A high-affinity aptamer with base-appended base-modified DNA bound to isolated authentic SARS-CoV-2 strains wild-type and B.1.617.2 (delta variant)

Minagawa, Hiroko; Sawa, Hirofumi; Fujita, Tomoko; Kato, Shintaro; Inaguma, Asumi; Hirose, Miwako; Orba, Yasuko; Sasaki, Michihito; Tabata, Koshiro; Nomura, Naoki; Shingai, Masashi; Suzuki, Yasuhiko; Horii, Katsunori

doi:10.1016/j.bbrc.2022.04.071

Cited by 10 publications

(8 citation statements)

References 37 publications

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“…Ikuo et al designed an adenine-appended modification strategy, and successfully screened an aptamer A ad1 against human β-defensin 2 (Minagawa et al, 2020) with the K D value of 6.8 nM. Recently, Horii's group applied base-appended modification strategy to select SARS-CoV-2 aptamer (Minagawa et al, 2022). These aptamers had extremely low K D value (1.2 nM and <1 nM) to the receptor-binding domain (RBD) and spike trimer of the SARS-CoV-2, respectively.…”

Section: Base-appended Base Modificationsmentioning

confidence: 99%

Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding

Chen

Luo

Gubu

et al. 2023

Front. Cell Dev. Biol.

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Nucleic acid aptamers are ssDNA or ssRNA fragments that specifically recognize targets. However, the pharmacodynamic properties of natural aptamers consisting of 4 naturally occurring nucleosides (A, G, C, T/U) are generally restricted for inferior binding affinity than the cognate antibodies. The development of high-affinity modification strategies has attracted extensive attention in aptamer applications. Chemically modified aptamers with stable three-dimensional shapes can tightly interact with the target proteins via enhanced non-covalent bonding, possibly resulting in hundreds of affinity enhancements. This review overviewed high-affinity modification strategies used in aptamers, including nucleobase modifications, fluorine modifications (2′-fluoro nucleic acid, 2′-fluoro arabino nucleic acid, 2′,2′-difluoro nucleic acid), structural alteration modifications (locked nucleic acid, unlocked nucleic acid), phosphate modifications (phosphorothioates, phosphorodithioates), and extended alphabets. The review emphasized how these high-affinity modifications function in effect as the interactions with target proteins, thereby refining the pharmacodynamic properties of aptamers.

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Section: Base-appended Base Modificationsmentioning

confidence: 99%

Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding

Chen

Luo

Gubu

et al. 2023

Front. Cell Dev. Biol.

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“…Since the onset of the COVID‐19 pandemic, many aptamers that recognize protein biomarkers from SARS‐CoV‐2 have been reported, [19–40] most of which target the spike protein (S‐protein) of the virus for binding largely because the S‐protein is on the surface of viral particles (and thus is easily accessible) and plays essential roles in virus fusion into host cells [41,42] . These aptamers were isolated using different selection methods (beads‐, filtration‐ or electrophoresis‐based SELEX) and various forms of S‐proteins as binding targets (receptor‐binding domain (RBD), subunit S1, trimeric S‐protein, pseudovirus with S‐protein expressed) [43] .…”

Section: Introductionmentioning

confidence: 99%

Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS‐CoV‐2 Variants

Zhang

Amini

et al. 2023

Analysis & Sensing

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Many DNA aptamers have been reported to target the spike protein (S‐protein) of SARS‐CoV‐2. These aptamers display different affinities or recognize different epitopes of the S‐protein. We conducted a comparative study of 9 DNA aptamers for binding to several variants of the S‐protein and pseudoviruses using the same testing methods, including dot‐blot assays and enzyme‐linked aptamer binding assays, to evaluate their affinity ranking and analytical utility. Moreover, the binding sites of these aptamers on the S‐protein were examined using aptamer competition assays to understand the effect of S‐protein mutations on aptamer affinity and the degree of overlapping of the binding sites by these aptamers.

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“…Recent emergence of COVID-19 and the causal virus, SARS-CoV-2, have had a serious impact on human society. So far, several anti-SARS-CoV-2 aptamers are reported. − Most of the previous SELEX targets the spike protein, especially the receptor binding domain (RBD), which is used for virus-host interaction . Using as diagnostic reagents is one of the possible applications of anti-SARS-CoV-2 aptamers.…”

mentioning

confidence: 99%

“…16,17 Minagawa et al reported a novel anti-SARS-CoV-2 aptamer using baseappended-base. 17 There remains a variety of nucleotide combinations to be tested. Collectively, anti-SARS-CoV-2 aptamers and their applications have attracted growing interest.…”

mentioning

confidence: 99%

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RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein

Adachi,

Nakamura,

Michishita

et al. 2024

Biochemistry

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Optimization of aptamers in length and chemistry is crucial for industrial applications. Here, we developed aptamers against the SARS-CoV-2 spike protein and achieved optimization with a deep-learning-based algorithm, RaptGen. We conducted a primer-less SELEX against the receptor binding domain (RBD) of the spike with an RNA/DNA hybrid library, and the resulting sequences were subjected to RaptGen analysis. Based on the sequence profiling by RaptGen, a short truncation aptamer of 26 nucleotides was obtained and further optimized by a chemical modification of relevant nucleotides. The resulting aptamer is bound to RBD not only of SARS-CoV-2 wildtype but also of its variants, SARS-CoV-1, and Middle East respiratory syndrome coronavirus (MERS-CoV). We concluded that the RaptGen-assisted discovery is efficient for developing optimized aptamers.

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A high-affinity aptamer with base-appended base-modified DNA bound to isolated authentic SARS-CoV-2 strains wild-type and B.1.617.2 (delta variant)

Cited by 10 publications

References 37 publications

Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding

Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding

Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS‐CoV‐2 Variants

RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein

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