A Peptide-PNA Hybrid Beacon for Sensitive Detection of Protein Biomarkers in Biological Fluids

Specific and rapid detection of proteins in biological fluids poses a challenging problem. In biological fluids, many proteins are present at low concentrations, requiring high affinity and specificity of the beacon-protein interaction. We report the design of a peptide-PNA hybrid beacon that exploits the dimeric nature of a target protein, S100B, a biomarker for brain trauma, to enhance binding affinity and specificity. The complementary base-pairing of the PNA bases brings the two arms of the beacon, one carrying an Alexa tag and the other carrying a Dabcyl moiety, into proximity, thus quenching Alexa fluorescence. Each of the arms carries a sequence that binds to one of the subunits. Binding to the target separates the quencher from the probe lifting the quenching of fluorescence. Enhanced affinity and specificity resulting from simultaneously binding to two sites allowed specific detection of S100B at low-nanomolar concentrations in the presence of serum. The design can be easily adapted for the detection of proteins containing multiple binding sites and could prove useful for rapid and sensitive biomarker detection.

Aptamer Displacement Reaction from Live-Cell Surfaces and Its Applications

The DNA strand displacement reaction has had sustained scientific interest in building complicated nucleic acid-based networks. However, extending the fundamental mechanism to more diverse biomolecules in a complex environment remains challenging. Aptamers bind with targeted biomolecules with high affinity and selectivity, thus offering a promising route to link the powers of nucleic acid with diverse cues. Here, we describe three methods that allow facile and efficient displacement reaction of aptamers from the living cell surface using complement DNA (cDNA), toehold-labeled cDNA (tcDNA), and single-stranded binding protein (SSB). The kinetics of the DNA strand displacement reaction is severely affected by complex physicochemical properties of the natural membrane. Toehold-mediated and SSB-mediated aptamer displacement exhibited significantly enhanced kinetics, and they completely removed the aptamer quickly to avoid a false signal caused by aptamer internalization. Because of its simplicity, aptamer displacement enabled detection of membrane protein post-translation and improved selection efficiency of cell-SELEX.

Coiled-Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection

The understanding of protein folding and assembly is of central importance for the design of proteins and enzymes with novel or improved functions. Minimalistic model systems, such as coiled-coils, provide an excellent platform to improve this understanding and to construct novel molecular devices. Along those lines, we designed a conformational switch that is composed of two coiled-coil forming peptides and a central binding epitope. In the absence of a binding partner, this switch adopts a hairpin-like conformation that opens upon receptor binding. Variation of the coiled-coil length modulates the strength of the intramolecular constraint. The two conformational states of this switch have been linked with characteristic fluorescent properties, which enables the detection of the receptor in real-time.

DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery

Herein, we review and summarise the development and biological applications of DNA tetrahedron, including cellular biosensors and drug delivery systems.

Designing a Biostable L-DNAzyme for Lead(II) Ion Detection in Practical Samples

A promising biosensor for effectively lead (II) ion detection in practical applications was developed by constructing a Pb2+-specific L-DNAzyme, the enantiomer of the natural nucleic acid-constructed D-DNAzyme. This fluorescent sensor contains the L-enzyme strand with a quencher at the 3' end, and the L-substrate strand with a fluorophore at the 5' and a quencher at the 3' ends that formed a complex. In the presence of Pb2+, the L-substrate is cut into two fragments, leading to the recovery of fluorescence. The sensor shows high sensitivity and selectivity for Pb2+ detection with a linear response in the range of 5-100 nM and a detection limit of 3 nM in aqueous solution. Importantly, based on that L-DNAzyme consists of non-natural nucleic acids, which is insensitive to nuclease digestion, protein adsorption and D-DNA hybridization, our sensor shows specific response to Pb2+ in practical water and serum samples. Therefore, it is expected that our L-DNAzyme-based strategy may offer a new method for developing simple, rapid and sensitive sensors in complex systems.

Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking

Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.

Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products

This study presents a novel dual hairpin-like molecular beacon (MB) for the selective and sensitive detection of melamine (MA) based on the conjugation of MA and thymine. In this protocol, the coordination between coralyne and adenosine (A) leaded a dual hairpin-like MB and the fluorophore-quencher pair is close proximity resulting in the fluorescence quenching. With the addition of MA, it conjugated with thymine in the loop part of dual hairpin-like MB by triple H-bonds, triggering the dissociation of the dual hairpin-like MB. The resulting spatial separation of the fluorophore from quencher induced the enhancement in fluorescence emission. Under the optimized conditions, the sensor exhibited a wide linear range of 8×10(-9)-1.6×10(-5) M (R(2)=0.9969) towards MA, with a low detection limit of 5 nM, approximately 4000 times lower than the Drug Administration and the US Food estimated MA safety limit. The real milk samples were also investigated with a satisfying result.

