Identification of new human mesenchymal stem cell biomarker by aptamers / Identificação de novos biomarcadores de células tronco mesenquimais de origem humana por meio de aptâmeros

Stem cells are undifferentiated cells that can be distinguished from others by their ability to self-renew and to differentiate into new specific cell types. Mesenchymal stem cells (MSC) are adult stem cells that can be obtained from different sources, such as adipose tissue, bone marrow, dental pulp, and umbilical cord. They can either replicate, originating new identical cells, or differentiate into cells of mesodermal origin and from other germ layers. MSC have been studied as new tools for regenerative therapy. Although encouraging results have been demonstrated, MSC-based therapies still face a great barrier: the difficulty of isolating these cells from heterogeneous environments. MSC are currently characterized by immunolabelling through a set of multiple surface membrane markers, including CD29, CD73, CD90 and CD105, which are also expressed by other cell types. Hence, the present work aimed to identify new specific biomarkers for the characterization of human MSC using DNA aptamers produced by the SELEX (Systematic Evolution of Ligands by EXponential Enrichment) technique. Our results showed that MSC from different origins bound to DNA candidate aptamers, that is, DNA or RNA oligonucleotides selected from random libraries that bind specifically to biological targets. Aptamer-bound MSC could be isolated by fluorescenceactivated cell sorting (FACS) procedures, enhancing the induction of differentiation into specific phenotypes (chondrocytes, osteocytes and adipocytes) when compared to the whole MSC population. Flow cytometry analyses revealed that candidate aptamers bound to 50% of the MSC population from dental pulp and did not present significant binding rates to human fibroblasts or lymphocytes, both used as negative control. Moreover, immunofluorescence images and confocal analyses revealed staining of MSC by aptamers localized in the surfacemembrane of these cells. The results also showed internal staining of human monocytes by our investigated aptamers. A non-specific control aptamer (CNTR APT) obtained from the random pool was then utilized to compare the specificity of the aptamers bound to the analyzed non-apoptotic cells, showing no staining for MSC. However, 40% of the monocytes bound to the CNTR APT. Normalized data based on the cells bound to candidate aptamers compared to those bound to the CNTR APT, revealed a 10 to 16-fold higher binding rate for MSC against 2-fold for monocytes. Despite its low specificity, monocyte-aptamer binding occurs probably due to the expression of shared markers with MSC, since monocytes are derived from hematopoietic stem cells and are important for the immune system ability to internalize/phagocyte external molecules. Given that, we performed a pull-down assay followed by mass spectrometry analysis to detect which MSC-specific protein or other target epitope not coexpressed by monocytes or the CNTR APT would bind to the candidate aptamer. Distinguishing between MSC and monocyte epitopes is important, as both cells are involved in immunomodulatory effects after MSC transplantations. ADAM17 was found to be a target of the APT10, emerging as a possible biomarker of MSC, since its involvement in the inhibition of the TGF signaling cascade, which is responsible for the differentiation of MSC. Thus, MSC with a higher stemness profile should overexpress the protein ADAM17, which presents a catalytic site with affinity to APT10. Another target of Apt 10 is VAMP3, belonging to a transmembrane protein complex that is involved in endocytosis and exocytosis processes during immune and inflammatory responses. Overall, proteins identified as targets of APT10 may be cell surface MSC biomarkers, with importance for MSC-based cell and immune therapies

