Molecular engineering of DNA: molecular beacons

Single-layer transition metal dichalcogenide nanosheet-based nanosensors for rapid, sensitive, and multiplexed detection of DNA

Single-layer transition metal dichalcogenide nanosheets, including MoS2, TiS2, and TaS2, are used as novel sensing platforms for sensitive and selective detection of DNA, based on their high fluorescence-quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a single-layer TaS2 nanosheet-based multiplexed DNA sensor is also developed.

Synthesis of fluorescent dye-doped silica nanoparticles for target-cell-specific delivery and intracellular microRNA imaging

MicroRNA (miRNA) is found to be up-regulated in many kinds of cancer and therefore is classified as an oncomiR. Herein, we design a multifunctional fluorescent nanoprobe (FSiNP-AS/MB) with the AS1411 aptamer and a molecular beacon (MB) co-immobilized on the surface of the fluorescent dye-doped silica nanoparticles (FSiNPs) for target-cell-specific delivery and intracellular miRNA imaging. The FSiNPs were prepared by a facile reverse microemulsion method from tetraethoxysilane and silane derivatized coumarin that was previously synthesized by click chemistry. The as-prepared FSiNPs possess uniform size distribution, good optical stability and biocompatibility. In addition, there is a remarkable affinity interaction between the AS1411 aptamer and the nucleolin protein on the cancer cell surface. Thus, a target-cell-specific delivery system by the FSiNP-AS/MB is proposed for effectively transferring a MB into the cancer cells to recognize the target miRNA. Using miRNA-21 in MCF-7 cells (a human breast cancer cell line) as a model, the proposed multifunctional nanosystems not only allow target-cell-specific delivery with the binding affinity of AS1411, but also can track simultaneously the transfected cells and detect intracellular miRNA in situ. The proposed multifunctional nanosystems are a promising platform for a highly sensitive luminescent nonviral vector in biomedical and clinical research.

Nanoporous molybdenum carbide nanowires: a novel sensing platform for DNA detection

Nanoporous Mo₂C nanowires have been successfully demonstrated as an effective sensing platform for nucleic acid detection for the first time.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

A label-free fluorescent molecular switch for a DNA hybridization assay utilizing a G-quadruplex-selective auramine O

A G-quadruplex molecular switch (G4-MS) assembled using auramine O and the G-rich single stranded DNA is developed for a DNA assay.

A smart DNA–gold nanoparticle probe for detecting single-base changes on the platform of a quartz crystal microbalance

A design of DNA–gold nanoparticle probe-fueled DNA strand displacements for detecting single-base changes on the platform of a quartz crystal microbalance with random sequences was developed.

Intracellular detection of ATP using an aptamer beacon covalently linked to graphene oxide resisting nonspecific probe displacement

Fluorescent aptamer probes physisorbed on graphene oxide (GO) have recently emerged as a useful sensing platform. A signal is generated by analyte-induced probe desorption. To address nonspecific probe displacement and the false positive signal, we herein report a covalently linked aptamer probe for adenosine triphosphate (ATP) detection. A fluorophore and amino dual modified aptamer was linked to the carboxyl group on GO with a coupling efficiency of ∼50%. The linearity, specificity, stability, and regeneration of the covalent sensor were systematically studied and compared to the physisorbed probe. Both sensors have similar sensitivity, but the covalent one is more resistant to nonspecific probe displacement by proteins. The covalent sensor has a dynamic range from 0.125 to 2 mM ATP in buffer at room temperature and is resistance to DNase I. Intracellular ATP imaging was demonstrated using the covalent sensor, which generated a higher fluorescence signal than the physisorbed sensor. After the cells were stimulated with 5 mM Ca(2+) for ATP production, the intracellular signal enhanced by 31.8%. This work highlights the advantages of covalent aptamer sensors using GO as both a quencher and a delivery vehicle for intracellular metabolite detection.

Isothermal amplified detection of DNA and RNA

This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.

Catalytic activity of a dual-hemin labelled oligonucleotide: conformational dependence and fluorescent DNA sensing

The conformation-dependent peroxidase activity of a dual-hemin labelled oligonucleotide was identified and conveniently utilized to design a sensitive homogenous fluorescent method for DNA sensing.

