Advances of aptamers screened by Cell-SELEX in selection procedure, cancer diagnostics and therapeutics

Zhong, Yi; Zhao, Jiayao; Li, Jiazhao; Liao, Xin; Chen, Fengling

doi:10.1016/j.ab.2020.113620

Cited by 56 publications

(40 citation statements)

References 150 publications

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“…The aligned N49 regions showed some conserved sequences such as 'GTTG' (Apt2, 6, 7, 8, 11, 13-16, 18, 23 and 25); 'X 1 GCTGCX 2 ' where X 1 can be either T or A and X 2 can be G or C (Apt8 and 22); 'TGGTX' where X can be either C, T or G (Apt2, 8, 9 and 23); 'X 1 TTG CCG X 2 ' where X 1 can be G or A and X 2 can be G, C or A (Apt2, 6,8,11,15,17,23,25); 'XCAAGTX' where X can be both either G or A (Apt5 and 6); 'XGAGT' where X can be T, C or G (Apt1, 4, 7, 8, 10, 11, 16, 19 and 21); ' AAGT' (Apt1-3, 5, 6, 8, 11, 14 and 21); 'X 1 GGAGX 2 ' where X 1 can be G, A or C and X 2 can be G, T or C (Apt7, 8, 10, 11 and 21); and 'GCCG' (Apt2, 3, 5, 6, 8, 10, 11 and 14-25) (Fig. 2A).…”

Section: Identification Of Ssdna Aptamer Candidates Aided By Bioinformentioning

confidence: 99%

“…An emerging strategy in tumor-targeted therapies consists of using specific ligands, such as aptamers that are able to bind a variety of targets including proteins, small molecules, viruses, bacteria and live cells with high affinity, specificity and selectivity [9][10][11] . Aptamers exhibit many advantages over other ligands, such as the antibodies, since they can be easily synthesized and chemically modified, are non-toxic, and possess rapid tissue penetration and low immunogenicity 12 .…”

mentioning

confidence: 99%

“…Aptamers are short single-stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) oligonucleotides derived from random oligonucleotide libraries through an in vitro iterative method so-called Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which involves repetitive rounds of partitioning and enrichment commonly performed with purified target proteins immobilized on a solid support 13,14 . Cell-SELEX enables the generation of aptamers directed towards cell-surface molecules by using whole living cells as targets 11,15 . It allows the screening of cell-specific aptamers without any prior knowledge of molecular signatures of the target cells, besides offering the unique ability to target specific phenotypes by performing positive-negative selection cycles to find proteins only present on the target cells 16,17 .…”

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confidence: 99%

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Selection of aptamers against triple negative breast cancer cells using high throughput sequencing

Ferreira

Barbosa

Sousa

et al. 2021

Sci Rep

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Triple-negative breast cancer is the most aggressive subtype of invasive breast cancer with a poor prognosis and no approved targeted therapy. Hence, the identification of new and specific ligands is essential to develop novel targeted therapies. In this study, we aimed to identify new aptamers that bind to highly metastatic breast cancer MDA-MB-231 cells using the cell-SELEX technology aided by high throughput sequencing. After 8 cycles of selection, the aptamer pool was sequenced and the 25 most frequent sequences were aligned for homology within their variable core region, plotted according to their free energy and the key nucleotides possibly involved in the target binding site were analyzed. Two aptamer candidates, Apt1 and Apt2, binding specifically to the target cells with $$K_{d}$$ K d values of 44.3 ± 13.3 nM and 17.7 ± 2.7 nM, respectively, were further validated. The binding analysis clearly showed their specificity to MDA-MB-231 cells and suggested the targeting of cell surface receptors. Additionally, Apt2 revealed no toxicity in vitro and showed potential translational application due to its affinity to breast cancer tissue sections. Overall, the results suggest that Apt2 is a promising candidate to be used in triple-negative breast cancer treatment and/or diagnosis.

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Section: Identification Of Ssdna Aptamer Candidates Aided By Bioinformentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Selection of aptamers against triple negative breast cancer cells using high throughput sequencing

Ferreira

Barbosa

Sousa

et al. 2021

Sci Rep

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“…The eliciting of sequence-specific nucleic acids (aptamers) recognizing low-molecular-weight ligands, macromolecules and even cells by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedure [1][2][3][4] introduced revolutionary means to apply nucleic acids as functional materials for bioanalytical [5,6], catalytic [7][8][9] and biomedical [9][10][11][12] applications. The selective formation of aptamer-ligand complexes enabled the application of aptamers as versatile recognition elements for the development of sensor devices and sensing platforms, aptasensors [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Vázquez‐González

Willner

2021

IJMS

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Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions “nucleoapzymes”. In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

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“…Meanwhile, aptamer screening has been greatly improved by combining microfluidic chip technology with SELEX technology, and aptamer screening for multiple targets can be completed in just a few hours [20,21]. Nucleic acid aptamers not only have a good application prospect in diagnosis of tumors and diseases, but also can be used in combination with a variety of drugs or nanomaterials for targeted therapy of tumors to improve drug delivery efficiency, reduce toxicity to normal cells, alleviate stress, assuage side effects, and improve the quality of life of cancer patients [22,23].…”

Section: Introductionmentioning

confidence: 99%

Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing

et al. 2021

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Nucleic acid aptamers are small fragments of DNA or RNA molecules binding specifically to targets, which can be obtained through in vitro screening via systematic evolution of ligands by exponential enrichment (SELEX). Lactate dehydrogenase (LDH) is an important tumor marker, whose level in patients is of great significance for diagnosis of many diseases. Here, we report the identification of LDH aptamers by 9 rounds of screening from a length-mixed single-stranded DNA library using the SELEX technology. After the 3rd and 7th rounds of aptamer screening, affinity was significantly improved, and fluorescence quantitative analysis showed stronger affinity for the aptamers selected from the 7th to 9th rounds of screening. After highthroughput sequencing, motif analysis, and secondary structure prediction, we finally chose and further investigated 15 candidate LDH aptamer sequences with obvious differences in secondary structure in the 7th to 9th rounds of screening. Among them, LDH7-1, LDH7-9, LDH8-2, and LDH9-1 were shown to bind to LDH protein with high affinity and specificity with K d < 25 nM. This study provides new ideas for rapid detection of LDH protein content and enzyme activity, thus contributing to the development of rapid medical detection.

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Advances of aptamers screened by Cell-SELEX in selection procedure, cancer diagnostics and therapeutics

Cited by 56 publications

References 150 publications

Selection of aptamers against triple negative breast cancer cells using high throughput sequencing

Selection of aptamers against triple negative breast cancer cells using high throughput sequencing

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing

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