Células tronco são células indiferenciadas que podem ser distinguidas de outros tipos celulares por meio da habilidade de se auto renovarem e de se diferenciarem em novos tipos celulares. Células tronco mesenquimais (MSC) são células tronco adultas encontradas em diferentes tecidos como tecido adiposo, polpa de dente e cordão umbilical. Estas células podem se autodividir em células idênticas ou se diferenciarem em células de origem mesodermal. Estas células têm sido estudadas em novas aplicações que envolvem terapia regenerativas. Embora resultados encorajadores tenham sido demonstrados, terapias que utilizam MSC ainda encontram uma grande barreira: a dificuldade no isolamento destas células a partir de um ambiente heterogêneo. MSC são caracterizadas por populações positivas em ensaios de imunomarcação para os epítopos membranares CD29, CD73, CD90 e CD105, presentes também em outros tipos celulares. Assim, o presente trabalho tem o objetivo de identificar novos biomarcadores de MSC de origem humana, utilizando aptâmeros de DNA produzidos pela técnica SELEX (Systematic Evolution of Ligands by EXponential Enrichment) como ferramenta. Nossos resultados mostraram que MSC de diferentes origens ligam-se a aptâmeros (oligonucleotídeos de DNA ou RNA que atuam como ligantes específicos de alvos moleculares) de DNA candidatos que atuam no isolamento de MSC por meio da técnica FACS de separação celular, promovendo uma maior indução de diferenciação em células específicas (condrócitos, osteócitos e adipócitos) comparada com a população total de MSC. Análises de citometria de fluxo mostraram que os aptâmeros candidatos se ligam a 50% das MSC de polpa de dente e não apresentam taxa de ligação significante para fibroblastos e linfócitos de origem humana - utilizados como controles negativo. Além domais, imagens de imunofluorescência e confocal mostraram ligação na superfície da membrana de MSC e a marcação interna de monócitos a estes aptâmeros. Portanto, um aptâmero controle (CNTR APT) foi utilizado para comparar a especificidade dos aptâmeros ligados a células viáveis, mostrando a não ligação deste aptâmero a MSC. Porém, 40% da população de monócitos ligou-se ao CNTR APT. Uma normalização baseada na comparação entre as taxas de ligação entre células ligadas com aptâmeros candidatos e o aptâmero controle gerou uma taxa de especificidade entre 10-16 vezes maior para MSC contra 2,5 vezes para os monócitos. Deste modo, embora os resultados tenham mostrado uma taxa de ligação entre monócitos e aptâmeros, as MSC ligadas aos aptâmeros candidatos possuem uma maior taxa de especificidade devido a uma maior presença de antígenos que são expressos em ambas as células. Um ensaio de Pull Down seguido de espectrometria de massas foi utilizado para a identificação de biomarcadores que se ligariam aos aptâmeros candidatos, e que não seriam co-expressos por monócitos e por antígenos ligados ao aptâmero controle. Deste modo, a proteína ADAM17 foi identificada nas amostras de APT10 ligadas às MSC. Tal proteína está relacionada à inibição de uma cascata de sinalização da família de proteínas TGF, responsável pela diferenciação de MSC. Assim, MSC com maior potencial tronco deveriam expressar ADAM17 em maior quantidade. Tal proteína apresenta um sítio catalítico que demonstra interagir com o APT10, de acordo com predição Docking entre proteína e DNA. Foi identificada também, a proteína VAMP3, que pertence a um complexo proteico transmembranar responsável pelos processos de endocitose e exocitose, e que podem ter um papel importante na liberação de citocinas e outras moléculas relacionadas às respostas imune e inflamatórias. Deste modo, o APT10 identificou proteínas importantes que devem estar relacionas com a melhora de imunoterapias que utilizam MSC

Screening and Identification of Nucleic Acid Aptamers Specifically Binding to Human Lipocalin 6 / 中国生物化学与分子生物学报

It is an urgent and difficult task to establish a simple and efficient method for identifying and isolating sperm cells from mixed stains in forensic science. Nucleic acid aptamers targeting sperm cell-surface proteins can be used for the separation and purification of sperms from mixed stain samples. Human lipocalin 6 (hLCN6) is an epididymal secreted protein that binds to the head and tail of sperm cells and is associated with sperm maturation. Using the systematic evolution of ligands by the exponential enrichment (SELEX) technique, magnetic bead-bound hLCN6 was used as the target molecule to screen for aptamers with high affinity and specificity to hLCN6 from a random single-stranded DNA (ssDNA) library. Through 15 rounds of positive selection and 3 rounds of negative selection, 24 clones were selected and subjected to sequence analysis. Subsequently, 4 candidate aptamers were selected and further examined for their binding affinity and specificity by enzyme-linked oligonucleotide adsorption (ELONA) and cell binding assays. One aptamer (H2) against hLCN6 with a high affinity and specificity was isolated and investigated by dot blotting and immunofluorescence staining. The result revealed that the candidate aptamer H2 with a dissociation constant of (3. 21 ± 0. 75) nmol/ L was able to recognize and specifically bind to hLCN6. The aptamer H2 also showed high affinity and specificity to human sperms in vitro, which establishes the foundation for the separation of sperm cells from mixed stain based on nucleic acid-protein interactions and provides a new scheme.

