A RuO2 Nanosheet as a Novel Quencher-free Platform for the Detection of Nucleic Acids in a Homogeneous Solution

A fluorescent dye-labeled DNA probe was adsorbed and quenched on the monolayer of RuO₂ nanosheets. Significant fluorescent recovery was observed upon the addition of complementary DNA due to desorption of the probe from the surface of the RuO₂ nanosheet through duplex formation. The efficiency of fluorescence recovery was higher than that for graphene oxide, which was known as a quencher-free platform for the detection of nucleic acids in a homogeneous solution.

DNA nanosheet as an excellent fluorescence anisotropy amplification platform for accurate and sensitive biosensing

Recently, various inorganic nanomaterials have been used as fluorescence anisotropy (FA) enhancers for biosensing successfully. However, most of them are size-uncontrollable and possess an intensive fluorescence quenching ability, which will seriously reduce the accuracy and sensitivity of FA method. Herein, we report a two-dimensional DNA nanosheet (DNS) without fluorescence quenching effect as a novel FA amplification platform. In our strategy, fluorophore-labeled probe DNA (pDNA) is linked onto the DNS surface through the hybridization with the handle DNA (hDNA) that extended from the DNS, resulting in the significantly enhanced FA value. After the addition of target, the pDNA was released from the DNS surface due to the high affinity between the hDNA and target, and the FA was decreased. Thus, target could be detected by the significantly decreased FA value. The linear range was 10-50 nM and the limit of detection was 8 nM for the single-stranded DNA detection. This new method is general and has been also successfully applied for the detection of ATP and thrombin sensitively. Our method improved the accuracy of FA assay and has great potential to detect series of biological analytes in complex biosensing systems.

A dandelion-like liposomes-encoded magnetic bead probe-based toehold-mediated DNA circuit for the amplification detection of MiRNA

The development of facile and sensitive miRNA quantitative detection methods is a central challenge for the early diagnosis of miRNA-related diseases. Herein, we propose a strategy for a liposome-encoded magnetic bead-based DNA toehold-mediated DNA circuit for the simple and sensitive detection of miRNA based on a toehold-mediated circular strand displacement reaction (TCSDR) coupled with a personal glucometer (PGM ). In this strategy, a glucoamylase-encapsulated liposomes (GELs)-encoded magnetic bead (GELs-MB) probe is designed to integrate target binding, magnetic separation, and signal response. Upon sensing the target miRNA-21, a GELs-MB probe-based toehold-mediated circular strand displacement reaction (TCSDR) was initiated with the help of fuel-DNA, constructing a DNA circuit system, and realizing target recycling amplification and the disassembly of the liposomes. The disassembled liposomes were finally removed via magnetic separation, and the encapsulated glucoamylase was liberated to catalyze amylose hydrolysis with multiple turnovers to glucose for a PGM readout. Benefiting from target recycling amplification initiated by the toehold-mediated DNA circuit and the liposome multiple-label amplification, a small quantity of target miRNA-21 can be transformed into a large glucose signal. The strategy realized the quantification of miRNA-21 down to a level of 0.7 fM without enzymatic amplification or precise instrumentation. Moreover, the high-density GELs-MB probe allows the sensitive detection of miRNA-21 to be accomplished within 1.5 h. Furthermore, this strategy exhibits the advantages of specificity and simplicity, since a toehold-mediated strand displacement reaction, magnetic separation and portable PGM were used. Importantly, this strategy has been demonstrated to allow the high-confidence quantification of miRNA. Therefore, with the advantages of low cost, ease of use, portability, and sensitivity, the reported method holds great potential for the early diagnosis of miRNA-related diseases.

An ATP-fueled nucleic acid signal amplification strategy for highly sensitive microRNA detection

Herein, an adenosine triphosphate (ATP)-fueled nucleic acid signal amplification strategy based on toehold-mediated strand displacement (TMSD) and fluorescence resonance energy transfer (FRET) was proposed for highly sensitive detection of microRNA-21. More importantly, the target microRNA-21 could be regenerated with ATP as the fuel rather than a nucleotide segment in conventional approaches, which made the proposed strategy simple and efficient due to the high affinity and strength of the aptamer-target interaction.

Stepwise nanoassembly of a single hairpin probe and its biosensing

Herein, we describe a novel trigger-induced DNA nanoassembly method using only one loop-stem shaped hairpin probe (HP) that consists of three different functional regions as a single building unit. The Region I is designed complementary to the trigger, while the Region II and Region III are projected to complementary with each other. When hybridized with the trigger, a toehold mediated strand displacement (TMSD) occurred on the strand of Region I, leading to the release of Region III for further hybridization with the Region II on another HP molecule and in turn inducing a stepwise growth of HP with the aid of polymerase. Unlike the conventional assembly approaches that rely on the sophisticated sequence design and complex operation, the single-HP nanoassembly is easy and fast. Moreover, because many HPs are opened during the assembly process, we exemplified the nanoassembly strategy by re-designing a new labeled hairpin probe to analyze the Kras oncogene with a high sensitivity and specificity. The present study demonstrated a novel promising DNA nanoassembly strategy for biological applications.

