In Vitro Selection of DNA Aptamers to Glioblastoma Multiforme

Bayraç, Abdullah Tahir; Sefah, Kwame; Parekh, Parag; Bayraç, Ceren; Gülbakan, Basri; Öktem, Hüseyin Avni; Tan, Weihong

doi:10.1021/cn100114k

Cited by 99 publications

(53 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Cell-SELEX without employing negative selection steps was used to obtain DNA aptamer against glioma A172 cells by Byrac et al (20). Here the authors have used 454-pyrosequencing and bioinformatics analyses for identification of oligonucleotide sequences based on sequence comparison between the initial pool and enriched populations following rounds of selection.…”

Section: Selex Application For Gbm-targeting Aptamersmentioning

confidence: 99%

Aptamer for imaging and therapeutic targeting of brain tumor glioblastoma

Delač

Motaln

Ulrich³

et al. 2015

Cytometry Pt A

View full text Add to dashboard Cite

Aptamers are short single-stranded nucleic acids (RNA or ssDNA), identified by an in vitro selection process, denominated SELEX, from a partially random oligonucleotide library. They bind to a molecular target, a protein or other complex macromolecular structures of interest with high affinity and specificity, comparable to those of antibodies. Recently, aptamer selection protocols were developed for targeting living cells, including tumors. Chemical modifications of the aptamers and modalities of their detection and delivery systems are already available with high selectivity and targeting ability for the desired cancer cell type, making them promising for diagnosis and therapy. Glioblastoma multiformae represents the most malignant and fatal stage of glioma, and is also the most frequent brain tumor. Glioblastoma-specific aptamers were developed by either targeting the whole cell surface or known glioma biomarkers. These aptamers may gain importance for imaging, tumor cell isolation from biopsies and drug delivery. In biomedical imaging techniques, aptamers coupled with radionuclide or fluorescent labels, bioconjugates and nanoparticles offer an advanced, noninvasive manner for defining the glioblastoma tissue border. Though single modality aptamer imaging probes have some limitations, these are overcome by the use of multimodal probes. Due to selectivity and chemical characteristics, aptamers can be coupled to functionalized nanoparticles and loaded with a drug, appeared promising for in vivo targeting of glioblastoma. Finally, aptamers are effective mediators for gene silencing when coupled to small interfering RNA and a viral vector, thus providing a novel tool with enhanced targeting capability in drug delivery, designed for tailored treatment of glioblastoma patients. V C 2015 International Society for Advancement of Cytometry Key terms aptamer; SELEX; cancer biomarkers; cell and target protein; imaging; drug delivery; glioblastoma; nanoparticles APTAMERS AND THE SELEX TECHNOLOGY IN CANCER APTAMERS, first introduced by Tuerk and Gold (1) and Ellington and Szostak (2), are short chains of DNA or RNA oligonucleotides that bind to small molecules, peptides, and macromolecules, such as proteins of various sizes and conformations. These are identified by an in vitro selection method in a stepwise evolutionary process from a combinatorial library of partial randomized oligonucleotides, consisting of up to 10 15 different sequences and secondary and tertiary structures by a method called SELEX (Systematic Evolution of Ligands by EXponential enrichment). It begins with a pool of variable oligonucleotide sequences with multiple rounds of target exposure of the combinatorial RNA or DNA library, followed by elution of target binders and enrichment of those by RT-PCR or PCR procedures are performed. These results in exponential increase of oligonucleotides with improved ligand to target binding in the previously combinatorial library, which finally is narrowed down to a homogeneous population of high-affinity...

show abstract

Section: Selex Application For Gbm-targeting Aptamersmentioning

confidence: 99%

Aptamer for imaging and therapeutic targeting of brain tumor glioblastoma

Delač

Motaln

Ulrich³

et al. 2015

Cytometry Pt A

View full text Add to dashboard Cite

show abstract

“…That is because the periods of cell-SELEX are at least 2-3 months; it is hard to obtain enough live cells with stable performance in this long period by primary cell culture. Although cell-SELEX without counter selection has been reported able to generate aptamers that broadly recognize common cancer biomarkers [12,29], more specific aptamers for desired cell lines need to be selected by combining a counter selection step. In order to generate aptamers that only recognize the molecular signatures of the target cells, at least one control cell type is used for counter selection to eliminate the sequences that bind to the common molecules present in both types of cells.…”

