Label-free molecular beacons for biomolecular detection

An allosteric palindromic hairpin probe based dual-mode interactive strand displacement amplification enables robust miRNA biosensing

This study introduces an allosteric palindromic hairpin probe (APHP)-based dual-mode interactive strand displacement amplification (DMI-SDA) system for ultrasensitive detection of microRNA-155. The system achieves exceptional signal amplification and improved signal preservation using dimeric G-triplexes as signal reporters, enabling robust detection of miRNA-155, representing a promising avenue in molecular diagnosis.

Versatile DNA Balances via Adjacent Base Stacking for Homogeneous Assay of Energy Parameters, Small Molecules, And Ribonuclease

Homogeneous assays often obviate any separation and washing steps, thus minimizing the risks of contamination and false positive. DNA toehold exchange is a homogeneous, reversible process whose thermodynamic properties can be finely tuned for various assay applications. However, the developed probes often rely on direct interactions of analytes with DNA strands involved in toehold exchange, limiting the versatility of probe design. Here, the coaxial adjacent stacking between one auxiliary strand and another invading strand offers a favorable ΔG to shift one DNA balance, while the auxiliary strand is independent of the DNA balance itself. Therefore, such a DNA balance allowed fine tuning of the equilibrium via adjustment of the auxiliary strand alone. The energy contribution of base stacking can be quantified in a homogeneous solution based on the difference in the equilibrium constant. Besides, the proof of concept for DNA balance allows effective assay of a small molecule or ribonuclease in a homogeneous solution. This novel DNA balance via adjacent base stacking provides an interesting alternative to homogeneously assay various analytes.

Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms

Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.

Application of the Dimeric G-Quadruplex and toehold-mediated strand displacement reaction for fluorescence biosensing of ochratoxin A

Ochratoxin A (OTA) is one of the most toxic mycotoxins that exists in various agro-products and foods. Here, a non-label and enzyme-free fluorescence biosensor for highly specific detection of OTA has been developed by the combination of toehold-mediated strand displacement reaction (TMSD) and G-quadruplex dimer/ThT (G-dimer/ThT). The DNA duplex (aptamer-IP) is composed of the anti-OTA aptamer and a single stranded initiation probe (IP). In the presence of OTA, the attachment of target to aptamer leads to the liberation of the IP, which activates the cycle TMSD amplifications of two hairpin probes (H1 and H2) accompanied by the production of numerous H1-H2 assemblies. This double-stranded H1-H2 structure results in the proximity between the 5'-end overhang tail of H1 and the 3'-end stem of H2 to liberate the pre-blocked G-dimer sequence for lighting up ThT. In addition, the method displayed a stable fluorescence emission in the high-salt media. It was successfully applied to analyze OTA in real food samples. Hence, the constructed fluorescence biosensing platform might provide a new way for OTA and other toxin analysis detection.

Beyond amyloid proteins: Thioflavin T in nucleic acid recognition

Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.

Expanding the codes: The development of density-encoded hydrogel microcarriers for suspension arrays

Although suspension array technology (SAT), which uses encoded microspheres, provides high-quality results with versatile applicability for information-intensive bioanalytic applications, current encoding strategies limit the number of codes that can be distinguished. In this paper, we introduce density-encoded hydrogel microcarriers (DMs), which employ the intrinsic density property of biomaterials as a high-capacity coding dimension. Two hydrogel monomers were employed at different ratios to synthesize microgels with distinctive densities. DMs not only can be simultaneously decoded and separated using density gradient centrifugation, but also are compatible with flow cytometry detection. The size and color of DMs have been used as extra coding parameters, to construct an 8 × 2 × 4 (density × size × color) three-dimensionally encoded hydrogel microcarrier library. With aptamer-functionalized DMs (ADMs), we developed a 4-plex protein quantification method for the label-free detection of plasma biomarkers with sub-nanomolar detection limits and good linearities. Moreover, ADMs can be used for label-free naked-eye detection of tumor-derived exosomes. We believe that the simplicity and functionality of DMs will advance the field of suspension arrays and inspire the development of DM-based diagnostic applications.