Systematic comparison between toehold exchange and toehold displacement: exploration for highly specific and sensitive DNA detection

The detection of nucleic acid variations with high specificity and sensitivity is essential for the good practice of precision medicine.

Oxo-Functionalized Graphene as a Cell Membrane Carrier of Nucleic Acid Probes Controlled by Aging

We applied a fluorescein-containing oligonucleotide (ON) to probe surface properties of oxidized graphene (oxo-G) and observed that graphene-like patches are formed upon aging of oxo-G, indicated by enhanced probe binding and by FTIR spectroscopic analysis. By using a recently developed fluorogenic endoperoxide (EP) probe, we confirmed that during the aging process the amount of EPs on the oxo-G surface is reduced. Furthermore, aging was found to strongly affect cell membrane carrier properties of this material. In particular, freshly prepared oxo-G does not act as a carrier, whereas oxo-G aged for 28 days at 4 °C is an excellent carrier. Based on these data we prepared an optimized oxo-G, which has a low-defect density, binds ONs, is not toxic, and acts as cell membrane carrier. We successfully applied this material to design fluorogenic probes of representative intracellular nucleic acids 28S rRNA and β-actin-mRNA. The results will help to standardize oxidized graphene derivatives for biomedical and bioanalytical applications.

Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection

Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

A microRNA-activated molecular machine for non-enzymatic target recycling amplification detection of microRNA from cancer cells

The presence of the microRNA-141 target molecules activates the DNA molecular machine powered by the DNA fuel strands, leading to non-enzymatic target cyclic reuse of microRNA-141 and significantly amplified fluorescent signals for sensitive monitoring of microRNA-141 from low numbers of human prostate cancer cells.

A target responsive aptamer machine for label-free and sensitive non-enzymatic recycling amplification detection of ATP

Based on a new target-triggered aptamer molecular machine, a label-free and non-enzymatic target recycling amplification strategy for sensitive fluorescence detection of ATP in human serums is described. The presence of the target ATP together with the DNA fuel strand initiates the operation of the aptamer machine and leads to cyclic reuse of ATP and the release of many G-quadruplex sequences, which associate with a fluorescent dye to generate significantly amplified fluorescence signals to achieve sensitive detection of ATP.

What Controls the "Off/On Switch" in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles?

In DNA dynamic nanotechnology, a toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements a displacing action is conjugated on gold nanoparticles. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, i.e., the abrupt jump in behavior of an "off/on switch", in the reaction rate when the invading toehold was extended to eight bases from seven bases. These phenomena are attributed to the effect of steric hindrance arising from the high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.

Fabrication of enzyme-immobilized halloysite nanotubes for affinity enrichment of lipase inhibitors from complex mixtures

Lipase is the key enzyme for catalyzing triglyceride hydrolysis in vivo, and lipase inhibitors have been used in the management of obesity. We present the first report on the use of lipase-adsorbed halloysite nanotubes as an efficient medium for the selective enrichment of lipase inhibitors from natural products. A simple and rapid approach was proposed to fabricate lipase-adsorbed nanotubes through electrostatic interaction. Results showed that more than 85% lipase was adsorbed into nanotubes in 90 min, and approximately 80% of the catalytic activity was maintained compared with free lipase. The specificity and reproducibility of the proposed approach were validated by screening a known lipase inhibitor (i.e., orlistat) from a mixture that contains active and inactive compounds. Moreover, we applied this approach with high performance liquid chromatography-mass spectrometry technique to screen lipase inhibitors from the Magnoliae cortex extract, a medicinal plant used for treating obesity. Two novel biphenyl-type natural lipase inhibitors magnotriol A and magnaldehyde B were identified, and their IC50 values were determined as 213.03 and 96.96 μM, respectively. The ligand-enzyme interactions of magnaldehyde B were further investigated by molecular docking. Our findings proved that enzyme-adsorbed nanotube could be used as a feasible and selective affinity medium for the rapid screening of enzyme inhibitors from complex mixtures.

The graphene/nucleic acid nanobiointerface

In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.

A novel graphene oxide amplified fluorescence anisotropy assay with improved accuracy and sensitivity

A novel and versatile graphene oxide (GO) amplified fluorescence anisotropy (FA) strategy with improved accuracy and sensitivity has been successfully developed.