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.     

A Fluorescent Polymeric Quantum Dot/Aptamer Superstructure and Its Application for Imaging of Cancer Cells

In this work, a novel polymeric quantum dot/aptamer superstructure with a highly intense fluorescence was fabricated by a molecular engineering strategy and successfully applied to fluorescence imaging of cancer cells. The polymeric superstructure, which is composed of both multiple cell‐based aptamers and a high ratio of quantum dot (QD)‐labeled DNA, exploits the target recognition capability of the aptamer, an enhanced cell internalization through multivalent effects, and cellular disruption by the polymeric conjugate. Importantly, the polymeric superstructure exhibits an increasingly enhanced fluorescence with recording time and is thus suitable for long‐term fluorescent cellular imaging. The unique and excellent fluorescence property of the QD superstructure paves the way for developing polymeric QD superstructures that hold promise for applications such as in vivo imaging.     

Self‐Assembled Aptamer‐Based Drug Carriers for Bispecific Cytotoxicity to Cancer Cells

Monovalent aptamers can deliver drugs to target cells by specific recognition. However, different cancer subtypes are distinguished by heterogeneous biomarkers and one single aptamer is unable to recognize all clinical samples from different patients with even the same type of cancers. To address heterogeneity among cancer subtypes for targeted drug delivery, as a model, we developed a drug carrier with a broader recognition range of cancer subtypes. This carrier, sgc8c‐sgd5a (SD), was self‐assembled from two modified monovalent aptamers. It showed bispecific recognition abilities to target cells in cell mixtures; thus broadening the recognition capabilities of its parent aptamers. The self‐assembly of SD simultaneously formed multiple drug loading sites for the anticancer drug doxorubicin (Dox). The Dox‐loaded SD (SD–Dox) also showed bispecific abilities for target cell binding and drug delivery. Most importantly, SD–Dox induced bispecific cytotoxicity in target cells in cell mixtures. Therefore, by broadening the otherwise limited recognition capabilities of monovalent aptamers, bispecific aptamer‐based drug carriers would facilitate aptamer applications for clinically heterogeneous cancer subtypes that respond to the same cancer therapy.     

Engineering target-responsive hydrogels based on aptamer-target interactions

In this communication, we report a simple, but highly adaptable, method of constructing selective target-responsive hydrogels using DNA aptamers. The simplicity of the design is accomplished by using linear polymer chains as the hydrogel backbone and a DNA aptamer as the cross-linker. In this design, competitive binding of target to the aptamer causes the decrease of cross-linking density and, hence, dissolution of the hydrogel. The adaptability of this strategy for therapeutic applications was demonstrated using two different types of targets, small molecules and proteins. Our results indicated that this molecular engineering provides a highly selective and controllable release system whereby efficient release of therapeutic agents can occur at specific environments in which the target biomarker is found.     

核酸适体偶联药物的生物偶联构建技术与应用

核酸适体被称为“化学抗体”, 具有与抗体类似或更加优异的特异性和亲和力, 可以精准地靶向靶蛋白, 与靶蛋白特异性结合. 此外, 核酸适体还具有获取简单、 合成简便、 易于进行化学修饰、 不易变性、 靶标范围广、 免疫原性低及细胞内化快等优点, 已被广泛应用于众多研究领域. 在癌症治疗领域, 核酸适体作为一种优异的靶向识别工具和药物递送载体, 可实现抗肿瘤药物的精准递送. 将核酸适体与药物分子偶联, 可通过核酸适体的靶向作用使药物分子随核酸适体共同进入靶细胞, 实现药物分子在靶细胞内的富集, 进而促进靶细胞的死亡. 近年来, 核酸适体偶联药物已成为癌症靶向治疗的前沿新兴领域, 希望通过该领域的深入研究为癌症靶向治疗领域提供新思路. 本文综合评述了以生物偶联技术构建的核酸适体偶联药物及其应用研究.     

核酸适配体在肿瘤靶向治疗方面的研究进展

传统的抗肿瘤药物大多不具有选择性,在临床治疗中产生了严重的毒副作用。核酸适配体是一种小分子核酸,能够与靶标高亲和性、高特异性地结合。选择与癌症发生发展过程密切相关的生物标记物为靶标进行SELEX过程筛选出的核酸适配体自身可作为药物,也可与药物、siRNA、纳米粒等结合构成靶向给药体系,该体系能靶向作用于特定的肿瘤细胞,降低对正常细胞的毒性,用药量显著降低,药效提高。本文综述了近年来核酸适配体直接作为抗肿瘤药物、药物载体、siRNA载体以及作为纳米材料靶向剂构成多元复合靶向给药体系在肿瘤靶向治疗领域的研究进展。     

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.     

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。     

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.     

