An Aptamer-Based Competitive Fluorescence Quenching Assay for IgE

A simple competitive fluorescence quenching assay based on aptamer was developed for IgE detection. Two DNA probes were used. One is 5′-end fluorescein-labeled IgE aptamer; the other is 3′-end DABCYL-labeled short DNA, which would hybridize with IgE aptamer to quench the fluorescence. In the presence of IgE, the aptamer-IgE complex formed is strong enough to prevent the short DNA probes hybridizing with the bounded aptamer probes, which results in the less decrease of fluorescence intensity. The signal change was found to be proportional to the concentration of IgE from 0.35 to 35 nM with a detection limit of 0.17 nM.     

Aptamer-Based Fluorescence Nanoprobe for Sensitive and Selective Detection of Potassium

A new aptamer-based fluorescence nanoprobe for potassium ion (K⁺) has been developed. The nanoprobe employs gold nanoparticles (AuNPs) as the sensing platform and Rhodamine B as the fluorescence indicator. Aptamer acts as the switch of fluorescence signal of Rhodamine B. In the presence of K⁺, aptamer departs from AuNPs as a result of the formation of G-quartets with K⁺, leading to the decrease of fluorescence signals. Under the optimum conditions, the limit of detection (LOD) for K⁺ is as low as 3.8 nM. The proposed method was successfully applied in the determination of K⁺ in human saliva sample.     

Assessment of aptamer-steroid binding using stacking-enhanced capillary electrophoresis

The binding affinity of 17β-estradiol with an immobilized DNA aptamer was measured using capillary electrophoresis. Estradiol captured by the immobilized DNA was injected into the separation capillary using pH-mediated sample stacking. Stacked 17β-estradiol was then separated using micellar electrokinetic capillary chromatography and detected with UV-visible absorbance. Standard addition was used to quantify the concentration of estradiol bound to the aptamer. Following incubation with immobilized DNA, analysis of free and bound estradiol yielded a dissociation constant of 70 ± 10 μM. The method was also used to screen binding affinity of the aptamer for estrone and testosterone. This study demonstrates the effectiveness of capillary electrophoresis to assess the binding affinity of DNA aptamers.     

适配体生物传感器在病原微生物检测中的应用

适配体是通过指数富集系统进化技术(SELEX)体外筛选得到的一类能够特异性地结合小分子物质、蛋白,甚至整个细胞的寡核苷酸序列.由于具有制备简便、易于修饰、稳定性好等特点,适配体已广泛应用于构建生物传感器,实现对病原微生物的识别和检测.本文在阐述适配体基本原理的基础之上,结合近年来病原微生物适配体研究领域的最新研究成果,综述以病原微生物为目标的适配体筛选技术的最新进展;列举目前已经筛选获得的病原微生物(原生生物、病毒、细菌)适配体;综述适配体生物传感器在病原微生物检测中的应用.并展望了适配体生物传感器在病原微生物检测领域的发展趋势.     

Spectrofluorometry of Ions and Small Molecules Based on Conformational Changes of Specific Oligonucleotides with o-Phthalaldehyde-β-mercaptoethanol

Specific oligonucleotides such as telomere DNA and aptamer often undergo conformational changes upon ligand binding. Composite reagent composed of o-phthalaldehyde and β-mercaptoethanol(OPAME) has been extensively applied to fluorescent detection of amino compounds based on the reaction of primary amino-group, herein we proposed a general spectrofluorometry for ions and small molecules due to conformational changes upon ligand binding taking K+ and ATP as examples. In a borate controlled buffer medium, telomere DNA could react with OPAME, giving a thio-subtituted isoindole compound with strong fluorescence emission at 455 nm when excited at 340 nm. It was found that however, the fluorescence emission was greatly reduced in the presence of K+ since the formation of the quadruplex structure inhibits the reaction activity of amino-groups of telomere DNA. In order to testify the general application of OPAME reagent based on the conformational change of oligonucleotides, we further proposed a sensitive method of ATP based on its highly selective interaction with ATP-aptamer. The above mentioned applications show that the spectrofluorometry with the aid of OPAME reagent is simple, label free that is expected to be potentially general for DNA conformational change-based target detection.     

