Methods for Improving Aptamer Binding Affinity

Hasegawa, Hijiri; Savory, Nasa; Abe, Koichi; Ikebukuro, Kazunori

doi:10.3390/molecules21040421

Cited by 195 publications

(143 citation statements)

References 72 publications

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“…This experimental process was repeated 3 times, and the K d (dissociation constant) was determined to be 100.9 nM. This value is much lower than those of several small molecule‐binding aptamers displaying affinities in the low to the midmicromolar range . Thus, this nanomolar K d value indicates that NPE‐01 has a high binding affinity for the target, NPE.…”

Section: Resultsmentioning

confidence: 99%

“…The reason for the result against NP could be the similar hydrophobic sites of the 2 chemicals. The interaction between aptamer and target molecule is generally based on noncovalent bond, but hydrophobic interaction is limited by the low hydrophobicity of nucleic acids . But, the other result showed that the aptamer not only interact with ethoxylate chain which is the hydrophilic site of NPE.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Development of a ssDNA aptamer system with reduced graphene oxide (rGO) to detect nonylphenol ethoxylate in domestic detergent

Kim

Jung

et al. 2018

J of Molecular Recognition

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Endocrine‐disrupting chemicals are a major public health problem throughout the world. In the human body, these compounds functionalize the same as sexual hormones, inducing precocious puberty, gynecomastia, etc. To help prevent this occurrence, a simple detection system is needed. In this study, a nonylphenol ethoxylate (NPE)‐specific aptamer was selected by reduced graphene oxide‐systematic evolution of ligands by exponential enrichment. A random ssDNA library was incubated with rGO for adsorption, followed by elution with the target molecule. As a result of screening, a DNA aptamer was found that specifically bounds to the target with high binding affinity (Kd = 100.9 ± 13.2 nM) and had a low limit of detection (LOD = 696 pM). Furthermore, this NPE‐binding aptamer bounds selectively to the target. Characterization of the aptamer was confirmed by measuring the fluorescence signal recovery from rGO. In addition, detection of NPE was performed with several water samples, and the detection accuracy was 100 ± 10%. From these results, we expect that this aptamer could be applied to an on‐site detection system for NPE in industrial sites or domestic fields.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Development of a ssDNA aptamer system with reduced graphene oxide (rGO) to detect nonylphenol ethoxylate in domestic detergent

Kim

Jung

et al. 2018

J of Molecular Recognition

View full text Add to dashboard Cite

show abstract

“…Further refinement of aptamers is needed to achieve desired affinities [161]. Dimerization of aptamers (identical and different) was performed by Hasegawa and co-workers [162].…”

Section: Multivalent and Dimerization Of Aptamersmentioning

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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“…However, effective aptamer sequences are usually shorter than 30 nt, although they have typically been selected from libraries with 30–60 nt randomized nucleotides. Therefore, use of longer sequences in the selection library to increase the contact area is not an effective methodology . Linking of two aptamers that bind to different epitopes on the same protein target can generate hetero‐bivalent interactions and would be expected to increase the aptamer affinity greatly.…”

Section: Introductionmentioning

confidence: 99%

DNA‐Nanoscaffold‐Assisted Selection of Femtomolar Bivalent Human α‐Thrombin Aptamers with Potent Anticoagulant Activity

Zhou

Liu

et al. 2019

ChemBioChem

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Multivalent aptamers that interact with their target proteins through multiple sites exhibit much stronger binding strengths than their monovalent counterparts. In this work, we have designed a single‐stranded DNA (ssDNA) library (1015 molecules, each 145 nt) based on a predefined DNA nanostructure designed to present two random‐loop sites for bivalent aptamer evolution. From this library, a group of ultra‐strong bivalent aptamers against human α‐thrombin (with apparent KD values of ≈340 fm) were easily identified through a simple seven‐round conventional systematic evolution of ligands by exponential enrichment (SELEX) procedure. The dominant bivalent aptamers consist of two components, one binding to exosite I and the other to exosite II. The best of these bivalent aptamers show strong allosteric attenuation of the thrombin cleavage activity and also display an extremely potent anticoagulation effect in human plasma, demonstrating their great potential in therapeutic applications. The method developed here can easily be adapted to conventional SELEX techniques, opening a new route for fast selection of multivalent aptamers with superior binding affinity for other targets.

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Methods for Improving Aptamer Binding Affinity

Cited by 195 publications

References 72 publications

Development of a ssDNA aptamer system with reduced graphene oxide (rGO) to detect nonylphenol ethoxylate in domestic detergent

Development of a ssDNA aptamer system with reduced graphene oxide (rGO) to detect nonylphenol ethoxylate in domestic detergent

Aptamers Chemistry: Chemical Modifications and Conjugation Strategies

DNA‐Nanoscaffold‐Assisted Selection of Femtomolar Bivalent Human α‐Thrombin Aptamers with Potent Anticoagulant Activity

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