核酸适配体在癌症诊断中的研究进展

核酸适配体是通过指数富集配体系统进化技术(SELEX)从体外合成的寡核苷酸文库中筛选得到的短的寡核苷酸分子(ssDNA或RNA).核酸适配体能够通过折叠成特定的空间结构与靶标分子进行特异性结合,与抗体相比,适配体具有高亲和力、易修饰、低成本、易于合成和低免疫原性等优势,可以针对细胞、蛋白质、组织、生长因子进行癌症生物标...     

Use of quantum dots in the development of assays for cancer biomarkers

Biomarker assays may be useful for screening and diagnosis of cancer if a set of molecular markers can be quantified and statistically differentiated between cancerous cells and healthy cells. Markers of disease are often present at very low concentrations, so methods capable of low detection limits are required. Quantum dots (QDs) are nanoparticles that are emerging as promising probes for ultrasensitive detection of cancer biomarkers. QDs attached to antibodies, aptamers, oligonucleotides, or peptides can be used to target cancer markers. Their fluorescent properties have enabled QDs to be used as labels for in-vitro assays to quantify biomarkers, and they have been investigated as in-vivo imaging agents. QDs can be used as donors in assays involving fluorescence resonance energy transfer (FRET), or as acceptors in bioluminescence resonance energy transfer (BRET). The nanoparticles are also capable of electrochemical detection and are potentially useful for “lab-on-a-chip” applications. Recent developments in silicon QDs, non-blinking QDs, and QDs with reduced-size and controlled-valence further make these QDs bioanalytically attractive because of their low toxicity, biocompatibility, high quantum yields, and diverse surface modification flexibility. The potential of multiplexed sensing using QDs with different wavelengths of emission is promising for simultaneous detection of multiple biomarkers of disease.

核酸适配体荧光探针在生化分析和生物成像中的研究进展

核酸适配体是指通过体外筛选技术从核酸文库中筛选出来,能够高特异性、高亲和力识别靶标物的寡核苷酸序列,具有靶标类型广泛、合成简单、相对分子质量小、化学稳定性高、易于进行生物化学修饰等优点。 核酸适配体能够通过折叠成特定的二维或三维构型与靶标物特异性结合,加上合适的信号转导机制,为重要靶标物的研究提供理想的分子识别与分子检测探针。 荧光检测技术具有高灵敏、高分辨率、易于实现多元分析等优点。 将核酸适配体的分子识别特性与荧光优异的光学检测性能相结合,在生命科学研究领域有着广泛的应用空间。 本文主要综述了核酸适配体荧光探针常见的分子设计和信号响应方式,及其在细胞成像、亚细胞成像中的应用研究,并对核酸适配体探针目前面临的一些挑战进行了讨论,最后对其未来的发展方向进行了展望。     

基于核酸适体的外泌体分子识别研究进展

自研究者证实外泌体承担了细胞外RNA等物质的运输功能以来, 关于外泌体来源与功能的研究一直备受关注. 近年来外泌体被发现具有作为疾病生物标志物的潜力, 使得拥有特定表面蛋白以及特定装载物的外泌体成为分析化学领域有价值的检测对象. 从化学本质角度来说, 外泌体的获取与分析需要依赖特异性的分子识别过程. 核酸适体作为分子识别单元, 因其特异性强、 亲和力高、 生物活性稳定、 易于合成和保存、 而且其序列和结构上具有可编程性, 易于设计和修饰, 已成功地用在外泌体相关的生物传感体系中. 本文从外泌体的化学组成及其具有生理、 病理意义的组分出发, 从外泌体通用生物标志物识别、癌细胞来源外泌体的检测及外泌体蛋白谱的分析这3个方面综述了以核酸适体作为分子识别单元在外泌体分析领域的代表性工作, 总结了现有的靶向外泌体的核酸适体序列信息以及应用场景, 阐述了利用化学合成与修饰以及DNA自组装等化学调控手段增强核酸适体分子识别性能的最新进展, 并从适用于外泌体分子识别的核酸适体的筛选以及化学修饰的角度, 对未来的研究方向进行了展望.     

Cell-SELEX-based aptamer-conjugated nanomaterials for enhanced targeting of cancer cells

Early detection and treatment of cancer depends on developing highly sensitive and specific methods for targeting cancer cells. To do this, aptamers, which are generated by a novel technique called cell-SELEX (systematic evolution of ligands by exponential enrichment), have been widely applied in cancer cell targeting based on such merits as high target affinity and specificity, small size, minimal immunogenicity, and ease of chemical modification. Furthermore, aptamers can gain more flexibility as cancer c...     