Comparative evaluation and design of a G-triplex/thioflavin T-based molecular beacon

Both G-quadruplex (G4) and G-triplex (G3) can bind thioflavin T (ThT) to light up the fluorescence of ThT. G4/ThT and G3/ThT can be used as fluorescent indicators to construct a label-free molecular beacon (MB). In this work, we present a comparative perspective of G3/ThT-based MB and G4/ThT-based MB. The results showed that the G3/ThT-based MB had higher sensitivity and faster response speed than the G4/ThT-based MB. Furthermore, we systematically studied the effect of stem length and varying pairs on the response of the G3/ThT-based MB, and then proposed one rational design of the G3/ThT-based MB. This work demonstrates that the shorter G3 is more suitable for constructing the MB stem. This present work opens a promising way to develop a sensitive, simple and homogeneous biosensing method.

Label-free and enzyme-free fluorescence detection of microRNA based on sulfydryl-functionalized carbon dots via target-initiated hemin/G-quadruplex-catalyzed oxidation

Carbon dots (CDs)-based biosensors have attracted considerable interest in reliable and sensitive detection of microRNA (miRNA) because of their merits of ultra-small size, excellent biosafety and tunable emission, whereas complicated labeling procedure and expensive bioenzyme associated with current strategies significantly limit their practical application. Herein, we developed a label-free and enzyme-free fluorescence strategy based on strand displaced amplification (SDA) for highly sensitive detection of miRNA using sulfydryl-functionalized CDs (CDs-SH) as probe. CDs-SH displayed excellent response to G-quadruplex DNA against other DNAs based on based on the catalytic oxidation of -SH into -S-S- by hemin/G-quadruplex. Further, CDs-SH were employed to detect miRNA, using miRNA-21 as target model, which triggered the SDA reaction of P1 and P2 to generate hemin/G-quadruplex, subsequently making CDs-SH transform from dot to aggresome along with the quenched fluorescence. Therefore, label-free, enzyme-free, and highly sensitive analysis of miRNA-21 was readily acquired with a limit of detection at 0.03 pM. This proposed biosensor couples the advantages of CDs and label-free/enzyme-free strategy, and thus has a significant potential to be used in early and accurate diagnosis of cancer.

Dimeric G-Quadruplex: An Effective Nucleic Acid Scaffold for Lighting Up Thioflavin T

As a recently identified higher-order quadruplex (G4) structure, the G4 dimer possesses unique structure and biological functions. In this work, we found accidentally that two tandem PW17 (one known G4-forming DNA) sequences can fold into a stable G4 dimer, and the G4 dimer can enhance dramatically the fluorescence intensity of thioflavin T (ThT). The G4 dimer/ThT fluorescence intensity is about ninefold that of the corresponding G4 monomer/ThT. Meanwhile, compared with the common G4/ThT system, G4 dimer/ThT exhibited more stable fluorescence emission in the media with various concentrations of Na⁺ and K⁺. On the basis of these findings, G4 dimer/ThT was used as a fluorescence indicator to construct one arched DNA probe for label-free detection of DNA. By incorporating a G4 dimer sequence in amplified products, we further designed one rolling circle amplification-based biosensing strategy to show the utility of this G4 dimer/ThT fluorescence indicator. This study demonstrates that dimeric G4 is an effective nucleic acid scaffold for lighting up ThT, showing promising applications in a label-free bioassay.

