522 nm and was enhanced by about 19.4-fold in the presence of the target peptide. An oligonucleotide-based reduction-triggered fluorescence probe was successfully applied to the detection of the Rev peptide in solution.

Efficient nucleic acid detection by templated reductive quencher release

RNA-templated fluorescence activation is a nucleic acid detection strategy that offers the possibility of direct visual detection of genetic information in living cells. Here we describe a new reaction strategy for fluorescence activation in which a phosphine on one DNA probe reduces an azide group in a linker on a second probe, resulting in linker cleavage and release of a fluorescence quenching group. These "Q-STAR" probes are shown to yield a strong fluorescence turn-on signal in approximately 20 min, with very low background and substantial amplification by turnover on the template. A green/red pair of such probes allowed the discrimination of two bacterial species by a single nucleotide difference in their 16S rRNA. The beneficial properties of the reductive quencher release design make these probes promising candidates for widespread application in the detection of nucleic acids in vitro and in cells.