Section: Choice and Maintenance Of Cancer Cellsmentioning

confidence: 99%

“…Reprinted from Ref. [16] New sequencing technology (454 pyrosequencing) together with bioinformatics (MAFFT 6.0, Perl, Jalview 2.4 and ATV 4.0.5 programs) have also been used to analyze the sequences in enriched pools of different rounds of selection in a large scale [29,30]. The usage of new sequencing technologies with the help of bioinformatics can provide early and detailed information for progress of SELEX by displaying the intensity of selected sequences in the earlier rounds, as well as provide more information for the choice of candidate aptamers.…”

Section: Cloning and Sequencingmentioning

confidence: 99%

Cell-SELEX: Aptamer Selection Against Whole Cells

Shangguan

Bing

Zhang

2015

Aptamers Selected by Cell-Selex for Theranostics

View full text Add to dashboard Cite

Changes at the molecular level always occur at different stages in diseased cells. The detection of these changes is critical for understanding the molecular mechanisms underlying pathogenesis, as well as accurately diagnosing disease states and monitoring therapeutic modalities. Cell-SELEX is a foundational tool used to select probes able to recognize molecular signatures on the surface of diseased cells. This technology has been increasingly used in biomarker discovery, as well as cancer diagnosis and therapy. In this chapter, the whole cell-SELEX process is described, including aptamer selection, identification, and validation. In addition, we will explore the challenges and prospects for cell-SELEX now and in the coming years. It is anticipated that this chapter will guide readers toward a better understanding of the working principles underlying the cell-SELEX technology and serve as a practical reference for bench scientists engaged in cell and molecular biology.

show abstract

“…Bunların yanında modifiye ve sentetik nükleik asitlerden yapılmış bazı aptamerler de mevcuttur. Literatürde etanolamin, asetilkolin gibi küçük organik molekülleri [3,4] büyük protein komplekslerini [5,6] hatta farklı hücreleri [7] hedef alan birçok aptamer bulunmaktadır. Aptamer-hedef kompleksleri pikomolar-submikromolar aralığında ayrışma sabiti değerlerine (Kd) sahip olabilmektedir [8].…”

Section: Introductionunclassified

Domuz Jelatinine Özgü DNA Aptamerlerinin Seçilimi ve Karakterizasyonu

Bayraç¹,

Kandemir²

2017

SDÜ Fen Bil Enst Der

View full text Add to dashboard Cite

Anahtar KelimelerAptamer, SELEX, Jelatin, Domuz Özet: Aptamerler farklı hedeflere yüksek etkin ve özgünlükte bağlanabilen DNA ve RNA moleküllerdir. Bu çalışmada domuz jelatininin algılanmasında kullanılmak üzere DNA aptamerleri geliştirilmiştir. Aptamerlerin seçilimi için tekrarlı, negatif seçilim bulunan bir SELEX metodu takip edilmiş ve kütüphaneler bu yolla zenginleştirilmiştir. Zenginleştirilen kütüphaneler tarafımızca modifiye edilmiş bir metagenomik dizileme metodu kullanılarak yeni nesil dizileme sistemi Miseq ile dizilenmiş ve elde edilen yüksek hacimli veriden aday aptamer dizileri uygun biyoinformatik araçlar kullanılarak belirlenmiştir. Floresan modifiye olarak üretilen aday DNA aptameri domuz jelatinine karşı yüksek afinite göstermekte balık ve sığır jelatinine görece düşük afinite ile bağlanmaktadır. Bu çalışmada geliştirilen aptamer gıda tağşişlerinin belirlenmesi için kullanılacak sensörlerin geliştirilmesinde potansiyel algılama ajanı olarak kullanılabilecektir. Selection and Characterization of Porcine Gelatine Specific DNA Aptamers KeywordsAptamer, SELEX, Gelatine, Porcine Abstract: Aptamers are DNA or RNA molecules that can bind to their target in high affinity and specificity. In this study we developed DNA aptamers to use in the detection of porcine gelatine. Selection of aptamers was performed by repetitive SELEX procedure with negative selection and libraries are enriched by this method. Enriched libraries were sequenced by a new generation sequencing system Miseq using a modified metagenomics method and bioinformatics tools were used to identify candidate aptamers from high throughput data. Florescence modified DNA aptamer showed high affinity to porcine gelatine, and low affinity to fish and bovine gelatine. Aptamer generated in this study has potential use in the detection of adulteration in food as sensing agent.

show abstract

In Vitro Selection of DNA Aptamers to Glioblastoma Multiforme

Cited by 99 publications

References 28 publications

Aptamer for imaging and therapeutic targeting of brain tumor glioblastoma

Aptamer for imaging and therapeutic targeting of brain tumor glioblastoma

Cell-SELEX: Aptamer Selection Against Whole Cells

Domuz Jelatinine Özgü DNA Aptamerlerinin Seçilimi ve Karakterizasyonu

Contact Info

Product

Resources

About