Hg2+-mediated stabilization of G-triplex based molecular beacon for label-free fluorescence detection of Hg2+, reduced glutathione, and glutathione reductase activity

G-triplexes have been reported recently with the similar function to G-quadruplex that can combine with thioflavin T (ThT) and emit strong fluorescence but easier to be controlled and excited. In this work, we report an Hg²⁺-mediated stabilization of G-triplex based functional molecular beacon (G3TMB) sensing system for the label-free detection of Hg²⁺, reduced glutathione (GSH), and glutathione reductase (GR) activity. In the presence of Hg²⁺, the extended G-triplex sequence containing the "T" bases can form a stable hairpin structure due to the strong interactions of "T-Hg²⁺-T", resulting in the locking of G-tracts in the stem of the G3TMB effectively. However, the hairpin structure of the G3TMB can be opened by the introduction of GSH through the stronger "GSH-Hg²⁺" interaction. Therefore, by employing the fact that GR can catalyze the reduction of oxidized glutathione (GSSG) into GSH, this concept can be applied to fluorescence "off-on" detection of GR activity, with a linear range of 0.02-30 mU/mL and detection limit of 0.01 mU/mL. This work may expand a new perspective of G-triplex based functional molecular beacon as the label-free fluorescent probes in the detection of small biomolecule and enzyme activity.

Evaluation of Rationally Designed Label-free Stem-loop DNA Probe Opening in the Presence of miR-21 by Circular Dichroism and Fluorescence Techniques

The characteristic features of stem-loop structured probes make them robust tools to detect targets with high sensitivity and selectivity. The basis of the hairpin based sensors operation is a conformational change that occurs upon hybridization of target with stem-loop probe. The design of the stem-loop probe has an important role in target recognition. Therefore, we designed a label-free stem loop probe for targeting miR-21 as a cancer biomarker investigated by web-based tools; its thermodynamic parameters obtained by thermal UV spectroscopy. The efficiency of stem-loop structure opening in the presence of target and non-target sequences was evaluated by fluorescence spectroscopy and circular dichroism spectro-polarimetry. The results showed that the target sequence opens the structure of hairpin efficiently in comparison to non-target sequences. To optimize the stem-loop hybridization to its target, the buffer ionic strength was changed by adding different concentrations of NaCl, KCl and MgCl₂. It was shown that buffering conditions have a significant role in loop structure opening and its optimization, led to an increase in sensitivity detection and have improved LOD from 60 pM to 45 pM.

A label-free G-quadruplex-based fluorescence assay for sensitive detection of alkaline phosphatase with the assistance of Cu2

The level of alkaline phosphate (ALP) is a significant biomarker index in organism. In this work, a label-free and sensitive G-quadruplex fluorescence assay for monitoring ALP activity has been developed with the assistance of Cu²⁺ based on the competitive binding effect between pyrophosphate (PPi) and G-quadruplex-N-methylmesoporphyrin (G4/NMM) complex to Cu²⁺. In the sensing assay, the G4/NMM complex is employed as a signal indicator, while the Cu²⁺ as a quencher and the PPi as recovery agent as well as the hydrolytic substance for ALP. In details, the fluorescence of the G4/NMM complex was efficiently quenched by introducing Cu²⁺ due to the proximal carboxylate groups of NMM coordinating with the Cu²⁺ as well as the unfolding of G-quadruplex by Cu²⁺, while the higher affinity between PPi and Cu²⁺ could lead to the fluorescence recovery. However, in the presence of ALP, the PPi was hydrolyzed to phosphate ions (Pi) which cannot integrate with Cu²⁺, resulting in the fluorescence quenching once again. Thus, a simple and facile way to inspect ALP has been exploited. The proposed assay shows a good linear relationship in the range from 0.5 to 100 U/L with the detection limit of 0.3 U/L. Moreover, the fabricated method is succeeded in detecting ALP in human serum samples, indicating the potential as a profitable candidate in biological and biomedical application.

Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues

Aptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current systems are limited by relatively low enhancement of fluorescence upon dye binding. Here, we added duplex modules to G4 structures, which supposedly cause the formation of a dye-binding cavity between two modules. Screening of multiple synthetic GFP chromophore analogues and variation of the duplex module resulted in the selection of dyes that light up after complex formation with two-module structures and their RNA analogues by up to 20 times compared to parent G4s. We demonstrated that the short duplex part in TBA25 is preferable for fluorescence light up in comparison to parent TBA15 molecule as well as TBA31 and TBA63 stabilized by longer duplexes. Duplex part of TBA25 may be partially unfolded and has reduced rigidity, which might facilitate optimal dye positioning in the joint between G4 and the duplex. We demonstrated dye enhancement after binding to modified TBA, LTR-III, and Tel23a G4 structures and propose that such architecture of short duplex-G4 signaling elements will enforce the development of improved aptasensors.

Ratiometric Multicolor Analysis of Intracellular MicroRNA Using a Chain Hybrid Substitution-Triggered Self-Assembly of Silver Nanocluster-Based Label-Free Sensing Platform

A simple and label-free sensing platform with low background based on the chain-displacement triggered self-assembly of Ag NCs was developed for ratiometric visual analysis of intracellular miRNA-21. Based on this sensitively ratiometric sensing approach, a picomole limit detection for miRNA-21 can be obtained. Most importantly, compared with the traditional single base mismatch detection method, our proposed method can realize single base mismatch detection according to the remarkable fluorescence color conversion, rather than simple fluorescence intensity change, which can obviously improve the accuracy and reliability. In addition, successful multicolor real-time monitoring of intracellular miRNA-21 makes the probe a potential candidate for miRNA-21 inhibiting drug screening. Furthermore, MCF-7, HeLa, and normal L02 cells can also be visually differentiated according to the fluorescence color by using the label-free sensing platform, showing its potential prospect in target visual analysis.

A rapid label- and enzyme-free G-quadruplex-based fluorescence strategy for highly-sensitive detection of HIV DNA

Because rapid, convenient, and selective methods for HIV detection are urgently needed, herein, a simple label-free and enzyme-free strategy is constructed for sensitive fluorescence detection of HIV DNA using the fluorescent intercalating dye thioflavin T (THT) as the detection signal source. This strategy utilizes a hairpin DNA sequence (H1) and two assistant strands. H1 is wisely designed with a G-quadruplex sequence in the stem. Target DNA, when present in solution, will hybridize with H1 to form H1/target duplexes and release the G-quadruplexes. Additionally, the assistant probes hybridize with the unfolded H1 to form a stable DNA double strand, resulting in the displacement of the target to participate in another similar reaction cycle. Consequently, many G-quadruplex structures are generated, leading to a significantly amplified fluorescence signal of THT. The linear range is from 0.1 nM to 50.0 nM with a limit of detection of 13 pM. Results can be achieved within 40 min, because the cyclic amplification involves only one DNA hairpin and two auxiliary chains. Furthermore, this platform exhibited good selectivity with one base mismatch or other DNA sequences. This strategy could be used as a simple, sensitive, and selective tool to detect other DNA biomarkers.

Dendrimer-Functionalized Superparamagnetic Nanobeacons for Real-Time Detection and Depletion of HSP90α mRNA and MR Imaging

Background & Aims: The use of antisense oligonucleotide-based nanosystems for the detection and regulation of tumor-related gene expression is thought to be a promising approach for cancer diagnostics and therapies. Herein, we report that a cubic-shaped iron oxide nanoparticle (IONC) core nanobeacon is capable of delivering an HSP90α mRNA-specific molecular beacon (HSP90-MB) into living cells and enhancing T₂-weighted MR imaging in a tumor model.

Methods: The nanobeacons were built with IONC, generation 4 poly(amidoamine) dendrimer (G4 PAMAM), Pluronic P123 (P123) and HSP90-MB labeled with a quencher (BHQ1) and a fluorophore (Alexa Fluor 488).