Selection and appraisement of nucleic acid aptamers for castration resistant prostate cancer cells based on Cell-SELEX / 西安交通大学学报(医学版)

【Objective】 To screen nucleic acid aptamers that can specifically recognize castration-resistant prostate cancer （CRPC） cells by Cell-SELEX. 【Methods】 For Cell-SELEX selection， CRPC cell lines C4-2 were used as positive control cells， while androgen-dependent prostate cancer cell lines LNCap were used as negative control cells. The 5’end of the upstream primers was labeled with FITC， and the 5’end of the downstream primers was labeled with biotin. Single-stranded DNA （ssDNA） collected from each round of screening was used as template for PCR amplification and purification. The biotin-streptavidin magnetic bead separation was used to isolate PCR product for the next round of screening. The process of Cell-SELEX was analyzed by flow cytometry. ssDNA products of the last round were collected for PCR amplification， purification， cloning and DNA sequencing. The secondary structure of selected DNA aptamers was predicted. Dissociation constants of the two aptamers were calculated. Flow cytometry and confocal microscopy were used to evaluate selective binding of aptamers to CRPC cells and tissues. 【Results】 The binding rate of DNA products to CRPC cells gradually increased with the increase of selection cycles， reaching the highest in the last round. DNA structure prediction analysis showed that the secondary structure of aptamers CRPC-1 and CRPC-2 was mainly stem-loop structure. Flow cytometry analysis and confocal images showed that both CRPC-1 and CRPC-2 could specifically target C4-2 cells. In addition， immunohistofluorescence assay showed that CRPC-1 could specifically target CRPC tissues. 【Conclusion】 Cell-SELEX can be used to screen aptamers that specifically target CRPC cells and tissues， which provides experimental basis for early screening and targeted diagnosis of CRPC. It is of significance for treatment plan adjustment and prognosis improvement of prostate cancer.

Los aptámeros como novedosa herramienta diagnóstica y terapéutica y su potencial uso en parasitología / Aptamers as a novel diagnostic and therapeutic tool and their potential use in parasitology

Los aptámeros son secuencias de ADN o ARN de cadena sencilla que adoptan la forma de estructuras tridimensionales únicas, lo cual les permite reconocer un blanco específico con gran afinidad. Sus usos potenciales abarcan, entre otros, el diagnóstico de enfermedades, el desarrollo de nuevos agentes terapéuticos, la detección de riesgos alimentarios, la producción de biosensores, la detección de toxinas, el transporte de fármacos en el organismo y la señalización de nanopartículas. El pegaptanib es el único aptámero aprobado para uso comercial por la Food and Drug Administration (FDA). Otros aptámeros para el tratamiento de enfermedades están en la fase clínica de desarrollo. En parasitología, se destacan los estudios que se vienen realizando en Leishmania spp., con la obtención de aptámeros que reconocen la proteína de unión a poliA (LiPABP) y que pueden tener potencial utilidad en la investigación, el diagnóstico y el tratamiento de la leishmaniasis. En cuanto a la malaria, se han obtenido aptámeros que permiten identificar eritrocitos infectados e inhiben la formación de rosetas, y otros que prometen ser alternativas para el diagnóstico al detectar de forma específica la proteína lactato deshidrogenasa (PfLDH). Para Cryptosporidium parvuum se han seleccionado aptámeros que detectan ooquistes a partir de alimentos o aguas contaminadas. Para Entamoeba histolytica se han aislado dos aptámeros llamados C4 y C5, que inhiben la proliferación in vitro de los trofozoítos y tienen potencial terapéutico. Los aptámeros contra Trypanosoma cruzi inhiben la invasión de células LLC-MK2 (de riñón de mono) en un 50 a 70 % y aquellos contra T. brucei transportan moléculas tóxicas al lisosoma parasitario como una novedosa estrategia terapéutica. Los datos recopilados en esta revisión destacan los aptámeros como una alternativa para la investigación, el diagnóstico y el tratamiento contra parásitos de interés nacional.

