A highly sensitive DNA-AIEgen-based “turn-on” fluorescence chemosensor for amplification analysis of Hg~(2+) ions in real samples and living cells

Functional nucleic acids(FNAs)-based biosensors have shown great potential in heavy metal ions detection due to their low-cost and easy to operate merits. However, in most FNAs based fluorescence probes, the ingenious designs of double-labeled(fluorophore and quencher group) DNA sequence, not only bring the annoyance of organic synthesis, but also restrict its use as a robust biosensor in practical duties. In this paper, we design a simple AIEgens functional nucleic acids(AFNAs) probe which consists of only fluorogen but no quencher group. With the help of duplex-specific nuclease(DSN) enzyme based target recycling, high fluorescence signal and superior sensitivity towards Hg~(2+) are achieved. This robust assay allows for sensitive and selective detection of Hg~(2+) in real water samples and mapping of intracellular Hg~(2+), without double-labeling of oligonucleotide with a dye-quencher pair, nor the multiple assay steps.     

A highly sensitive DNA-AIEgen-based “turn-on” fluorescence chemosensor for amplification analysis of Hg<Superscript>2+</Superscript> ions in real samples and living cells

Functional nucleic acids (FNAs)-based biosensors have shown great potential in heavy metal ions detection due to their low-cost and easy to operate merits. However, in most FNAs based fluorescence probes, the ingenious designs of double-labeled (fluorophore and quencher group) DNA sequence, not only bring the annoyance of organic synthesis, but also restrict its use as a robust biosensor in practical duties. In this paper, we design a simple AIEgens functional nucleic acids (AFNAs) probe which consists of only fluorogen but no quencher group. With the help of duplex-specific nuclease (DSN) enzyme based target recycling, high fluorescence signal and superior sensitivity towards Hg²⁺ are achieved. This robust assay allows for sensitive and selective detection of Hg²⁺ in real water samples and mapping of intracellular Hg²⁺, without double-labeling of oligonucleotide with a dye-quencher pair, nor the multiple assay steps.     

Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling

We have developed a new class of surface-enhanced Raman scattering beacons (SERS beacons) that can be turned on and off by long-range plasmonic coupling, induced by biomolecular recognition and binding events. The beacons are based on colloidal gold nanocrystals in two sizes (40 and 60 nm) and are prepared by spectral encoding with a Raman reporter molecule, functionalized with thiolated DNA probes, and stabilized and protected by low molecular weight poly(ethylene glycol)s (PEGs). The results show the SERS signal intensities increase by 40-200-fold when the nanoparticle beacons are activated by plasmonic coupling, much higher than the bright-to-dark intensity ratios reported for traditional molecular beacons. Multivalent gold nanoparticles also have exquisite specificity and are able to recognize single-base mismatches or mutations. This class of SERS nanoparticle beacons has novel mechanisms for molecular detection and signal amplification, and its long-range coupling nature raises new opportunities in developing plasmonic probes to detect proteins, cells, and intact viruses.     

A ligation-triggered DNAzyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal

Many types of fluorescent sensing systems have been reported for biological small molecules. Particularly, several methods have been developed for the recognition of ATP or NAD(+), but they only show moderate sensitivity, and they cannot discriminate either ATP or NAD(+) from their respective analogues. We have addressed these limitations and report here a dual strategy which combines split DNAzyme-based background reduction with catalytic and molecular beacon (CAMB)-based amplified detection to develop a ligation-triggered DNAzyme cascade, resulting in ultrahigh sensitivity. First, the 8-17 DNAzyme is split into two separate oligonucleotide fragments as the building blocks for the DNA ligation reaction, thereby providing a zero-background signal to improve overall sensitivity. Next, a CAMB strategy is further employed for amplified signal detection achieved through cycling and regenerating the DNAzyme to realize the true enzymatic multiple turnover (one enzyme catalyzes the cleavage of several substrates) of catalytic beacons. This combination of zero-background signal and signal amplification significantly improves the sensitivity of the sensing systems, resulting in detection limits of 100 and 50 pM for ATP and NAD(+), respectively, much lower than those of previously reported biosensors. Moreover, by taking advantage of the highly specific biomolecule-dependence of the DNA ligation reaction, the developed DNAzyme cascades show significantly high selectivity toward the target cofactor (ATP or NAD(+)), and the target biological small molecule can be distinguished from its analogues. Therefore, as a new and universal platform for the design of DNA ligation reaction-based sensing systems, this novel ligation-triggered DNAzyme cascade method may find a broad spectrum of applications in both environmental and biomedical fields.     

Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute‐2 Cleavage (miRACle) Beacons

MicroRNA detection is a valuable method for determining cell identity. Molecular beacons are elegant sensors that can transform intracellular microRNA concentration into a fluorescence intensity. While target binding enhances beacon fluorescence, the degree of enhancement is insufficient for demanding applications. The addition of specialty nucleases can enable target recycling and signal amplification, but this process complicates the assay. We have developed and characterized a class of beacons that are susceptible to the endogenous nuclease Argonaute‐2 (Ago2). After purification of the complex by co‐immunoprecipitation, microRNA:Ago2 cleavage (miRACle) beacons undergo site‐ and sequence‐specific cleavage, and show a 13‐fold fluorescence enhancement over traditional beacons. The system can be adapted to any microRNA sequence, and can cleave nuclease‐resistant, non‐RNA bases, potentially allowing miRACle beacons to be designed for cells without interference from non‐specific nucleases.     

Combination of Mass Signal Amplification and Isotope‐Labeled Alkanethiols for the Multiplexed Detection of miRNAs

We report a fast and sensitive method for the multiplexed detection of miRNAs by combining mass signal amplification and isotope‐labeled signal reporter molecules. In our strategy, target miRNAs are captured specifically by immobilized DNAs on gold nanoparticles (AuNPs), which carry a large number of small molecules, called amplification tags (Am‐tags), as the reporter for the detection of target miRNAs. For multiplexed detection, we designed and synthesized four Am‐tags containing 0, 4, 8, 12 isotopes so that they had same molecular properties but different molecular weights. By observing the mass signals of the Am‐tags on AuNPs decorated along with different probe DNAs, four types of miRNAs in a sample could be easily discriminated, and the relative amounts of these miRNAs could be quantified. The practicability of our strategy was further verified by measuring the expression levels of two miRNAs in HUVECs in response to different CuSO₄ concentrations.     

Enzymatic cleavage and mass amplification strategy for small molecule detection using aptamer-based fluorescence polarization biosensor

Fluorescence polarization (FP) assays incorporated with fluorophore-labeled aptamers have attracted great interest in recent years. However, detecting small molecules through the use of FP assays still remains a challenge because small-molecule binding only results in negligible changes in the molecular weight of the fluorophore-labeled aptamer. To address this issue, we herein report a fluorescence polarization (FP) aptamer assay that incorporates a novel signal amplification strategy for highly sensitive detection of small molecules. In the absence of adenosine, our model target, free FAM-labeled aptamer can be digested by nuclease, resulting in the release of FAM-labeled nucleotide segments from the dT-biotin/streptavidin complex with weak background signal. However, in the presence of target, the FAM-labeled aptamer–target complex protects the FAM-labeled aptamer from nuclease cleavage, allowing streptavidin to act as a molar mass amplifier. The resulting increase in molecular mass and FP intensity of the aptamer–target complex provides improved sensitivity for concentration measurement. The probe could detect adenosine from 0.5 μM to 1000 μM, with a detection limit of 500 nM, showing that the sensitivity of the probe is superior to aptamer-based FP approaches previously reported for adenosine. Importantly, FP could resist environmental interferences, making it useful for complex biological samples without any tedious sample pretreatments. Our results demonstrate that this dual-amplified, aptamer-based strategy can be used to design fluorescence polarization probes for rapid, sensitive, and selective measurement of small molecules in complicated biological environment.     

基于滚环合成的聚分子信标用于 凝血酶的靶向检测

采用滚环扩增(RCA)合成得到的DNA长链打开带适配体的分子信标, 由于RCA长链上带有多个与分子信标(MB)互补的重复序列, 其打开分子信标的能力比单一互补短链提高了上百倍. 所形成的聚多价分子信标组装体, 在分子信标浓度相同的情况下, 打开后的荧光强度也大幅上升; 并且由于组装体上多价适配体的存在, 聚分子信标对凝血酶的靶向能力显著增强. 实验结果表明, 聚分子信标结合凝血酶后, 其荧光信号与凝血酶浓度呈线性关系, 检测灵敏度达到0.2 nmol/L, 该体系的构建有利于实现对凝血酶的高灵敏、 特异性检测.     

Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA‐Programmed Nanoparticle Disassembly

Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low‐abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal‐to‐background ratio of conventional molecular imaging probes. Herein, we report a class of DNA‐templated gold nanoparticle (GNP)–quantum dot (QD) assembly‐based probes for catalytic imaging of cancer‐related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA‐programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non‐catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.     

Multiplexed Immunosensing Platform Coupled to Hybridization Chain Reaction for Electrochemical Determination of MicroRNAs in Clinical Samples

There is an urgent need for development of rapid and inexpensive techniques for detection of microRNAs (miRNAs), which are potential biomarkers of various types of cancer. In this paper, we describe a multiplexed electrochemical platform for determination of three cancer‐relevant miRNAs: miR‐21, let‐7a and miR‐31. The strategy combines the use of magnetic beads (MBs) modified with a commercial antibody for the efficient capture of the heteroduplexes formed by hybridization of the target miRNA with DNA probe. Free non‐hybridized region of the DNA probe was thereafter hybridized with two biotin‐labeled auxiliary DNA probes in a process of hybridization chain reaction (HCR), resulting in a long hybrid bearing a large number of biotin molecules. Labeling of these multiple biotin units with streptavidin‐peroxidase conjugates allowed an amplification of the amperometric signal measured after capturing the modified MBs at a screen‐printed carbon electrode array of eight electrodes. The combined strategy demonstrated in a similar assay time significantly higher sensitivity than those previously described using modified MBs with the same capture antibody (without amplification by HCR) or a HCR strategy implemented on the surface of MBs, respectively. The methodology exhibits a good selectivity for discriminating single mismatches and was applied to the determination of the three target miRNAs in total RNA (RNA_t) extracted from various cancer cell lines and from cervical precancerous lesions.     

Dumbbell probe-mediated cascade isothermal amplification: A novel strategy for label-free detection of microRNAs and its application to real sample assay

Considering the great significance of microRNAs (miRNAs) in cancer detection and typing, the development of sensitive, specific, quantitative, and low-cost methods for the assay of expression levels of miRNAs is desirable. We describe a highly efficient amplification platform for ultrasensitive analysis of miRNA (taking let-7a miRNA as a model analyte) based on a dumbbell probe-mediated cascade isothermal amplification (DP-CIA) strategy. The method relies on the circularization of dumbbell probe by binding target miRNA, followed by rolling circle amplification (RCA) reaction and an autonomous DNA machine performed by nicking/polymerization/displacement cycles that continuously produces single-stranded G-quadruplex to assemble with hemin to generate a color signal. In terms of the high sensitivity (as low as 1 zmol), wide dynamic range (covering 9 orders of magnitude), good specificity (even single-base difference) and easy operation (one probe and three enzymes), the proposed label-free assay is successfully applied to direct detection of let-7a miRNA in real sample (total RNA extracted from human lung tissue), demonstrating an attractive alternative for miRNA analysis for gene expression profiling and molecular diagnostics, particularly for early cancer diagnosis.     

基于核酸适配体信号置换结合循环扩增的液相色谱法检测4种生物胺

生物胺的含量是衡量食品卫生状况和药物纯度的重要标志之一,建立食品药品中生物胺的精准、灵敏检测具有重要的实际意义。该文基于核酸适配体置换生物胺信号源并结合荧光信号循环扩增的策略,建立了一种新型的同时检测鱼肉、猪肉和抗生素中4种生物胺的高效液相色谱法(HPLC)。首先通过两步信号置换,将无荧光信号的目标物转换为有荧光信号的核酸探针;再结合双链特异性核酸酶辅助信号扩增策略,获取大量不同长度和碱基序列的核酸探针;最后借助HPLC平台实现实际样品中多种生物胺信号的精确识别。文章研究了核酸探针的碱基序列和长度对出峰时间和前后顺序的影响,以提高荧光信号的区分度。通过正交实验探讨了柱温、流速和梯度洗脱过程、反应温度、孵化时间等对信号分离的影响,确定最优条件,提高信号的分离效率。该方法对目标物酪胺、组胺、精胺和色胺的检出限分别为0.25、0.21、0.27和0.19 pmol/L,线性范围为1 pmol/L~1 μmol/L。通过对硫酸大庆霉素、鱼肉和猪肉样品中生物胺含量进行检测,研究了该方法检测实际样品的可行性。该方法可精准识别、捕获和分离复杂基质样品中的生物胺组分,能有效提高对目标分析物的选择性,并降低实际样品中的基质干扰,有望为食品药品分析领域提供一种新的思路。     

Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes

The rational and straightforward design of hairpin ribozymes that can be sequence-specifically induced by external oligonucleotides is described. Due to intrinsic signal amplification, their sensitivity is at least an order of magnitude increased compared to standard molecular beacons. We applied this system to the detection of microRNAs, a recently discovered class of small endogenous RNA molecules that are involved in gene regulation. We show that the cognate microRNA can reliably and sensitively be detected at low concentrations in a mix of other microRNA sequences. These probes may be useful in applications that require direct detection of minute amounts of small DNAs or RNAs.     

Pyrene excimer signaling molecular beacons for probing nucleic acids

Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.     

Target-triggered hairpin-free chain-branching growth of DNA dendrimers for contrast-enhanced imaging in living cells by avoiding signal dispersion

The development of amplification strategies is one of the central challenges for detection of lowabundance targets. One-to-many(1:M) amplification strategies in which one target lights many signal probes, has improved the detection sensitivity in bulk solution, but with discounted contrast in cell imaging, because the lighted probes are dissociative and dispersible. In this work, a one-to-large(1:L) signaling mechanism, in which the lighted probes were orderly connected to each other, was concep...     

Label-free fluorescence turn-on detection of microRNA based on duplex-specific nuclease and a perylene probe

A novel fluorescence turn-on microRNA (miRNA) detection method based on duplex-specific nuclease (DSN) and a perylene probe is presented in this study. A positively charged perylene derivative (compound 1) was used as the fluorescent probe. Compound 1 exhibits strong monomer fluorescence in an aqueous buffer solution. It is well known that single-stranded DNA is a polyanion in nature. Thus, it can induce the aggregation of compound 1 through strong electrostatic, hydrophobic and π−π stacking interactions. As a result, the fluorescence of compound 1 was efficiently quenched. When the target miRNA was added, the formation of DNA-RNA hybridized duplex initiated the cleavage of the DNA strand by DSN cycle reaction, which resulted in disaggregation of compound 1. A fluorescence turn-on signal was detected, and a novel miRNA sensing method was therefore established. The presented method is label-free, simple, cost effective, sensitive and selective.     

Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification

Using a cascade signal amplification strategy, an ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon (MB) mediated circular strand displacement polymerization (CSDP) and hyperbranched rolling circle amplification (HRCA) was proposed. The hybridization of MB probe to target DNA resulted in a conformational change of the MB and triggered the CSDP in the presence of bio-primer and Klenow fragment (KF exo⁻), leading to multiple biotin-tagged DNA duplex. Furthermore, the HRCA was implemented to product amounts of double-stranded DNA (ds-DNA) fragments using phi29 DNA polymerase via biotin-streptavidin interaction. After the product of HRCA binded numerous biotinylated detection probes, an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor exhibited excellent detection sensitivity and specificity with a log-linear response to target DNA from 0.01 fM to 10 pM as low as 8.9 aM. The proposed method allowed DNA detection with simplicity, rapidness, low cost and high specificity, which might have the potential for application in clinical molecular diagnostics and environmental monitoring.     

High-throughput quantitative detection of triple-negative breast cancer-associated expressed miRNAs by rolling circle amplification on fluorescence-encoded microspheres

Compared with other types of breast cancer, triple-negative breast cancer(TNBC) has the characteristics of a high degree of malignancy and poor prognosis. Early diagnosis of TNBC through biological markers and timely development of effective treatment methods can reduce its mortality. Many Research experiments have confirmed that some specific mi RNA expression profiles in TNBC can used as markers for early diagnosis. However, detecting the expression profiles of multiple groups of miRNAs accord...