Femtosecond studies of protein-DNA binding and dynamics: histone I

In this contribution, we report studies of the nature of binding interactions and dynamics of protein histone I (H1) with ligands in solution and as a complex with DNA, an important biological process for the higher-order structure in chromatin. With femtosecond time resolution, we examined the role of solvation by water, the micropolarity at the interface of the binding site(s) of H1, and the rigidity of the complex structure. We used two biologically common fluorescent probes: 2-(p-toluidino)naphthalene-6-sulfonate (TNS) and 5-(dimethylamino)naphthalene-1-sulfonyl chloride (DC). By noncovalently attaching TNS and covalently adducting DC to the binding sites we found that the solvation dynamics, which occur within 1 ps, for the probe at the protein surface and in bulk solution are comparable, indicating the significant contribution of bulk water shells. However, the local polarity changes significantly, reflecting the change in dielectric properties at the protein/water interface. The binding structure of the protein-DNA complex was examined by the local orientational motion of the probe. The covalently bound DC molecule, sandwiched between the protein and DNA, was found to be frozen, revealing the very rigid structure at the recognition site, while, for noncovalently bound TNS, the complexes displace the probe. The dynamical rigidity of the complex, and the role of solvation and interface polarity, elucidate the strong recognition mechanism between DNA and the protein by electrostatic interactions, which are important to the compactness and to chromatin condensation in the biological function.

Highly sensitive multiplexed DNA detection using multi-walled carbon nanotube-based multicolor nanobeacon

A highly sensitive and selective multi-walled carbon nanotube (MWCNT)-based multicolor fluorescent nanobeacon is developed for multiplexed analysis of DNA in homogeneous solution. In this work, three different dye-labeled DNA hairpins were adsorbed on MWCNTs surface via π-stacking, which brings the dyes and MWCNTs into close proximity and leads to the quenching of fluorescence of the dyes. When target DNAs were added to the solution, the target DNAs specifically hybridize with the probes to form stable DNA duplexes, which weakens the interactions between the probes and MWCNTs, and results in the fluorescence recovery of the dyes. By using three 15-mer DNA fragments as proof-of-principle analytes, the proposed method showed good analytical performance. The limits of detection obtained were in the range of 35-42 pM. Moreover, this method also exhibits an excellent ability to discriminate between single nucleotide polymorphisms.

Mercury/homocysteine ligation-induced ON/OFF-switching of a T-T mismatch-based oligonucleotide molecular beacon

A molecular beacon (MB) with stem-loop (hairpin) DNA structure and with attached fluorophore-quencher pair at the ends of the strand has been applied to study the interactions of Hg(2+) ions with a thymine-thymine (T-T) mismatch in Watson-Crick base-pairs and the ligative disassembly of MB·Hg(2+) complex by Hg(2+) sequestration with small biomolecule ligands. In this work, a five base-pair stem with configuration 5'-GGTGG...CCTCC-3' for self-hybridization of MB has been utilized. In this configuration, the four GC base-pair binding energy is not sufficient to hybridize fully at intermediate temperatures and to form a hairpin MB conformation. The T-T mismatch built-in into the stem area can effectively bind Hg(2+) ions creating a bridge, T-Hg-T. We have found that the T-Hg-T bridge strongly enhances the ability of MB to hybridize, as evidenced by an unusually large MB melting temperature shift observed on bridge formation, ΔT(m) = +15.1 ± 0.5 °C, for 100 nM MB in MOPS buffer. The observed ΔT(m) is the largest of the ΔT(m) found for other MBs and dsDNA structures. By fitting the parameters of the proposed model of reversible MB interactions to the experimental data, we have determined the T-Hg-T bridge formation constant at 25 °C, K(1) = 8.92 ± 0.42 × 10(17) M(-1) from mercury(II) titration data and K(1) = 1.04 ± 0.51 × 10(18) M(-1) from the bridge disassembly data; ΔG° = -24.53 ± 0.13 kcal/mol. We have found that the biomarker of oxidative stress and cardiovascular disease, homocysteine (Hcys), can sequester Hg(2+) ions from the T-Hg-T complex and withdraw Hg(2+) ions from MB in the form of stable Hg(Hcys)(2)H(2) complexes. Both the model fitting and independent (1)H NMR results on the thymidine-Hg-Hcys system indicate also the high importance of 1:1 complexes. The high value of K(1) for T-Hg-T bridge formation enables analytical determinations of low concentrations of Hg(2+) (limit of detection LOD = 19 nM or 3.8 ppb, based on 3σ method) and Hcys (LOD = 23 nM, 3σ method). The conditional stability constants for Hg(Hcys)H(2)(2+) and Hg(Hcys)(2)H(2) at 52 °C have been determined, β(112) = 5.37 ± 0.3 × 10(46) M(-3), β(122) = 3.80 ± 0.6 × 10(68) M(-4), respectively.