Results: After internalization by malignant cells overexpressing HSP90α, the fluorescence of the nanobeacon was recovered, thus distinguishing cancer cells from normal cells. Meanwhile, MB-mRNA hybridization led to enzyme activity that degraded DNA/RNA hybrids and resulted in downregulation of HSP90α at both the mRNA and protein levels. Furthermore, the T₂-weighted MR imaging ability of the nanobeacons was increased after PAMAM and P123 modification, which exhibited good biocompatibility and hemocompatibility.

Conclusions: The nanobeacons show promise for applicability to tumor-related mRNA detection, regulation and multiscale imaging in the fields of cancer diagnostics and therapeutics.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

A rapid fluorometric method for determination of aflatoxin B1 in plant-derived food by using a thioflavin T-based aptasensor

A fluorometric aptamer-based method is described for the determination of aflatoxin B₁ (AFB₁). The fluorescent dye thioflavin T (ThT) forms a complex with the aptamer against AFB₁ (aptamer/ThT), and the fluorescence of the complex is strongly enhanced. On addition of AFB₁, it will bind to the aptamer and release ThT. The fluorescence of free ThT is much weaker. The fluorescence of the system, best measured at excitation/emission wavelengths of 440/487 nm, drops gradually in the AFB₁ concentration range from 0.2 to 200 ng·mL^-1, exhibiting good linearity. The detection limits are 0.2 ng·mL^-1 in buffer solution, and 1 ng·mL^-1 when applied to plant-derived food. The recovery of AFB₁ from spiked foodstuff ranges from 74.7% to 121%. The assay can be performed within 20 min. Graphical abstract Schematic presentation of label-free thioflavin T (ThT)-based fluorescence aptasensor using aflatoxin B₁(AFB₁) aptamer/ThT G-quadruplex complex and the AFB1 aptamer/AFB1 complex fluorescent signal system for the rapid and sensitive detection of AFB1 in soy sauce, spirits, rice, corn and peanuts.

Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons

Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence ( Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016 , 52 , 4041 - 4044 ). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the  inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.

A G-triplex based molecular beacon for label-free fluorescence "turn-on" detection of bleomycin

Since bleomycins (BLMs) play a prominent role in the clinical treatment of various cancers, the development of convenient and sensitive detection assays for BLM is of great significance in cancer therapy and related biological mechanism research. Here, taking advantage of the easily controllable and excitation of the G-triplex DNA structure, we reported a facile, label-free G-triplex based functional molecular beacon (G3MB) sensing system for fluorescence "turn-on" detection of BLM based on BLM-Fe(ii) mediated DNA strand scission. In the presence of BLM, the stable hairpin structure of G3MB undergoes an irreversible cleavage in the loop region that contains a 5'-GT-3' recognition site for BLM. The released G-tract DNA fragment self-assembles into a G-triplex-ThT complex showing a strong fluorescence. Owing to the effective locking of G-tracts in the stem of the G3MB and the specific DNA strand scission by BLM which is like a key for the release of G-tracts, the assay shows high sensitivity and selectivity with a detection limit of 0.2 nM. In addition, satisfactory results were obtained for the detection of BLM in human serum samples. Critically, the convenient "mix-and-detect" protocol, fast response and no need for modifying DNA offered a potential application of the proposed strategy for BLM assay in biomedical and clinical studies.

G-triplex based molecular beacon with duplex-specific nuclease amplification for the specific detection of microRNA

Based on the G-triplex molecular beacon (MBG3), we have developed a duplex-specific nuclease signal amplification (DSNSA) assay for highly selective miRNA detection.

Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation

Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).