Aptamers are single-stranded DNA or RNA sequences that adopt unique three-dimensional structures that allow them to recognize a specific target with high affinity. They can potentially be used for the diagnosis of diseases, as new therapeutic agents, for the detection of food risks, as biosensors, for the detection of toxins, and as drug carriers and nanoparticle markers, among other applications. To date, an aptamer called pegaptanib is the only aptamer approved by the Food and Drug Administration (FDA) for commercial use. Other aptamers are in different clinical stages of development for the treatment of different diseases. In parasitology, investigations carried out with parasites such as Leishmania spp. allowed the acquisition of aptamers that recognize the polyA-binding protein LiPABP and may have potential applications in research and diagnosis and even as therapeutic agents. Regarding malaria, aptamers have been obtained that allow the identification of infected erythrocytes or inhibit the formation of rosettes, along with those that provide promising alternatives for diagnosis by specifically detecting the protein lactate dehydrogenase (PfLDH). In Cryptosporidium parvum allow the detection of oocysts in contaminated food or water. In Entamoeba histolytica, two aptamers called C4 and C5, which inhibit the proliferation of trophozoites in vitro and have potential use as therapeutic agents, have been isolated. Aptamers obtained against Trypanosoma cruzi inhibit the invasion of LLC-MK2 (from monkey kidney) cells by 50-70%, and in T. brucei, aptamers with the potential to transport toxic molecules to the parasitic lysosome were identified as a novel therapeutic strategy. The data collected in this review highlight aptamers as a novel alternative in the research, diagnosis, and treatment of parasites of national interest.

Aptamers: Trending Prospective in Therapeutics

Aptamers are short stretches of Ribonucleic acid or Deoxyribonucleic acid having a specific 3D shape which form complexes with the target site with high affinity. Systemic Evolution of Ligands by Exponential Enrichment (SELEX) is responsible for the high affinity and specificity of aptamers to bind the target molecules. Due to some unique features of Aptamers, it attracts the attention of many scientists to use them as a tool in the treatment & diagnosis of various diseases and syndromes. The results obtained from the various clinical data shows that Aptamers can be used in the treatment and diagnosis of various diseases including cancer and syndromes like AIDS, severe acute respiratory syndrome etc. Many viral infections like human immunodeficiency virus, hepatitis B virus and Ebola virus are now treated or diagnosed with the help of aptamers. Along with viral infections, aptamers are also promising Chemical antibodies in the treatment of various kinds of cancer like breast cancer, lung cancer, colorectal cancer, etc. Aptamers have several advantages over conventional antibodies in context to its size, thermal stability, immunogenicity, ease of modification, etc. Aptamers are smaller than conventional antibodies, this property allows aptamers to access in tissue and cell. Aptamers are synthetic agents and we scale up its production as per requirement and it eliminate the various regulatory requirements associated with bio- production. The various roles of aptamers in the treatment and diagnosis of many life- threatening diseases, syndromes and viral infections like cancer, AIDS, Ebola virus lead aptamers to serve as Future Pharmaceutical dosage form or prospective Future of Modern Medical Science.

Cytological study on aptamer selection for bladder cancer through CELL-SELEX / 医学研究生学报

ObjectiveThe methods based on bladder cancer markers which could be applied to early diagnosis and postoperative recurrence monitoring of bladder cancer were current research hotspots. This study aims to screen aptamers that specifically recognize human bladder cancer cell lines (EJ, T24, BIU87) through cell-based systematic evolution of ligand by exponential enrichment (CELL-SELEX).MethodsFor CELL-SELEX screening, bladder cancer cell lines EJ, T24, and BIU87 were used as positive control cells. HCV 29 (human normal urothelial cell line), 293T (human embryonic kidney cell line), huh7 (human hepatocellular carcinoma cell line) were used as negative control cells. PCR upstream primers were labeled with FITC, downstream primer was labeled with Biotin. ssDNA fragments collected from each round were amplified by PCR, and the amplified product was then purified using a DNA purification Kit. The biotin-streptavidin magnetic separation methods were used to isolate the PCR product to obtain secondary FITC-ssDNA for the next CELL-SELEX round. The screening process was monitored by flow cytometry. ssDNA pool with the highest binding rates to bladder cancer cell lines(EJ, T24, and BIU87) was selected to PCR amplification, product purification, molecular cloning, and sequencing. According to the sequencing results, the secondary structure of the aptamer was pre-simulated by Dnaman software. Aptamer labeled with FITC was synthesized in vitro, flow cytometry was used to detect the binding rate of the aptamer to bladder cancer cell lins (EJ, T24 and BIU87).ResultsWith the advance of the CELL-SELEX process, the binding rate of FITC-ssDNA to bladder cancer cell lins (EJ, T24, and BIU87) increased gradually. By the 15th round, the binding rate of FITC-ssDNA to EJ cells reached the highest level. The apt1 had the highest enrichment among the 15th round ssDNA pool. By the 18th round, the binding rate of FITC-ssDNA to T24 or BIU87 cells reached the highest level. The apt2 and apt3 had the highest enrichment among the 18th round ssDNA pool. DNA structure prediction showed that the secondary structure of apt1, apt2, and apt3 was mainly stem-loop structure. Flow cytometry showed that the highest binding rate was FITC-apt1 to EJ cells, FITC-apt2 to T24 cells, and FITC-apt3 to BIU87 cells, respectively. There is no significant combination between these aptamers with the negative cells.ConclusionIn this study, three kinds of aptamers with high specificity for bladder cancer cell lines were successfully screened by CELL-SELEX. The apt1 can specifically recognize EJ cells, apt2 can specifically recognize T24 cells and apt3 can specifically recognize BIU87 cells, all of which provide experimental evidence for early diagnosis and targeted therapy technology research of bladder cancer.