Single cell gene expression analysis in injury-induced collective cell migration

Collective cell behavior in response to mechanical injury is central to various regenerative and pathological processes. Using a double-stranded locked nucleic acid probe for monitoring real-time intracellular gene expression, we examined the spatiotemporal response of epithelial cells during injury-induced collective migration and compared to the blocker assay with minimal injury as control. We showed that cells ∼150 μm from the wound edge exhibit a gradient in response to mechanical injury, expressing different genes depending on the wounding process. While release of contact inhibition is sufficient to trigger the migratory behavior, cell injury additionally induces reactive oxygen species, Nrf2 protein, and stress response genes, including heat shock protein 70 and heme oxygenase-1, in a spatiotemporal manner. Furthermore, we show that Nrf2 has an inhibitory role in injury-induced epithelial-mesenchymal transition, suggesting a potential autoregulatory mechanism in injury-induced response. Taken together, our single-cell gene expression analyses reveal modular cell responses to mechanical injury, manipulation of which may afford novel strategies for tissue repair and prevention of tumor invasion in the future.

A fluorescence turn-on detection of copper(II) based on the template-dependent click ligation of oligonucleotides

In this work, a fluorescence turn-on method for copper(II) detection is reported. A molecular beacon (MB) was designed as a template. Cu(2+) was reduced to Cu(+) in the presence of a reductant (ascorbic acid). Two short single-stranded oligonucleotides one was labeled with a 5'-alkyne and the other with 3'-azide group, proceeded a template-dependent chemical ligation through the Cu(I)-catalyzed azide-alkyne cycloaddition. The newly generated click-ligated long chain oligonucleotide, which was complementary to the MB, opened the MB hairpin structure and resulted in a turn on fluorescence. The increase in fluorescence intensity is directly proportional to the amount of Cu(2+) added to the assay solution. The present assay is quite sensitive and allows the detection of 2 nM Cu(2+). The described assay also exhibits high selectivity over other metal ions.

The synaptoneurosome transcriptome: a model for profiling the emolecular effects of alcohol

Chronic alcohol consumption changes gene expression, likely causing persistent remodeling of synaptic structures via altered translation of mRNAs within synaptic compartments of the cell. We profiled the transcriptome from synaptoneurosomes (SNs) and paired total homogenates (THs) from mouse amygdala following chronic voluntary alcohol consumption. In SN, both the number of alcohol-responsive mRNAs and the magnitude of fold-change were greater than in THs, including many GABA-related mRNAs upregulated in SNs. Furthermore, SN gene co-expression analysis revealed a highly connected network, demonstrating coordinated patterns of gene expression and highlighting alcohol-responsive biological pathways, such as long-term potentiation, long-term depression, glutamate signaling, RNA processing and upregulation of alcohol-responsive genes within neuroimmune modules. Alterations in these pathways have also been observed in the amygdala of human alcoholics. SNs offer an ideal model for detecting intricate networks of coordinated synaptic gene expression and may provide a unique system for investigating therapeutic targets for the treatment of alcoholism.

Nanometer-sized manganese oxide-quenched fluorescent oligonucleotides: an effective sensing platform for probing biomolecular interactions

We propose a novel template-assisted strategy to prepare nanometer-sized manganese oxide (nano-MnO2) by self-assembly of some MnO2 platelets and demonstrate its application as a new class of biosensing platform for probing DNA hybridization and aptamer-target interaction in a homogeneous solution.