顺铂前药接枝修饰硫代DNA及其自组装靶向纳米药物研究

选用具有良好生物相容性的硫代修饰嵌段核酸为载体,将其非硫代修饰部分设计为靶向MUC-1蛋白的核酸适配体序列,同时在其硫代修饰部分通过硫代磷酸酯基团（Phosphorothioate,PS）接枝修饰四价顺铂前药,制备了两亲性核酸-顺铂前药缀合物MUC-1/^PODNA-b-（^PSDNA-g-Pt）,并进一步自组装成类似球形核酸（Spherical nucleic acid,SNA）的含铂靶向纳米药物（MUC-1/Pt-SNAs）.结果表明,该纳米药物递送体系载药率高、形貌稳定、分散性好,能够高效靶向MUC-1蛋白过表达的MCF-7乳腺癌细胞,并在体内外实验中表现出优异的抗肿瘤效果和极低的毒副作用.     

Synthesis and biological evaluation of disulfide-linked HPMA copolymer-mesochlorin e6 conjugates

Novel polymeric delivery systems for the photosensitizer mesochlorin e6 (Mce6) were synthesized to overcome problems of systemic toxicity. A disulfide bond was included to allow for quick release of Mce6 from the N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer backbone once internalized in tumor tissue. The synthesized conjugates demonstrated a time-dependent reductive cleavage with an accompanying increase in the quantum yield of singlet oxygen generation on exposure to DTT. Quicker release kinetics and a higher cytotoxicity in SKOV-3 human ovarian carcinoma cells were obtained as compared to polymer conjugate with a proteolytically cleavable GFLG spacer. These novel conjugates hold promise as clinically relevant drug delivery systems for photodynamic therapy of cancer.     

Modified capillary electrophoresis based measurement of the binding between DNA aptamers and an unknown concentration target

The recognition of targets such as biomacromolecules, viruses and cells by their aptamers is crucial in aptamer-based biosensor platforms and research into protein function. However, it is difficult to evaluate the binding constant of aptamers and their targets that are hard to purify and quantify, especially when the targets are undefined. Therefore, we aimed to develop a modified capillary electrophoresis based method to determine the dissociation constant of aptamers whose targets are hard to quantify. A protein target, human thrombin, and one of its aptamers were used to validate our modified method. We demonstrated that the result calculated by our method, only depending on the aptamer’s concentrations, was consistent with the classical method, which depended on the concentrations of both the aptamers and the targets. Furthermore, a series of DNA aptamers binding with avian influenza virus H9N2 were confirmed by a four-round selection of capillary electrophoresis–systematic evolution of ligands by exponential enrichment, and we identified the binding constant of these aptamers by directly using the whole virus as the target with the modified method. In conclusion, our modified method was validated to study the interaction between the aptamer and its target, and it may also advance the evaluation of other receptor–ligand interactions.     

Evaluation of Relative Aptamer Binding to Campylobacter jejuni Bacteria Using Affinity Probe Capillary Electrophoresis

Abstract

A qualitative capillary electrophoresis immunoassay was developed for the first-time to evaluate aptamer binding to bacterial cells. Binding affinity of aptamers developed against a Campylobacter jejuni bacterial cell target, relative to other common food-borne pathogens was investigated and specific binding affinity was evidenced by pronounced mobility shift and peak broadening with increasing bacteria concentration for both aptamers. Little to no mobility shift was observed for food-borne pathogens, Salmonella typhirium and Escherichia coli, even when increasing concentrations 10-fold over target. These results suggest that affinity probe capillary electrophoresis could be useful for qualitative screening of aptamer candidates for bacterial cell targets.     

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.     

Syntheses,electrochemistry and cytotoxicity of ferrocene-containing polyaspartamides as water-soluble polymeric drug carrier/drug conjugates

A general strategy towards the syntheses of water-soluble polymeric drug carriers and their drug conjugates is described. Methods of drug uptake by cells, drug release from the polymeric carrier and the relevance of electrochemistry to drug activity of the ferrocenyl group are highlighted. The advantages of these polymeric systems are demonstrated utilising cytotoxicity results of a polyaspartamide-ferrocenyl conjugate.     

Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers

Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na⁺-binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na⁺ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm . Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.     

Sandwich-type aptasensor employing modified aptamers and enzyme-DNA binding protein conjugates

The use of aptamers in various analytical applications as molecular recognition elements and alternative to antibodies has led to the development of various platforms that facilitate the sensitive and specific detection of targets ranging from small molecules and proteins to whole cells. The goal of this work was to design a universal and adaptable sandwich-type aptasensor exploiting the unique properties of DNA binding proteins. Specifically, two different enzyme-DNA binding protein conjugates, GOx-dHP and HRP-scCro, were used for the direct detection of a protein using two aptamers for target capture and detection. The specific dsDNA binding sequence for each DNA binding protein tag was incorporated in the form of a hairpin at one end of each aptamer sequence during the synthesis step. Detection was accomplished by an enzymatic (GOx/HRP) cascade reaction after the binding of each enzyme conjugate to its corresponding binding sequence on each aptamer. The proposed sandwich-type aptasensor was validated for the detection of thrombin, which is one of the most commonly used model targets with known dual aptamers. The limit of detection accomplished was 0.92 nM which is comparable with other colorimetric platforms reported in the literature. The sensitivity of the aptasensor was easily modulated by changing the number of dsDNA binding sites incorporated in the aptamer sequences, thus controlling the enzyme stoichiometry. Finally, the potential use of the proposed sensing approach for real sample testing was demonstrated using spiked human plasma and no significant matrix effects were observed when up to 2% plasma was used.