Evolution of specific RNA aptamers via SELEX targeting recombinant human CD36 protein: A candidate therapeutic target in severe malaria

Objective: To isolate and characterize RNA aptamers that are specific to human CD36 protein using systematic evolution of ligands by exponential enrichment (SELEX) technology to identify candidates for adjunct therapy to reverse the binding of Plasmodium-infected erythrocytes. Methods: RNA aptamers were isolated using nitrocellulose membrane-based SELEX and binding analysis was screened using an electrophoretic mobility shift assay and enzyme-linked oligonucleotide assay. Results: Thirteen cycles of nitrocellulose membrane-based SELEX yielded three aptamers (RC60, RC25, RC04) exhibiting high binding against CD36 protein as shown on electrophoretic mobility shift assay. The sequence analysis revealed a G-quadruplex sequence within all the isolated aptamers that might contribute to aptamer binding and thermodynamic stability. The specificity assay further showed that RC60 and RC25 were highly specific to CD36. The competitive inhibition assay demonstrated that RC60 and RC25 shared a similar binding epitope recognized by mAb FA6-152, a specific monoclonal antibody against CD36. Conclusions: RC60 and RC25 are promising candidates as anti-cytoadherence for severe malaria adjunct therapy.

Evolution of specific RNA aptamers via SELEX targeting recombinant human CD36 protein: A candidate therapeutic target in severe malaria

To isolate and characterize RNA aptamers that are specific to human CD36 protein using systematic evolution of ligands by exponential enrichment (SELEX) technology to identify candidates for adjunct therapy to reverse the binding of Plasmodiuminfected erythrocytes. Methods: RNA aptamers were isolated using nitrocellulose membrane-based SELEX and binding analysis was screened using an electrophoretic mobility shift assay and enzyme-linked oligonucleotide assay. Results: Thirteen cycles of nitrocellulose membrane-based SELEX yielded three aptamers (RC60, RC25, RC04) exhibiting high binding against CD36 protein as shown on electrophoretic mobility shift assay. The sequence analysis revealed a G-quadruplex sequence within all the isolated aptamers that might contribute to aptamer binding and thermodynamic stability. The specificity assay further showed that RC60 and RC25 were highly specific to CD36. The competitive inhibition assay demonstrated that RC60 and RC25 shared a similar binding epitope recognized by mAb FA6-152, a specific monoclonal antibody against CD36. Conclusions: RC60 and RC25 are promising candidates as anticytoadherence for severe malaria adjunct therapy.

Isolation of MLL1 Inhibitory RNA Aptamers

Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (Systemic Evolution of Ligands by Exponential enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers—APT1 and APT2—represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5′-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3′. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.

Aptamers selection for tumor based on cell-SELEX and its application in tumor diagnosis and treatment / 国际肿瘤学杂志

Aptamers have shown great potential in early diagnosis,treatment of tumor because of its high specificity and affinity.The aptamers selected by cell-SELEX can identify tumor cells through target molecular changes,and then realize the prevention and treatment of tumors.At present,researchers have successfully selected a number of aptamers by using cell-SELEX technology combined with flow cytometry.To make up for the deficiencies and exert the advantages of aptamers can make aptamer technology really apply to clinical diagnosis and treatment.

