Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX

Dong, Lili; Tan, Qiwen; Ye, Wei; Liu, Dongli; Chen, Haifeng; Hu, Hongwei; Wen, Duo; Liu, Yang; Cao, Yang; Kang, Jingwu; Fan, Jia; Guo, Wei; Wu, Wei‐Zhong

doi:10.1038/srep15552

Cited by 88 publications

(51 citation statements)

References 30 publications

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“…The X‐ray structure of ATP was obtained from the Protein Data Bank. Because of the absence of an appropriate three‐dimensional (3D) structure for some ssDNA structures, the 3D structure of the aptamer could be designed using tools freely available on the Web and computational methods such as RNA‐composer (http://rnacomposer.ibch.poznan.pl), iFoldRNA (http://ifoldrna.dokhlab.org), SimRNA (http://genesilico.pl/SimRNAweb) and software package Hyperchem 8.0 . For this study, the SimRNA tool was used.…”

Section: Methodsmentioning

confidence: 99%

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

2018

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A new fluorimetric aptasensor was designed for the determination of adenosine triphosphate (ATP) based on magnetic nanoparticles (MNPs) and carbon dots (CDs). In this analytical strategy, an ATP aptamer was conjugated on MNPs and a complementary strand of the aptamer (CS) was labeled with CDs. The aptamer and its CS were hybridized to form a double helical structure. The hybridized aptamers could be used for the specific recognition of ATP in a biological complex matrix using a strong magnetic field to remove the interfering effect. In the absence of ATP, no CDs-CS could be released into the solution and this resulted in a weak fluorescence signal. In the presence of ATP, the target binds to its aptamer and causes the dissociation of the double helical structure and liberation of the CS, such that a strong fluorescence signal was generated. The increased fluorescence signal was proportional to ATP concentration. The limit of detection was estimated to be 1.0 pmol L with a dynamic range of 3.0 pmol L to 5.0 nmol L . The specific aptasensor was applied to detect ATP in human serum samples with satisfactory results. Moreover, molecular dynamic simulation (MDS) studies were used to analyze interactions of the ATP molecule with the aptamer.

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Section: Methodsmentioning

confidence: 99%

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

2018

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“…Moreover, some minor deviations in screening may negatively affect the quality of aptamer. Therefore, CE-SELEX, an improved method with high-efficiency, simplified-process and shortened-period was adopted in this study for screening aptamer (21,30,31).…”

Section: Discussionmentioning

confidence: 99%

“…The selection and identification of GPC3-bound aptamers were done on the P/ACE MDQ CE system (Beckman Coulter, Inc., Fullerton, CA, USA) installed with 32 Karat software according to a previous report (21). Briefly, CE of the purified GPC3 protein mixed with the ssDNA library was performed.…”

Section: Selection Of Gpc3-bound Aptamer By Cementioning

confidence: 99%

In vivo fluorescence imaging of hepatocellular carcinoma using a novel GPC3-specific aptamer probe

Zhao¹,

Dong²,

Liu³

et al. 2018

Quant. Imaging Med. Surg.

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Background: Glypican-3 (GPC3) is highly expressed in most of the hepatocellular carcinomas (HCCs), even in small HCCs. It may be used as a potential biomarker for early detection of HCC. The aptamer is a promising targeting agent with unique advantages over antibody. This study was to introduce a novel GPC3 specific aptamer (AP613-1), to verify its specific binding property in vitro, and to evaluate its targeting efficiency in vivo by performing near-infrared (NIR) fluorescence imaging on an HCC xenograft model.Methods: AP613-1 was generated from the systematic evolution of ligands by exponential enrichment. Conclusions: AP613-1 displays a specific binding affinity to GPC3 positive HCC. Fluorescently labeled AP613-1 could be used as an imaging probe to subcutaneous HCC in xenograft models.

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“…CE-SELEX separates the target bounded from unbounded sequences by the difference in electrophoretic mobility, which is a highly efficient separation method. This method enables the selection of aptamer candidates with high affinity while reducing the selection rounds to 1 to 4 from nearly 20 in conventional SELEX [41,42] Microfluidic SELEX (M-SELEX)…”

Section: Capillary Electrophoresis Selex (Ce-selex)mentioning

confidence: 99%

Aptamers Chemistry: Chemical Modifications and Conjugation Strategies

et al. 2019

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Soon after they were first described in 1990, aptamers were largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic, and therapeutic applications. Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. Their high binding specificity and affinity make them comparable to antibodies, but they are superior regarding a longer shelf life, simple production and chemical modification, in addition to low toxicity and immunogenicity. In the past three decades, aptamers have been used in a plethora of therapeutics and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamer research from bench to bedside has been challenged by several limitations that slow down the realization of promising aptamer applications as therapeutics at the clinical level. The main limitations include the susceptibility to degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional group diversity. The solution to overcome such limitations lies in the chemistry of aptamers. The current review will focus on the recent arts of aptamer chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze the advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will summarize the conjugation strategies of aptamers to nanocarriers for developing targeted drug delivery systems. Molecules 2020, 25, 3 2 of 51 molecules [2]. Nowadays, the aptamer field covers various biomedical applications, including [3], therapeutic [4-6], aptasensors [7], biosensors [8,9], diagnostic [10,11], and imaging systems [12].Aptamers need to be stabilized for in vivo use against nuclease degradation, and their small size makes them susceptible to renal filtration. Aptamers' stabilization can be attained by chemically modifying them using different approaches. Moreover, introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of aptamers and thereby their target spectrum [12]. Modified aptamers may show improved chemical diversity relative to aptamers composed entirely of natural DNA or RNA nucleotides and expand their applications in diagnostics, therapeutics, and nanotechnology [1].Chemical modifications of aptamer oligonucleotides are needed mainly to enhance their resistance to nuclease degradation and lowering their renal filtration. Additionally, chemical modifications, in some cases, may increase the aptamer-binding affinity [13]. Many approaches have been introduced to promote the stability of aptamers without altering their binding affinity and specificity against their targets. These approaches include chemical modification of the phosphate...

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Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX

Cited by 88 publications

References 30 publications

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

In vivo fluorescence imaging of hepatocellular carcinoma using a novel GPC3-specific aptamer probe

Aptamers Chemistry: Chemical Modifications and Conjugation Strategies

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