A gold-based nanobeacon probe for fluorescence sensing of organophosphorus pesticides

A nanomaterials-based novel molecular beacon has attracted growing attentions in fluorescent assays as many nanomaterials possess excellent quenching efficiency. In this work, a gold-based nanobeacon probe was established to detect organophosphorus pesticides for the first time. The constructed gold-based nanobeacon acted as a signal indicator and could display the decreasing of the intensity in the presence of targets, which competitively bound to single strand DNA. To achieve a high sensitive probe, some parameters including solution pH, temperature and reaction time were investigated and optimized. The gold-based nanobeacon probe assay was proved to be rapid and sensitive to achieve a detection limit of 0.035 μM for isocarbophos, 0.134 μM for profenofos, 0.384 μM for phorate and 2.35 μM for omethoate, respectively. The prepared nanobeacon effectively reduced the background and improved the detection sensitivity and selectivity. The probe is stable, easy to operate and does not need sophisticated instruments. These features makes the probe feasible for screening trace organophosphorus pesticides in real samples.     

Switchable Fluorescent Light-Up Aptamers Based on Riboswitch Architectures

Fluorescent light-up RNA aptamers (FLAPs) such as Spinach or Mango can bind small fluorogens and activate their fluorescence. Here, we adopt a switching mechanism otherwise found in riboswitches and use it to engineer switchable FLAPs that can be activated or repressed by trigger oligonucleotides or small metabolites. The fluorophore binding pocket of the FLAPs comprises guanine (G) quadruplexes, whose critical nucleotides can be sequestered by corresponding anti-FLAP sequences, leading to an inactive conformation and thus preventing association with the fluorophore. We modified the FLAPs with designed toehold hairpins that carry either an anti-FLAP or an anti-anti-FLAP sequence within the loop region. The addition of an input RNA molecule triggers a toehold-mediated strand invasion process that refolds the FLAP into an active or inactive configuration. Several of our designs display close-to-zero leak signals and correspondingly high ON/OFF fluorescence ratios. We also modified purine aptamers to sequester a partial anti-FLAP or an anti-anti-FLAP sequence to control the formation of the fluorogen-binding conformation, resulting in FLAPs whose fluorescence is activated or deactivated in the presence of guanine or adenine. We demonstrate that switching modules can be easily combined to generate FLAPs whose fluorescence depends on several inputs with different types of input logic.     

Discussion of the protein characterization techniques used in the identification of membrane protein targets corresponding to tumor cell aptamers

Aptamer is an oligonucleotide chain with specific binding ability to protein and other targets,which is widely used in ma ny fields.Because of its ability to screen the premise of unknown targets,it can be used to discover some novel tumor markers,i.e.,membrane proteins that are specifically highly expressed on the surface of tumor cells.Tumor markers can be used in many fields such as early diagnosis and treatment,and a new type of tumor marker proved to be effective can significantly improve the therapeutic effect of such tumors.However,further characterization of newly acquired membrane proteins is essential for their clinical use as tumor markers.This review first briefly introduced the process of obtaining novel tumor markers from nucleic acid aptamers.Next,the commonly used protein characterization methods could be used as a technical means to identify membrane protein targets corresponding to tumor cell aptamers,to clarify the principles,advantages and disadvantages of various means,and to analyze the most suitable situations for various experimental methods.Finally,the outlook was made and the characterization methods that should be used in such experiments were summarized.     

Label-free colorimetric aptasensor for sensitive detection of ochratoxin A utilizing hybridization chain reaction

The combination of high selectivity of aptamer with the peroxidase-mimicking property of DNAzyme has presented considerable opportunities for designing colorimetric aptasensor for detection of ochratoxin A (OTA). The activities of both aptamer (as biorecognition element) and DNAzyme (as signal amplification element) are blocked via base pairing in the hairpin structure. Hybridization chain reaction (HCR) between two hairpin DNAs was employed to further improve the sensitivity of this method. The presence of OTA triggers the opening of the hairpin structure and the beginning of HCR, which results in the release of many DNAzyme, and generates enhanced colorimetric signals, which is correlated to the amounts of OTA with linear range between 0.01 to 0.32 nM, and the limit of detection is 0.01 nM under optimal conditions. OTA in yellow rice wine and wheat flour samples was also detected using this method. We demonstrate that a new colorimetric method for the detection of OTA has been established, which is simple, easy to conduct, label-free, sensitive, high throughput, and cost-saving.     