Visual detection of cancer cells by colorimetric aptasensor based on aggregation of gold nanoparticles induced by DNA hybridization

A simple but highly sensitive colorimetric method was developed to detect cancer cells based on aptamer–cell interaction. Cancer cells were able to capture nucleolin aptamers (AS 1411) through affinity interaction between AS 1411 and nucleolin receptors that are over expressed in cancer cells, The specific binding of AS 1411 to the target cells triggered the removal of aptamers from the solution. Therefore no aptamer remained in the solution to hybridize with complementary ssDNA-AuNP probes as a result the solution color is red. In the absence of target cells or the presence of normal cells, ssDNA-AuNP probes and aptamers were coexisted in solution and the aptamers assembled DNA-AuNPs, produced a purple solution. UV–vis spectrometry demonstrated that this hybridization-based method exhibited selective colorimetric responses to the presence or absence of target cells, which is detectable with naked eye. The linear response for MCF-7 cells in a concentration range from 10 to 10⁵ cells was obtained with a detection limit of 10 cells. The proposed method could be extended to detect other cells and showed potential applications in cancer cell detection and early cancer diagnosis.     

Aptamers with Tunable Affinity Enable Single-Molecule Tracking and Localization of Membrane Receptors on Living Cancer Cells

Tumor cell-surface markers are usually overexpressed or mutated protein receptors for which spatiotemporal regulation differs between and within cancers. Single-molecule fluorescence imaging can profile individual markers in different cellular contexts with molecular precision. However, standard single-molecule imaging methods based on overexpressed genetically encoded tags or cumbersome probes can significantly alter the native state of receptors. We introduce a live-cell points accumulation for imaging in nanoscale topography (PAINT) method that exploits aptamers as minimally invasive affinity probes. Localization and tracking of individual receptors are based on stochastic and transient binding between aptamers and their targets. We demonstrated single-molecule imaging of a model tumor marker (EGFR) on a panel of living cancer cells. Affinity to EGFR was finely tuned by rational engineering of aptamer sequences to define receptor motion and/or native receptor density.     

Cell-specific internalization study of an aptamer from whole cell selection

Nucleic acid aptamers have been shown many unique applications as excellent probes in molecular recognition. However, few examples are reported which show that aptamers can be internalized inside living cells for aptamer functional studies and for targeted intracellular delivery. This is mainly due to the limited number of aptamers available for cell-specific recognition, and the lack of research on their extra- and intracellular functions. One of the major difficulties in aptamers' in vivo application is that most of aptamers, unlike small molecules, cannot be directly taken up by cells without external assistance. In this work, we have studied a newly developed and cell-specific DNA aptamer, sgc8. This aptamer has been selected through a novel cell selection process (cell-SELEX), in which whole intact cells are used as targets while another related cell line is used as a negative control. The cell-SELEX enables generation of multiple aptamers for molecular recognition of the target cells and has significant advantages in discovering cell surface binding molecules for the selected aptamers. We have studied the cellular internalization of one of the selected aptamers. Our results show that sgc8 is internalized efficiently and specifically to the lymphoblastic leukemia cells. The internalized sgc8 aptamers are located inside the endosome. Comparison studies are done with the antibody for the binding protein of sgc8, PTK7 (Human protein tyrosine kinase-7) on cell surface. We also studied the internalization kinetics of both the aptamer and the antibody for the same protein on the living cell surface. We have further evaluated the effects of sgc8 on cell viability, and no cytotoxicity is observed. This study indicates that sgc8 is a promising agent for cell-type specific intracellular delivery.     

DNA aptamer selected for specific recognition of prostate cancer cells and clinical tissues

Prostate cancer is the most common malignancy in men lack of efficient early diagnosis and therapeutics, calling for effective molecular probes. Herein, we performed cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX) to obtain specific recognition of human prostate cancer cells PC- 3M. Four aptamers were successfully obtained that can bind to target cells with high affinity and specificity. A 51-nt truncated sequence named Xq-2-C1 was identified after further elaborative analysis on the secondary structure. More importantly, the achieved aptamer Xq-2-C1 not only demonstrated excellent specific to target cells, but also revealed specific recognition to clinical prostate cancer tissue. The tissue imaging results showed that Xq-2-C1 had better recognition ratio for clinical prostate cancer tissue samples (85%) compared to the random sequence (9%). These results demonstrate that these newly generated aptamers would furnish potential applications in the early diagnosis and clinical treatment of prostate cancer.     