Hybrid magnetic nanoparticle/nanogold clusters and their distance-dependent metal-enhanced fluorescence effect via DNA hybridization

To improve the metal-enhanced fluorescence (MEF) effect of nanogolds (AuNPs) and accurately detect specific DNA sequences via DNA hybridization, novel hybrid magnetic nanoparticles/nanogold clusters (HMNCs) were designed based on finite-difference time-domain simulation results and prepared by using Fe3O4 and nanogolds. The nanogolds outside the HMNC were then conjugated with thiol-terminated DNA molecules, thus DNA modified-HMNCs (DNA-HMNCs) were obtained. The size distributions of these nanostructures were measured by a Malvern size analyzer, and their morphology was observed via transmission electron microscopy (TEM). The ultraviolet (UV)-visible (vis) absorption spectra of the samples were recorded with a UV-2600 spectrophotometer. Fluorescence spectra and the MEF effect were recorded using a spectrophotofluorometer, and lifetimes were determined using a time-correlated single photon counting apparatus. The prepared HMNCs were stable in aqueous solutions and had an average diameter of 87 ± 3.2 nm, with six to eight AuNPs around a single Fe3O4 nanoparticle. Fluorescein isothiocyanate (FITC) tagged DNA-HMNC conjugates exhibited a significant MEF effect and could accurately detect specific DNA sequences after DNA hybridization. This result indicates their various potential applications in sensors and biomedical fields.

Fluorescence detection of DNA hybridization based on the aggregation-induced emission of a perylene-functionalized polymer

A perylene-functionalized polycation was synthesized by quaternization of poly(4-vinylpyridine) with bromomethyl-perylene and methyl iodide, which exhibited a unique aggregation-induced emission (AIE) effect. The synthesized polycation and polyanion ssDNA could form a complex probe to detect DNA hybridization. Upon adding noncomplementary ssDNA, the fluorescence of the complex probe increased due to the AIE effect; upon adding complementary ssDNA, the fluorescence intensity changed little due to the combined effects of AIE and duplex-quenching resulting from the intercalation of perylene into the duplex.

High-throughput bead-based identification of structure-switching aptamer beacons

We describe a new platform to identify structure-switching DNA beacon aptamers, which detect small molecules in a specific manner. By clonally amplifying a DNA library designed to fluoresce in response to binding events onto microbeads, aptamer beacons can be selected by stringent fluorescence-assisted sorting. We validated this method by isolating known and novel anti-steroid aptamers from two separate DNA libraries that were structurally enriched with three-way junctions. Importantly, aptamers were retrieved in only a few (three) rounds of selection by this approach and did not require further optimization, significantly streamlining the process of beacon development.

Bis-pyrene-modified unlocked nucleic acids: synthesis, hybridization studies, and fluorescent properties

Efficient synthesis of a building block for the incorporation of a bis-pyrene-modified unlocked nucleic acid (UNA) into oligonucleotides (DNA*) was developed. The presence of bis-pyrene-modified UNA within a duplex leads to duplex destabilization that is more profound in DNA*/RNA and less distinct in DNA*/DNA duplexes. Nevertheless, the destabilization effect of bis-pyrene-modified UNA is weaker than that of unmodified UNA. Some oligonucleotides with bis-pyrene-modified UNA incorporations displayed superior mismatch discrimination capabilities. UV/Vis absorption and molecular modeling studies indicate that the pyrene groups of bis-pyrene-modified UNA are located in the major groove of a duplex. Oligonucleotides containing two bis-pyrene-modified UNA monomers showed low pyrene monomer emission in bulge-containing duplexes, high pyrene monomer emission in fully matched duplexes, and 5-(pyrenyl)uracil:pyrene exciplex emission in the single-stranded form. Such fluorescent properties enable the application of bis-pyrene-modified UNA in the development of fluorescence probes for DNA/RNA detection and for detection of deletions at specific positions.

Fluorescent sensors using DNA-functionalized graphene oxide

In the past few years, graphene oxide (GO) has emerged as a unique platform for developing DNA-based biosensors, given the DNA adsorption and fluorescence-quenching properties of GO. Adsorbed DNA probes can be desorbed from the GO surface in the presence of target analytes, producing a fluorescence signal. In addition to this initial design, many other strategies have been reported, including the use of aptamers, molecular beacons, and DNAzymes as probes, label-free detection, utilization of the intrinsic fluorescence of GO, and the application of covalently linked DNA probes. The potential applications of DNA-functionalized GO range from environmental monitoring and cell imaging to biomedical diagnosis. In this review, we first summarize the fundamental surface interactions between DNA and GO and the related fluorescence-quenching mechanism. Following that, the various sensor design strategies are critically compared. Problems that must be overcome before this technology can reach its full potential are described, and a few future directions are also discussed.

