Highly Specific,Single-step Cancer Cell Isolation with Multi-Aptamer-Mediated Proximity Ligation on Live Cell Membranes

A single-step method for isolation of specific cells based on multiple surface markers will have unique advantages because of its scalability, efficacy, and mildness. Herein, we developed multi-aptamer-mediated proximity ligation method on live cell membranes that leverages a multi-receptor co-recognition design for enhanced specificity, as well as a robust in situ signal amplification design for improved sensitivity of cell isolation. We demonstrated the promising efficacy of our method on differentiating tumor cell subtypes in both cell mixtures and clinical samples. Owing to its simple and fast operation with excellent cell isolation sensitivity and accuracy, this approach will have broad applications in biological science, biomedical engineering, and personalized medicine.     

基于裂开型核酸适体非标记荧光法检测ATP

基于裂开型核酸适体序列短、能有效降低因探针形成二级结构产生假阳性信号等优点,选择裂开型核酸适体作为特异性识别探针,核酸染料噻唑橙（TO）为信号探针,用单壁碳纳米管（SWCNTs）降低背景信号,利用“适配体-目标分子-适配体”的“三明治”夹心方式,建立了一种检测ATP的新方法。在pH 8.0的Tris-HCl缓冲溶液中,裂开成两段的ATP适体特异性识别ATP分子,生成稳定的“适配体-ATP-适配体”复合结构。单壁碳纳米管对该复合结构的吸附力较弱,因此该复合物游离在溶液中,TO与其结合而产生强荧光。当不存在ATP时,核酸适体探针以单链状态存在,可通过π-π共轭作用结合到SWCNTs表面,进而不能与TO结合,TO游离在溶液中荧光非常微弱。反应体系中ATP浓度越高,形成的“适配体-ATP-适配体”夹心识别结构复合物越多,检测到的荧光强度越大,据此实现对ATP的检测。在优化实验条件下,在最大荧光发射波长550 nm处,ATP的浓度在9.0×10-9～1.0×10-7 mol·L-1范围内与ΔF/F₀值成线性关系,r=0.996 4。该方法加标回收率为95.2%～104%,相对标准偏差（RSD）为1.02%～4.54%,检出限达到2.67×10-9 mol·L-1。该方法基于功能核酸对目标物亲合力强、选择识别性高的特点,对ATP的检测表现出很好的选择性,实验结果表明,当相对误差控制在±5%以内时,200倍的UTP,GTP和CTP均不干扰ATP的测定。另外,该方法操作简单、快速、无需标记、灵敏准确,可用于血清样品中ATP的测定,在快速检测小分子物质领域中有较好的应用前景。     

光学适配体传感器检测赭曲霉毒素A的研究进展

赭曲霉毒素A(Ochratoxin A,OTA)是真菌产生的次级代谢产物,性质稳定,不易去除,人体摄入后将产生严重的健康危害。数十年来,核酸适配体不断发展,成为生物传感器的重要识别元件之一,适体传感器被广泛用于生物、医药、疾病等分析检测。本文总结了用于检测OTA的经典方法和基于核酸适配体的生物传感器方法,并主要从光学适配体传感器方面阐述了近年用于检测赭曲霉毒素A的适配体传感器,并对其进行了总结和展望。     

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one-round SELEX experiments using five different trimeric spike proteins from variants, followed by high-throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS-CoV-2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well-suited for molecular recognition of rapidly evolving targets such as those found in SARS-CoV-2.     

A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K⁺ or Sr²⁺. TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.     

An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Beyond labels: A review of the application of quantum dots as integrated components of assays, bioprobes, and biosensors utilizing optical transduction

A comprehensive review of the development of assays, bioprobes, and biosensors using quantum dots (QDs) as integrated components is presented. In contrast to a QD that is selectively introduced as a label, an integrated QD is one that is present in a system throughout a bioanalysis, and simultaneously has a role in transduction and as a scaffold for biorecognition. Through a diverse array of coatings and bioconjugation strategies, it is possible to use QDs as a scaffold for biorecognition events. The modulation of QD luminescence provides the opportunity for the transduction of these events via fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), charge transfer quenching, and electrochemiluminescence (ECL). An overview of the basic concepts and principles underlying the use of QDs with each of these transduction methods is provided, along with many examples of their application in biological sensing. The latter include: the detection of small molecules using enzyme-linked methods, or using aptamers as affinity probes; the detection of proteins via immunoassays or aptamers; nucleic acid hybridization assays; and assays for protease or nuclease activity. Strategies for multiplexed detection are highlighted among these examples. Although the majority of developments to date have been in vitro, QD-based methods for ex vivo biological sensing are emerging. Some special attention is given to the development of solid-phase assays, which offer certain advantages over their solution-phase counterparts.     

核酸适配体在重金属检测中的应用研究

随着工业化生产的快速发展,由重金属离子带来的环境污染也越来越引起了人们的高度重视.科研人员通过不同的检测方法对重金属离子进行检测.由于核酸适配体对重金属离子的选择性较高,使得其在重金属检测中的应用越来越广.     

非标记凝血酶阵列电化学适体传感器的研究

基于自制的集成化三阵列金膜电极,构建了一个简单、灵敏、非标记的凝血酶阵列电化学适体传感器。以聚乙烯不干胶掩膜版法结合金属溅射沉积技术,在FR-4玻璃纤维板上制作了由3个金膜工作电极、1个大面积金膜对电极和1个厚膜Ag/AgCl参比电极构成的集成化金膜阵列电极系统。以集成化金膜阵列电极作为基础电极,采用巯基自组装技术将带巯基的凝血酶适体固定在3个金工作电极表面,巯基己醇封闭后获得三阵列凝血酶适体传感器,以电活性物质铁氰化钾作为电化学探针,基于凝血酶适体和凝血酶结合前后铁氰化钾在电极表面传质的不同导致电流变化进行凝血酶的测定。采用方波脉冲伏安法,铁氰化钾氧化峰电流的变化值与凝血酶浓度在 1.52~63 nmol/L范围内呈良好的线性关系,检出限(S/N=3)为0.92 nmol/L。