核酸适体在癌症诊疗中的研究进展

核酸适体是通过体外筛选技术得到的可特异性结合靶标分子的单链寡核苷酸分子探针, 其表现出与抗体相当或更优异的特异性和亲和力, 且具有靶标范围广、 免疫原性低、 易于精准制备和修饰及设计灵活可控等优势. 为癌症的早期筛查、 诊断及靶向治疗提供了全新的分子工具, 在癌症诊疗领域获得了广泛的关注与应用. 本文聚焦核酸适体在癌症诊断及治疗中的应用, 对近年来取得的研究进展进行了系统性总结, 并对未来发展方向及前景进行了展望.     

基于Cell-SELEX的核酸适配体在生化分析与生物成像中的应用

基于Cell-SELEX的核酸适配体是指以活细胞为靶标物,通过指数富集的配基系统进化技术(Systematic evolution of ligands by exponential enrichment,SELEX)从人工合成的DNA/RNA文库中筛选得到的单链寡核苷酸.它能够与靶标细胞高亲和性、高特异性结合,具有分子量低、合成简单、化学稳定性好、免疫原性低、易于功能化修饰等优点,已广泛应用于生命科学研究领域.本文综述了基于Cell-SELEX技术筛选的核酸适配体在肿瘤细胞检测、分析和成像方面的研究进展,并对核酸适配体研究的发展前景和趋势进行了展望.     

In vivo Fluorescence Imaging of Tumors using Molecular Aptamers Generated by Cell‐SELEX

Poor sensitivity and low specificity of current molecular imaging probes limit their application in clinical settings. To address these challenges, we used a process known as cell‐SELEX to develop unique molecular probes termed aptamers with the high binding affinity, sensitivity, and specificity needed for in vivo molecular imaging inside living animals. Importantly, aptamers can be selected by cell‐SELEX to recognize target cells, or even surface membrane proteins, without requiring prior molecular signature information. As a result, we are able to present the first report of aptamers molecularly engineered with signaling molecules and optimized for the fluorescence imaging of specific tumor cells inside a mouse. Using a Cy5‐labeled aptamer TD05 (Cy5‐TD05) as the probe, the in vivo efficacy of aptamer‐based molecular imaging in Ramos (B‐cell lymphoma) xenograft nude mice was tested. After intravenous injection of Cy5‐TD05 into mice bearing grafted tumors, noninvasive, whole‐body fluorescence imaging then allowed the spatial and temporal distribution to be directly monitored. Our results demonstrate that the aptamers could effectively recognize tumors with high sensitivity and specificity, thus establishing the efficacy of these fluorescent aptamers for diagnostic applications and in vivo studies requiring real‐time molecular imaging.     

Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection,characterization and structural modeling

Detecting specific protein glycoforms is attracting particular attention due to its potential to improve the performance of current cancer biomarkers. Although natural receptors such as lectins and antibodies have served as powerful tools for the detection of protein-bound glycans, the development of effective receptors able to integrate in the recognition both the glycan and peptide moieties is still challenging. Here we report a method for selecting aptamers toward the glycosylation site of a protein. It allows identification of an aptamer that binds with nM affinity to prostate-specific antigen, discriminating it from proteins with a similar glycosylation pattern. We also computationally predict the structure of the selected aptamer and characterize its complex with the glycoprotein by docking and molecular dynamics calculations, further supporting the binary recognition event. This study opens a new route for the identification of aptamers for the binary recognition of glycoproteins, useful for diagnostic and therapeutic applications.

Binary recognition of the glycoprotein prostate specific antigen by aptamers: a tool for detecting aberrant glycosylation associated with cancer.     

Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing

The development of novel affinity probes for cancer biomarkers may enable powerful improvements in analytical methods for detecting and treating cancer. In this report, we describe our use of capillary electrophoresis (CE) as the separation mechanism in the process of selecting DNA aptamers with affinity for the ovarian cancer biomarker HE4. Rather than the conventional use of cloning and sequencing as the last step in the aptamer selection process, we used high-throughput sequencing on an Illumina platform. This data-rich approach, combined with a bioinformatics pipeline based on freely available computational tools, enabled the entirety of the selection process—and not only its endpoint—to be characterized. Affinity probe CE and fluorescence anisotropy assays demonstrate the binding affinity of a set of aptamer candidates identified through this bioinformatics approach.