基于聚间苯二胺为受体的UC-FRET传感器检测凝血酶

本文以上转换发光材料(UCPs)为供体,聚间苯二胺(PMPD)为受体,构建了基于荧光共振能量转移(FRET)的传感平台,并将其用于凝血酶的检测。一定浓度的PMPD加入到标记单链DNA的UCPs体系中,对上转换发光的猝灭效率可以达到70%。当加入浓度在0.2~5.0nmol/L范围内的目标物凝血酶时,其荧光恢复程度与浓度呈线性关系,检出限为0.18nmol/L。PMPD因其良好的水溶性、荧光猝灭能力及免标记的特点为基于FRET技术的生物样品检测提供了新的平台。     

Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation

Proteins play a central role in all domains of life, and precise regulation of their activity is essential for understanding the related biological processes and therapeutic functions. Nucleic acid aptamers, the molecular recognition components derived from systematic evolution of ligands by exponential enrichment(SELEX), can specifically identify proteins with antibody-like recognition characteristics and help to regulate their activity. This minireview covers the SELEX-based selection of protein-binding aptamers, membrane protein analytical techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins, including membrane receptors and non-membrane proteins(thrombin as a model), as well as the potential challenges and prospects regarding aptamer-mediated protein manipulation, aiming to supply some useful information for researchers in this field.     

脱氧核糖核酸分子设计在电化学生物传感器中的应用

基于特殊DNA序列的构型变化的电化学生物传感器是一种高灵敏、高特异性的生物分析方法.固定在电极表面的特殊DNA探针(茎环、核酸适配体、四聚体等)因为目标物质的结合而发生构型变化,从而产生可检测的电化学信号,这种策略操作简便而且特异性强,引起了研究者的广泛关注.本文总结了目前基于基因构型变化的电化学生物传感器的发展历程.     

An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells

Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six-letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six-letter DNA library to selectively bind liver cancer cells; and 2) in a six-letter self-assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer-nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer-targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.     

Label-free detection of adenosine based on fluorescence resonance energy transfer between fluorescent silica nanoparticles and unmodified gold nanoparticles

A sensitive and convenient strategy was developed for label-free assay of adenosine. The strategy adapted the fluorescence resonance energy transfer property between Rhodamine B doped fluorescent silica nanoparticles (SiNPs) and gold nanoparticles (AuNPs) to generate signal. The different affinities of AuNPs toward the unfolded and folded aptamers were employed for the signal transfer in the system. In the presence of adenosine, the split aptamer fragments react with adenosine to form a structured complex. The folded aptamer cannot be adsorbed on the surface of AuNPs, which induces the aggregation of AuNPs under high ionic concentration conditions, and the aggregation of AuNPs leads to the decrease of the quenching ability. Therefore, the fluorescence intensity of Rhodamine B doped fluorescent SiNPs increased along with the concentration of adenosine. Because of the highly specific recognition ability of the aptamer toward adenosine and the strong quenching ability of AuNPs, the proposed strategy demonstrated good selectivity and high sensitivity for the detection of adenosine. Under the optimum conditions in the experiments, a linear range from 98 nM to 100 μM was obtained with a detection limit of 45 nM. As this strategy is convenient, practical and sensitive, it will provide a promising potential for label-free aptamer-based protein detection.     

Evolution of Artificial Base Pairs with Hydrogen Bond Complementarity

Artificial base pairs,from the perspective of synthetic biology,are designed to contain the features of modularity,orthogonality,and manipulability.And the development of artificial base pairs has beat endowed with responsibility to understand the biological process,improve the recognition capacity and stability of aptamers,and develop the nucleoside drugs,diagnosis,and drag delivery.In this review,we first gave a concise introduction of artificial base pairs based on their interaction modes including alternative hydrogen bonding,hydrophobic interaction,and metal coordination.Then we displayed the detailed information of artificial base pairs with hydrogen bonding interaction,and analyzed how the changes of their structures affect their functions.Subsequently,we highlighted the applications of functional artificial base pairs in aptamer discovery,diagnosis,and drug delivery.Finally,an insight into the remaining challenges and future perspective of the artificial bases was provided.