     

A two-step stimulus-response cell-SELEX method to generate a DNA aptamer to recognize inflamed human aortic endothelial cells as a potential in vivo molecular probe for atherosclerosis plaque detection

Aptamers are single-stranded oligonucleotides that are capable of binding wide classes of targets with high affinity and specificity. Their unique three-dimensional structures present numerous possibilities for recognizing virtually any class of target molecules, making them a promising alternative to antibodies used as molecular probes in biomedical analysis and clinical diagnosis. In recent years, cell-systematic evolution of ligands by exponential enrichment (SELEX) has been used extensively to select aptamers for various cell targets. However, aptamers that have evolved from cell-SELEX to distinguish the “stimulus-response cell” have not previously been reported. Moreover, a number of cumbersome and time-consuming steps involved in conventional cell-SELEX reduce the efficiency and efficacy of the aptamer selection. Here, we report a “two-step” methodology of cell-SELEX that successfully selected DNA aptamers specifically against “inflamed” endothelial cells. This has been termed as stimulus-response cell-SELEX (SRC-SELEX). The SRC-SELEX enables the selection of aptamers to distinguish the cells activated by stimulus of healthy cells or cells isolated from diseased tissue. We report a promising aptamer, N55, selected by SRC-SELEX, which can bind specifically to inflamed endothelial cells both in cell culture and atherosclerotic plaque tissue. This aptamer probe was demonstrated as a potential molecular probe for magnetic resonance imaging to target inflamed endothelial cells and atherosclerotic plaque detection.

Aptamer sandwich assays: label-free and fluorescence investigations of heterogeneous binding events

We studied aptamer binding events in a heterogeneous format using label-free and fluorescence measurements for the purpose of developing an aptamer-based sandwich assay on a standard microtiter plate platform. The approach allowed visualization of the underlying aptamer immobilization and target binding events rather than relying on only an endpoint determination for method optimization. This allowed for a better understanding of these multi-step assays and optimal conditions specific to aptamers. α-thrombin was chosen as a prototypical analyte as two well-studied aptamers (15 and 29-mer) binding distinct epitopes are available. The Corning Epic? system, which utilizes a resonance waveguide diffraction grating in a 384-well microtiter plate format, was employed to measure relative immobilization and binding levels for various modified aptamers. Parameters investigated included the effects of aptamer orientation, label orientation, spacer length, spacer type, immobilization concentration, and binding buffer. Most notably, the 15-mer aptamer was preferable for capture over the 29-mer aptamer and aptamers with increasing poly(dT) spacer length between the biotin modification and the aptamer yielded decreased immobilization levels. This decreased immobilization resulted in increased α-thrombin binding ability for 15-mer aptamers with the poly(dT) spacer. Fluorescence measurements of fluorescein-labeled 29-mer aptamers with varying spacers were used to visualize sandwich complex formation. Using both label-free and traditional fluorescence measurements, an in-depth understanding of the overall assay was obtained, thus the inclusion of label-free measurements is recommended for future method development.     

Reversibly self-assembled pH-responsive PEG-p(CL-g-TMC) polymersomes

Polymersomes have gained much interest within the biomedical field as drug delivery systems due to their ability to transport and protect cargo from the harsh environment inside the body. For an improved drug efficacy, control over cargo release is however also an important factor to take into account. An often employed method is to incorporate pH sensitive groups in the vesicle membrane, which induce disassembly and content release when the particles have reached a target site in the body with the appropriate pH, such as the acidic microenvironment of tumor tissue or the endosome. In this paper, biodegradable poly(ethylene glycol)-poly(caprolactone-gradient-trimethylene carbonate)-based polymeric vesicles have been developed with disassembly features at mild acidic conditions. Modifying the polymer backbone with imidazole moieties results in vesicle disassembly upon protonation due to the lowered pH. Furthermore, upon increasing the pH efficient re-assembly into vesicles is observed due to the switchable amphiphilic nature of the polymer. When this re-assembly process is conducted in presence of cargo, enhanced encapsulation is achieved. Furthermore, the potency of the polymeric system for future biomedical applications such as adjuvant delivery is demonstrated.