Classical Triplex Molecular Beacons for MicroRNA-21 and Vascular Endothelial Growth Factor Detection

Triplex molecular beacons (tMBs) possess great potential in biological sensing because of the pH responsiveness and controllability of binding strength. Here, we systematically investigate and rationally design a classical tMB for convenient detection of microRNA-21, a well-known biomarker of cardio-cerebrovascular diseases. In the tMB, we employ the complementary sequence of miR-21 as the loop and the sequences of protonated cytosine-guanine-cytosine (C-G•C+) and thymine-adenine-thymine (T-A•T) as the triplex stem, in which both the Watson-Crick and Hoogsteen base-pairing control the binding strength in cooperation. It is demonstrated for the first time that the presence of miR-21 would only break the Hoogsteen base-pairing in the stem and hybridize with the tMB to form the rigid heterozygous hybrid duplex structure. These would hinder the fluorescence resonance energy transfer (FRET) between the fluorophore (FAM) and quencher (BHQ1) labeled at the ends of the oligonucleotide, and the fluorescence recovery degree of FAM can be used as the standard to quantitate the miR-21. More significantly, the excellent adjustability and sensitivity of our tMBs have been confirmed by constructing the corresponding duplex molecular beacon (dMB) for comparison. The fluorophore FAM in the tMB could be replaced by the fluorescent DNA/silver nanoclusters, which exhibits the universal applicability of energy donor and receptor selection for tMB. Furthermore, our proposed tMB could also be developed as an aptasensor for the detection of vascular endothelial growth factor (VEGF) by only introducing the complementary sequence of its aptamer into the tMB. This work is of great significance for the systematic study of tMBs for the detection of biomarkers such as nucleic acids and proteins.

A label-free fluorescent adenosine triphosphate biosensor via overhanging aptamer-triggered enzyme protection and target recycling amplification

Herein, a label-free fluorescent adenosine triphosphate (ATP) aptasensor is fabricated with a DNA hairpin and an overhanging aptamer. In the presence of ATP, the overhanging sequences of the aptamer may form preferred substrates of exo III, and thus trigger the enzyme-assisted amplification, which results in the release of G-rich sequences. Free G-rich sequences subsequently generate an enhanced flourescent signal by binding with thioflavin T. However, if ATP is absent, the overhanging sequence can induce steric hindrance and protect the DNA hairpin against the digestion of exo III, significantly reducing the noise of this biosensor. Accordingly, the signal-to-noise ratio of the sensing system is greatly improved, which ensures the desirable analytical performance of the proposed aptasensor both in pure samples and real samples.

Closing the Loop: Constraining TAT Peptide by γPNA Hairpin for Enhanced Cellular Delivery of Biomolecules

Based on the exceptionally high stability of γPNA duplexes, we designed a peptide/γPNA chimera in which a cell-penetrating TAT peptide is flanked by two short complementary γPNA segments. Intramolecular hybridization of the γPNA segments results in a stable hairpin conformation in which the TAT peptide is constrained to form the loop. The TAT/γPNA hairpin (self-cyclized TAT peptide) enters cells at least 10-fold more efficiently than its nonhairpin analog in which the two γPNA segments are noncomplementary. Extending one of the γPNA segments in the hairpin results in an overhang that can be used for binding and delivering a variety of nucleic acid-conjugated molecules into cells via hybridization to the overhang. We demonstrated efficient cellular delivery of a protein (as low as 10 nM) and a DNA tetrahedron by a TAT/γPNA hairpin.

A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation

We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.

Stable and Label-Free Fluorescent Probe Based on G-triplex DNA and Thioflavin T

G-triplexes have recently been identified as a new kind of DNA structures. They perhaps possess specific biological and chemical functions similar as identified G-quadruplex but can be formed by shorter G-rich sequences with only three G-tracts. However, until now, limited G-triplexes sequences have been reported, which might be due to the fact that their stability is one of the biggest concerns during their functional studies and application research. Herein, we found a G-rich sequence (5'-TGGGTAGGGCGGG-3') which can form a stable G-triplex (Tm ∼ 60 °C) at room temperature. The stable G-triplex can combine with thioflavin T and function as an efficient fluorescence light-up probe. Comparing with the traditional G-quadruplex based probe, this triplex based probe was easy to be controlled and excited. Finally, the probe was successfully applied into constructing a label-free molecular beacon for miRNA detection. Taking advantage of these abilities of the G-triplex based fluorescent probe, the challenges faced during designing G-rich sequences based fluorescent biosensors can be efficiently solved. These findings provide important information for the future application of G-triplex.