Biomolecule-to-fluorescent-color encoder: modulation of fluorescence emission via DNA structural changes

A biomolecule-to-fluorescent-color (B/F) encoder for optical readout of biomolecular information is proposed. In the B/F encoder, a set of fluorescence wavelengths and their intensity levels are used for coding of a biomolecular signal. A hybridization chain reaction of hairpin DNAs labeled with fluorescent reporters was performed to generate the fluorescence color codes. The fluorescence is modulated via fluorescence resonance energy transfer, which is controlled by DNA structural changes. The results demonstrate that fluorescent color codes can be configured based on two wavelengths and five intensities using the B/F encoder, and the assigned codes can be retrieved via fluorescence measurements.

A graphene-based biosensing platform based on the release of DNA probes and rolling circle amplification

We report a versatile biosensing platform capable of achieving ultrasensitive detection of both small-molecule and macromolecular targets. The system features three components: reduced graphene oxide for its ability to adsorb single-stranded DNA molecules nonspecifically, DNA aptamers for their ability to bind reduced graphene oxide but undergo target-induced conformational changes that facilitate their release from the reduced graphene oxide surface, and rolling circle amplification (RCA) for its ability to amplify a primer-template recognition event into repetitive sequence units that can be easily detected. The key to the design is the tagging of a short primer to an aptamer sequence, which results in a small DNA probe that allows for both effective probe adsorption onto the reduced graphene oxide surface to mask the primer domain in the absence of the target, as well as efficient probe release in the presence of the target to make the primer available for template binding and RCA. We also made an observation that the circular template, which on its own does not cause a detectable level of probe release from the reduced graphene oxide, augments target-induced probe release. The synergistic release of DNA probes is interpreted to be a contributing factor for the high detection sensitivity. The broad utility of the platform is illustrated though engineering three different sensors that are capable of achieving ultrasensitive detection of a protein target, a DNA sequence and a small-molecule analyte. We envision that the approach described herein will find useful applications in the biological, medical, and environmental fields.

Mesoporous phosphonate-TiO2 nanoparticles for simultaneous bioresponsive sensing and controlled drug release

The bioresponsive detection of DNA or proteins and the controlled release of drug molecules are two important research areas for both experimental studies and practical applications. However, the real incorporation of these two functions into one system is still untouched. Being different from the widely reported mesoporous silica nanoparticles that were used as the support, herein we report a smart system based on hybrid phosphonate-TiO(2) mesoporous nanostructures capped with fluorescein labeled oligonucleotides, which can realize simultaneous and highly-efficient biomolecule sensing and controlled drug release. The fluorescence of the labeled oligonucleotides is first quenched by the phosphonate-TiO(2) materials, which are related to the fluorescence resonance energy transfer mechanism. The addition of complementary DNA strands or protein target leads to the displacement of the capped DNA due to hybridization or protein-aptamer reactions. The opening of the pores can further cause the release of entrapped drugs as well as the restoration of dye fluorescence. The present method is proven to have high selectivity towards specific ssDNA and proteins.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Recent advances in fluorescent nucleic acid probes for living cell studies

Living cell studies can offer tremendous opportunities for biological and disease studies. Due to their high sensitivity and selectivity, minimum interference with living biological systems, ease of design and synthesis, fluorescent nucleic acid probes (FNAPs) have been widely used in living cell studies, such as for intracellular detection, cell detection, and cell-to-cell communication. Here, we review the general requirements and the recent developments in FNAPs for living cell studies. We broadly classify these designs as hybridization probes and aptamer probes. For hybridization probes, we describe recently developed designs, such as nanomaterial-based and amplification-based hybridization probes. For aptamer probes, we discuss four general paradigms that have appeared most frequently in the literature: nanomaterial-based, nanomachine-based, cell surface-anchored and activatable aptamer probe designs in vivo. FNAPs promise to open up new and exciting opportunities in biological marks detection for a wide range of biological and medical applications.

Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction

Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.