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Graphical Abstract A population of candidate aptamers is sequenced on an Illumina platform, enabling the process by which aptamers are selected over multiple SELEX rounds to be characterized. Bioinformatics tools are used to identify enrichment of selected aptamers and groupings into clusters based on sequence and structural similarity. A subset of sequenced aptamers may be intelligently chosen for in vitro testing.

     

全细胞的核酸适配体筛选的研究进展

核酸适配体(aptamer)是从人工合成的随机单链DNA(ssDNA)或RNA文库中筛选得到的,能够高亲和力、高特异性地与靶标结合的ssDNA或RNA。核酸适配体的靶标范围广,可包括小分子、蛋白质、细胞、微生物等多种靶标。其中以细胞为靶标的适配体在生物感应、分子成像、医学诊断、药物传输和疾病治疗等领域有很大的应用潜能。但全细胞的核酸适配体筛选过程复杂,筛选难度大,筛选的适配体性能不佳是导致目前可用的适配体非常有限的主要原因。由于细胞表面蛋白质在提取纯化过程中分子结构和形态会发生改变,故以膜表面蛋白质为靶标筛选的适配体很难应用于识别整体细胞。以全细胞为靶标的核酸适配体筛选则不需要准确了解细胞表面的分子结构,筛选过程中可保持细胞的天然状态,以全细胞为靶标筛选出的核酸适配体有望直接用于全细胞识别。本文总结了2008~2015年全细胞的核酸适配体筛选的研究进展,介绍了靶细胞的分类、核酸库的设计、筛选条件和方法以及核酸适配体的亲和力表征方法等。并列出全细胞靶标的核酸适配体序列。     

细菌的核酸适配体筛选的研究进展

核酸适配体(aptamer)是通过指数富集配体系统进化技术(SELEX)筛选的能够以高亲和力和高特异性识别靶标分子或细胞的核糖核酸(RNA)和单链脱氧核糖核酸(ssDNA)。作为化学抗体,核酸适配体的制备和合成比抗体的成本更低。核酸适配体的靶标范围极其广泛,包括小分子、生物大分子、细菌和细胞等。针对细菌靶标筛选的适配体,目前主要应用于食品、医药和环境中的细菌检测。细菌的核酸适配体筛选可以通过离心法将菌体-适配体复合物与游离的适配体分离,并通过荧光成像、荧光光谱分析、流式细胞仪分选、DNA捕获元件、酶联适配体分析等方法表征适配体与靶标的相互作用。筛选出的适配体可结合生物、化学检测方法用于细菌检测。本文介绍了细菌适配体的筛选和表征方法以及基于适配体的检测方法的最新进展,分析了不同检测方法的利弊,并列出了2011~2015年筛选的细菌的核酸适配体。     

Electrochemical Biosensors for Cancer Biomarkers Detection: Recent Advances and Challenges

Biomarkers are described as characteristics that provide information about biological conditions whether normal or pathological. Detection of biomarkers at the earliest stage of the cancer is of utmost importance for clinical diagnosis. Electrochemical biosensors allow detecting the low levels of specific analytes in blood, urine or saliva and providing a sensitive approach for direct measurement for cancer biomarker detection. Moreover, the integration of electrochemical devices with nanomaterials, such as carbon nanotubes, gold and magnetic particles offer amplification and multiplexing capabilities for simultaneous measurements of cancer biomarkers very sensitively. This review summarizes the recent developments of electrochemical biosensors systems for the detection of cancer biomarkers with emphasis on voltammetric, amperometric and impedimetric biosensors. A special attention is paid to aptamers and miRNAs that are very promising for the ultra‐sensitive and specific cancer biomarker detection.     

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.     

Aptamer-facilitated biomarker discovery (AptaBiD)

Here we introduce a technology for biomarker discovery in which (i) DNA aptamers to biomarkers differentially expressed on the surfaces of cells being in different states are selected; (ii) aptamers are used to isolate biomarkers from the cells; and (iii) the isolated biomarkers are identified by means of mass spectrometry. The technology is termed aptamer-facilitated biomarker discovery (AptaBiD). AptaBiD was used to discover surface biomarkers that distinguish live mature and immature dendritic cells. We selected in vitro two DNA aptamer pools that specifically bind to mature and immature dendritic cells with a difference in strength of approximately 100 times. The aptamer pools were proven to be highly efficient in flow- and magnetic-bead-assisted separation of mature cells from immature cells. The two aptamer pools were then used to isolate biomarkers from the cells. The subsequent mass spectrometry analysis of the isolated proteins revealed unknown biomarkers of immature and mature dendritic cells.