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson–Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C–C and T–T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved.

Hydroxyl-triggered fluorescence for location of inorganic materials in polymer-matrix composites

We present a locating technique for inorganic materials in polymer-matrix composites through a post-labeling approach based on specific covalent binding.

There is a long-standing challenge to realize in situ visualization of incorporated inorganic materials in organic–inorganic composites in a post-labeling manner, owing to the lack of specific fluorescent organic dye molecules for targeting inorganic materials. Herein, we observe that the specific covalent B–O binding between the hydroxyl groups of inorganic materials and commercially available aggregation-induced emission (AIE)-active boronic acid could lead to the formation of highly emissive solid-state fluorescent composite materials. The hydroxyl-triggered luminescent probe may serve as a practical method for in situ location of incorporated inorganic materials in polymer-matrix composites by simply dipping the composite film in boronic acid-modified AIE solution. This present work offers a non-invasive avenue to locate inorganic materials which possess hydroxyl-groups in polymer-matrix composites, thereby developing a convenient screening strategy for assessing the advanced properties of composites. This strategy can also be extended to the targeted tracing of other inorganic materials with inherent and functionalized carboxyl, amino, sulfhydryl and other groups via tuning the binding affinity between the inorganic materials and luminescent molecules.

Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties

Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.

A new AgNC fluorescence regulation mechanism caused by coiled DNA and its applications in constructing molecular beacons with low background and large signal enhancement

A AgNC fluorescence interference strategy caused by a coiled DNA sequence (A) and its applications in target DNA detection (B).

Thioflavin T behaves as an efficient fluorescent ligand for label-free ATP aptasensor

Here, we for the first time demonstrated thioflavin T (ThT) as an efficient fluorescent ligand for 27-mer ATP-binding aptamer (ABA27), providing a novel signal readout mode for label-free selective ATP detection. ABA27 can promote the fluorescence emission of ThT with an unprecedentedly high efficiency, attributed to the specific structure of ABA27 rather than the G-tracts. Polyacrylamide gel electrophoresis, fluorescence spectroscopy, and fluorometric titration reveal that ThT interacts with ABA27 with a lower binding affinity (Kd ~89 μM) than ATP, which allows ATP to easily compete with ThT for the DNA binder. In the presence of ThT, adding ATP induces ABA27 to undergo a structural change, thereby not favoring the binding to ThT, verified by circular dichroism and UV-Vis absorption spectroscopy. As a result, the fluorescence intensity of ThT decreases dramatically, enabling the sensitive detection of ATP with high selectivity over other analogs. Such a sensing strategy may make ThT able to serve as a facile signal reporter for DNA nanomechanical devices fueled with ATP. Graphical Abstract The principle of the displacement of ThT by ATP.

Light-up fluorophore--DNA aptamer pair for label-free turn-on aptamer sensors

We developed a light-up fluorophore-DNA aptamer pair for label-free aptamer sensors that fluoresce upon binding to the analyte. A 42mer DNA aptamer binding to the environment-sensitive fluorophore, dapoxyl, which increased the fluorescence by more than 700-fold upon binding, was successfully used to construct aptamer sensors by fusion with analyte-binding DNA aptamers.

Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures

Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.

Thioflavin T as a fluorescence probe for label-free detection of T4 polynucleotide kinase/phosphatase and its inhibitors

We have developed a new methodology for label-free fluorescence turn-on detection of T4 polynucleotide kinase/phosphatase activity (T4 PNKP) using a Thioflavin T probe. This method is very sensitive with a 0.01 unit/mL limit of detection, which is better than those with labeled fluorophores. Furthermore, T4 PNKP inhibition by the inhibitor heparin is shown, demonstrating the potential to screen suitable inhibitor drugs for T4 PNKP.