Selection of DNA aptamers to cervical intraepithelial neoplasia by SELEX / 生物工程学报

An in vitro synthesized random ssDNA library was subjected to 12 rounds of selection against anti-screening cells and sieving cells by SELEX. Normal and inflammatory cervical exfoliation cells were selected as anti-screening cells, and the cervical exfoliation cells of low-grade squamous intraepithelial lesion (CIN1), high-grade squamous intraepithelial lesion (CIN2, CIN3) and cervical carcinoma were selected as sieving cells during the screening process. Then, the highly specific aptamer CIN-Ap4 was established by the analysis of the specificity, affinity and cell immunofluorescence, which can be used as biomarker for Cervical Intraepithelial Neoplasia. Prime Premier 5.0 was applied to design a random ssDNA library. According to the fixed sequence at both ends of the library, a pair of primers were designed and synthesized. At the same time, the optimal annealing temperature, cycle times and primer concentration ratio of PCR procedure were selected. The results under the optimal condition are shown as follows. In the 50 μL reaction system, the optimum reaction conditions of symmetry PCR are as follows: annealing temperature is 49.5 ℃, number of cycles is 15. The optimal reaction conditions of indirect asymmetric PCR are as follows: the primer concentration ratio is 80:1, and the number of cycles is 35. The experiment proves that the oligonucleotide library is constructed successfully, and the highly specific dsDNA and ssDNA can be obtained under optimal PCR conditions with good repeatability, which establishes the foundation for the further exploration and experimentation.

Application of aptamer in the study of cancer stem cells / 国际肿瘤学杂志

Cancer stem cells have self-renewal and multilineage differentiation potentials,which play important roles in tumorigenesis,metastasis,recurrence and resistance to chemical therapy and radiotherapy,and so on.It is the hotspot of tumor research recently.Aptamer is a small molecular oligonucleotide with high targeting ability and affinity,which is a new type of nucleic acid in the diagnosis and treatment of cancer.Now more and more research is being done on the aptamer is applied in the diagnosis and treatment of cancer stem cells,which provides a new research tool for the diagnosis and treatment of cancer stem cells.

Aptamers from Cell-based Selection for Bioanalysis and Bioimaging / 分析化学

Aptamers are single-stranded oligonucleotides ( DNA or RNA ) selected through a technology termed "Systematic evolution of ligands by exponential enrichment" ( SELEX ) . In addition to high affinity and high specificity for their target molecules, aptamers have some advantages such as low molecular weight, easy synthesis, high chemical stability, low immunogenicity, and convenient modification. Based on the Cell-SELEX technique, a panel of aptamers which can specifically recognize target cell lines has been generated. By targeting specific membrane proteins in their native state, these aptamers can identify subtle molecular differences among different cell lines, thus have attracted a broad interest in biomedical research. In this review, we summarized the development of aptamers and their use in detection, profiling and imaging of tumor cells. Also, their perspectives were discussed.

Screening and identification of a novel DNA aptamer against albumin / 基础医学与临床

Objective To develop an albumin aptamer that may potentially serve as a selective ligand for albumin removal from experimental samples.Methods A single-stranded 59nt DNA library that contains 21 random oligo nucleotides was synthesized in vitro.An albumin aptamer A6 was developed by SELEX technique using bovine serum albumin (BSA) as target.The enrichment of aptamer and evaluation of its binding properties were monitored by flow cytometry.The secondary structure of A6 was predicted by MFord software.Results The aptamer A6 strongly bound to BSA with a Kd of 77.4 nmol/L,and had minimal cross reactivity with control proteins including ovalbu min,IgG,and trypsin.Conclusions Aptamer A6 may be a potential tool in albumin removal.

Selection and identification of aptamers for mesenchymal stem cells from different species / 军事医学

Objective To screen an ssDNA aptamer for rabbit mesenchymal stem cells (MSCs) and to identify the ability of the aptamer to recognize MSCs of a variety of species origin.Methods MSCs were isolated from the thigh bone of immature rabbits and identified by induced osteogenic and adipogenic differentiation,respectively.Aptamers were screened by cell SELEX (systematic evolution of ligands by exponential enrichment) technique targeting to isolated MSCs.Enrichment of the 5th pool was evaluated through binding assay of FAM modified pool to MSCs by confocal microscopy.The enriched 5th pool was then cloned into pGE-T vector and the cloned sequences were determined randomly.The candidates were chosen based on primary sequence conservation and predicted secondary structure by RNA structure and MEME online analysis.Flow cytometry analysis was used to identify the aptamers binding to MSCs of rabbit, rat, and human origin.Results The isolated MSCs had the potential of osteogenic differentiation and adipogenic differentiation under certain conditions.Aptamer 5-1-12 from 5th enriched pool was characterized as MSCs recognizing aptamer binding to MSCs of rabbit, rat and human origin.Conclusion Aptamer 5-1-12 that recognizes MSCs of different species origin is obtained through live cell-SELEX.