In vitro selection methodologies to probe RNA function and structure

Summary In vitro selection, or SELEX, has been used both to characterize the interaction of natural nucleic acids with proteins and to generate novel nucleic acid-binding species, or aptamers. Although numerous reports have demonstrated the power of the technique, they have not expanded on the methodologies that can be used for selection. This review focuses on the considerations and problems involved in selecting protein-binding aptamers from a random-sequence RNA pool. As an illustration, we describe two approaches to selecting aptamers to a particular target, the HTLV-I Rex protein. In the first, complete randomization is used to find an artificial, high-affinity RNA binding site. In the second, the contributions of individual nucleotides and/or base pairs to the natural Rex-binding element are determined by mutating the wild-type sequence and selecting active binding variants.     

Screening of Clenbuterol Hydrochloride Aptamers Based on Capillary Electrophoresis

Capillary electrophoresis based systematic evolution of ligands via exponential enrichment (CE-SELEX) was reported as a homogeneous efficient method for high-affinity selection of aptamer, with several merits involving screening in free solution without nonspecific binding, capable of high-efficient separation, low-sample consumption, and saving money. There are few studies regarding the aptamer selection against small molecule using CE-SELEX, resulting from the aspects of less binding sites and the negligible variety of its complex with nucleic acid in the electrophoretic mobility. In this study, we performed the aptamer selection towards a small molecule target of clenbuterol hydrochloride (Clen) by CE-SELEX. In brief, Clen were first incubated with an 80 nt ssDNA library, and CZE-UV approach was used to separate complex and random ssDNA. The complex was then collected into a vial followed by PCR amplification. Through three round selections, the third library was selected to clone and ten sequences were finally obtained. The dissociation constant (K_d) of three potential candidates (Apt 4, Apt 7 and Apt 12) were determined by CE-LIF, and showed high affinities of 9.315 × 10^?7 M, 1.040 × 10^?6 M and 1.143 × 10^?5 M, respectively. The result of m-Fold software analysis showed that the above three sequences could form stem-loop structure, and the Apt 4 gave the lowest free energy and the most stable structure. Using salbutamol as a control, three selected aptamers were verified with high specificity.     

Cell-imprinted polydimethylsiloxane for the selective cell adhesion

A cell-patterned substrate with aptamer functionalization was prepared, which holds promise in selective cell isolation fields such as the isolation of the circulating tumor cells.     

一种基于适配分子的偏振荧光检测法

凝血酶适配分子（aptamer)可与凝血酶以高亲和力结合，二者的结合可改变荧光素标记的适配分子溶液的荧光偏振强度，据此建立了适配分子荧光偏振法测定血酶的新方法。方法的线性范围是0.1-4IU/mL；检出限为0.09IU/mL。将该方法用于人体血浆中凝血酶含量分析，结果满意。     

Design of a dual aptamer-based recognition strategy for human matrix metalloproteinase 9 protein by piezoelectric biosensors

MMP-9, human matrix metalloproteinase 9, belongs to the family of zinc-dependent peptide-bond hydrolases and is involved in the degradation of the extracellular matrix (ECM). In clinics, it is well known that elevated MMP-9 serum levels are associated with cardiovascular dysfunctions, several aspects of the physiology and pathology of the central nervous system, neuropsychiatric disorders and degenerative diseases related to brain tumors, and excitotoxic/neuroinflammatory processes. Due to the large interest of diagnostics in this protein, efforts to set up sensitive methods to detect MMP-9 for early diagnosis of a number of metabolic alterations are rapidly increasing. In this panorama, biosensors could play a key role; therefore we explored for the first time the development of an aptamer-based piezoelectric biosensor for a sensitive, label free, and real time detection of MMP-9. The detecting strategy involved two different aptamers in a sandwich-like approach able to detect down to 100 pg mL⁻¹ (1.2 pM) of MMP-9 as detection limit in standard solution. As proof of principle, commercial serum was investigated in terms of possible interferents, their identification and role in MMP-9 detection. The estimated detection limit for MMP-9 is about 560 pg mL⁻¹ (6.8 pM) in untreated serum.