A reusable sensor for the label-free detection of specific oligonucleotides by surface plasmon fluorescence spectroscopy

The development of a reusable molecular beacon (MB)-based sensor for the label-free detection of specific oligonucleotides using surface plasmon fluorescence spectroscopy (SPFS) as the readout method is described. The MBs are chemisorbed at planar gold surfaces serving as fluorescence quenching units. Target oligonucleotides of 24 bases can be detected within a few minutes at high single-mismatch discrimination rates.

Ultrasensitive detection of 3′-5′ exonuclease enzymatic activity using molecular beacons

An ultrasensitive and rapid fluorescence assay was developed for the detection of 3′-5′ exonuclease activity using molecular beacons.

A rapid and sensitive detection of HBV DNA using a nanopore sensor

The simplest single-molecule nanopore sensor can be used for the rapid and sensitive detection of pathogenic DNA at the single-base recognition level.

Metal phosphonate hybrid materials: from densely layered to hierarchically nanoporous structures

Inorganic–organic metal phosphonate hybrid materials with great diversity in structure and properties exhibit application potential in various fields.

Cell-membrane-permeable and cytocompatible phospholipid polymer nanoprobes conjugated with molecular beacons

To enable the visualization of the distribution and dynamics of intracellular biomolecules and thereby understand the mechanisms of intracellular bioreactions, we developed a specific functional nanoprobe through the combination of a well-designed, cytocompatible phospholipid polymer and molecular beacons (MBs). A water-soluble, amphiphilic phospholipid polymer, poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-co-n-butyl methacrylate (BMA)-co-N-succinimidyloxycarbonyl tetra(ethylene glycol) methacrylate] (PMBS), was synthesized and conjugated with MBs to form nanoprobes via a chemical reaction between the ester group of N-hydroxysuccinimide and the amine group of the MBs. Surface tension measurements indicated that the polymeric nanoprobes had different conformations in aqueous solution, specifically at a concentration of 1.0 mg/mL. The PMBS, containing the large, hydrophobic BMA, formed polymer aggregates. The carcinoma cells used to test the probes remained 100% viable after incubation with PMBS-MB probes. The polymeric nanoprobes demonstrated not only a high target specificity but also resistance to nonspecific adsorption of proteins compared with unconjugated MBs and were able to penetrate the cytoplasm of the cells, allowing the live imaging of mRNA. In summary, MPC polymer-MB nanoprobes have great potential for practical application for the noninvasive monitoring of intracellular biomolecules and bioreactions in real time.

A novel sensitive and selective ligation-based ATP assay using a molecular beacon

In this paper, a novel, facile fluorometric ATP assay with high sensitivity and excellent selectivity has been reported. This approach utilizes a molecular beacon, T4 DNA ligase and two short oligonucleotides. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction and the ligation product restores the fluorescence of the molecular beacon. Owing to the high sensitivity of the molecular beacon and T4 DNA ligase's high substrate dependence, this novel ATP assay demonstrates exceptional selectivity and high sensitivity down to 0.14 nM in homogeneous solution. Cellular ATP concentrations in several cell lines have been determined by measuring the lysate sample containing 8.0 × 10(3) cells.

DNA nanomachines as evolved molecular beacons for in vitro and in vivo detection

Modern biosensors require high sensitivity, great signal enhancement and extensive applicability for detection and diagnostic purposes. Traditional molecular beacons (MBs) do not meet these requirements because of the lack of signal amplification. The current amplification pathways using enzymes, DNAzymes and nanoparticles are usually quite sophisticated and are limited to specific applications. Herein, we developed simple biosensors based on the structure of kissing-hairpin. Through hybridization amplification of these nanomachines, the evolved MBs could greatly enhance the detected signals (approximately 10-fold higher than the signals generated by traditional molecular beacons), reduce the sensing limits for targets and, remarkably, distinguish single-base mismatches specifically for nucleic acid detection. In addition, these new MBs can be directly applied in living cells. By introducing aptamer sequences, these novel sensors can also detect proteins and small molecules. These properties were exemplified by the detection of both the β-actin gene and thrombin. The simplicity, sensitivity and flexibility of these devices make them appropriate for more expansive applications.