Aptamers as a promising approach for the control of parasitic diseases

ABSTRACT Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host-parasite interactions from "omics" data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of "aptasensors" for parasite diagnosis, and "intramers" targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.

Screening specific recognition motif of RNA-binding proteins by SELEX in combination with next-generation sequencing technique / 生物工程学报

RNA-binding protein exerts important biological function by specifically recognizing RNA motif. SELEX (Systematic evolution of ligands by exponential enrichment), an in vitro selection method, can obtain consensus motif with high-affinity and specificity for many target molecules from DNA or RNA libraries. Here, we combined SELEX with next-generation sequencing to study the protein-RNA interaction in vitro. A pool of RNAs with 20 bp random sequences were transcribed by T7 promoter, and target protein was inserted into plasmid containing SBP-tag, which can be captured by streptavidin beads. Through only one cycle, the specific RNA motif can be obtained, which dramatically improved the selection efficiency. Using this method, we found that human hnRNP A1 RRMs domain (UP1 domain) bound RNA motifs containing AGG and AG sequences. The EMSA experiment indicated that hnRNP A1 RRMs could bind the obtained RNA motif. Taken together, this method provides a rapid and effective method to study the RNA binding specificity of proteins.

Aptasensors in viral detection

Background: Aptamers are single-stranded nucleic acids, so-called ‘artificial antibodies’, identified from the randomized combinatorial library against the target by the process called ‘SELEX’ (Systematic Evolution of Ligands by EXponential enrichment). Target can have any sizes from small molecules to the whole cell, attests the versatility of aptamers to bind a wide range of targets. Aptamers have several advantages over antibodies, such as they are easy to prepare, cheaper, have no batch variations, are easy to modify, stable and most importantly, non-immunogenic. Because of these positive characteristics, aptamers are incorporated in different fields, and most attractive in the applications involving therapeutics and diagnoses (theranostics). With either aptamers alone or complementing with antibodies, several high sensitive, portable sensors have been demonstrated for use in ‘bedside analysis’. Moreover, aptamers are more amenable to chemical modifications, making them capable of utilization with the most developed aptasensors (aptamerbased sensors). Significance: The development of more sensitive aptasensors could be useful and important for medical diagnosis, identification of pathogens for the quality control of consumable items, and surveillance of emerging diseases. In fact, aptasensors have already shown their efficacy in the detection of life threatening diseases caused by early stage of viral infections. In this review, role of aptasensors in detecting pathogenic viruses are overviewed. Keywords: Anti-virus; aptamer; aptasensor; bedside analysis; SELEX

Application progress of graphene oxide and aptamer in detection / 中国生化药物杂志

Aptamers are oligonucleotides which can combine targets with high affinity and specificity.Graphene oxide is a kind of new material with many unique physical and chemical properties.Recently, graphene oxide is gradually applied to the field of aptamers and has made a series of progress.This review focused on the application progress of graphene oxide and aptamers in the detection of different targets including small molecules and metal ion, biomacromolecules and cells in order to provide references for the mass application of graphene oxide and aptamers in the field of detection .

Screening and characterization of aptamers of human chronic myeloid leukemia (CML) fusion protein BCR-ABL and its structure analysis / 中国免疫学杂志

Objective:To screen and characterize aptamers against BCR-ABL fusion protein.Methods:A 90bp single stranded DNA( ssDNA) random library was subjected to 13 rounds of selection against BCR-ABL fusion protein by systematic evolution of ligands by expotential enrichment ( SELEX ) method, the selected aptamers were cloned and sequenced.The primary sequences and structure of aptamers were analyzed by Clustal W and DNA Folding Sever and the percentage of the ssDNA pool bound to BCR-ABL core protein were determinated.Results: after 13 rounds selection, the percentage of ssDNA pool bound to BCR-ABL fusion protein increased from 0.3%to 47.1%,the results showed that affinities of the Aptamers were different,the second structure analysis revealed possible stem-loops for binding to BCR-ABL fusion protein,the affinity of aptamer A2 to BCR-ABL fusion protein was highest with Kd values as low as 72 nmol/L.Conclusion:Aptamers against BCR-ABL fusion protein has been identified by SELEX methods from a 90 bp single stranded DNA library.And provide certain reference for the clinical treatment of chronic myelogenous.