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.

Molecular engineering of DNA: molecular beacons

Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.

Ultrasensitive optical biodiagnostic methods using metallic nanoparticles

Dramatic progress has been made over the recent decade in the applications of metallic nanoparticles in the field of biomolecule detection. The useful physical and chemical properties (e.g., availability of various synthetic methods of size- and shape-controlled nanoparticles, size- and shape-dependent optical properties, availability of various surface chemistries and biocompatibility) of metallic nanoparticles have brought development to the ultrasensitive detection of biomolecules at the attomolar level and this sensitivity enables the diagnosis of otherwise undetectable biomarkers of many fatal diseases, including Alzheimer’s disease. Furthermore, coupled with the strong physical properties and biocompatible nature of gold nanoparticles in in vivo conditions, the scope of applications for these particles have been broadened into the field of in vivo imaging, such as X-ray contrasting agents, and also cellular tracking. Here, we review synthetic methods and optical properties of metallic nanoparticles and their use in ultrasensitive, in vitro and in vivo biodiagnostic methods.

Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity

In order to gain deeper insight into the function and interplay of proteins in cells it is essential to develop methods that allow the profiling of protein function in real time, in solution, in cells, and in cell organelles. Here we report the development of a U-type oligonucleotide (molecular beacon) that contains a fluorophore and a quencher at the tips, and in addition a substrate analogue in the loop structure. This substrate analogue induces a hairpin cleavage in response to enzyme action, which is translated into a fluorescence signal. The molecular beacon developed here was used to characterize DNA-photolyase activity. These enzymes represent a challenge for analytical methods because of their low abundance in cells. The molecular beacon made it possible to measure the activity of purified class I and class II photolyases. Photolyase activity was even detectable in crude cell extracts.

Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase

The site-selective conjugation of peptide nucleic acids (PNA) with fluorescent reporter groups is essential for the construction of hybridisation probes that can report the presence of a particular DNA sequence. This paper describes convergent methods for the solution- and solid-phase synthesis of multiply labelled PNA oligomers. The solid-phase synthesis of protected PNA enabled the selective attachment of fluorescent labels at the C-terminal end (3' in DNA) which demonstrated that further manipulations on protected PNA fragments are feasible. For the conjugation to internal sites, a method is introduced that allows for the on-resin assembly of modified monomers thereby omitting the need to synthesise an entire monomer in solution. Furthermore, it is shown that the application of a highly orthogonal protecting group strategy in combination with chemoselective conjugation reactions provides access to a rapid and automatable solid-phase synthesis of dual labelled PNA probes. Real-time measurements of nucleic acid hybridisation were possible by taking advantage of the fluorescence resonance energy transfer (FRET) between suitably appended fluorophoric groups. Analogously to DNA-based molecular beacons, the dual labelled PNA probes were only weakly fluorescing in the single-stranded state. Hybridisation to a complementary oligonucleotide, however, induced a structural reorganisation and conferred a vivid fluorescence enhancement.

Design of a Molecular Beacon DNA Probe with Two Fluorophores

Fluorescence resonance energy transfer between two fluorophores (F₁ and F₂ ) attached to the two ends of a molecular beacon DNA probe containing a hairpin structure can be used for quantitative DNA/RNA studies. Concentrations of target-DNA as low as 1.7×10^-10  M could be determined with a commercial spectrometer by using coumarin and 6-carboxyfluorescein as the fluorophores. Measurements on the Förster energy transfer distance for the donor/acceptor pair can also be carried out using these DNA probes.