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

Zhang, Zijie; Li, Jiuxing; Amini, Ryan; Mansfield, Alexandria; Gu, Jimmy; Xia, Jianrun; Brennan, John D.; Li, Yingfu

doi:10.1002/anse.202300001

Cited by 5 publications

(7 citation statements)

References 80 publications

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“…In this regard, we set out to test the binding characteristics of the different aptamers using complementary analysis platforms. A recent cross-comparative study assessed the affinity of different aptamers binding to the SARS-CoV-2 spike protein through filter retention analysis and showed consistent binding of all tested aptamers [20]. In contrast, our comparative study reveals clear differences and suggests that the specificity for some of the aptamers might be influenced by the experimental conditions and that their binding is primarily directed to associated purification tags rather than to the spike protein.…”

Section: Of 13mentioning

confidence: 54%

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

Civit,

Moradzadeh,

Jonczyk

et al. 2024

IJMS

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The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2.

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Section: Of 13mentioning

confidence: 54%

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

Civit,

Moradzadeh,

Jonczyk

et al. 2024

IJMS

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show abstract

“…Utilizing this ELASA, Li et al [ 79 ] achieved sensitive detection of pseudo-lentiviruses with a limit of detection (LOD) of 400 fM in 50% saliva. Furthermore, Zhang et al [ 117 ] utilized nine previously discovered SARS-CoV-2 aptamer sequences to detect several variants of the S protein of pseudoviruses and determine the performance of these aptamers for variants of concern (VOCs) recognition ( Figure 3 ). Other colorimetric strategies used absorbance and color change methods.…”

Section: Aptamersmentioning

confidence: 99%

“…( C ) The data show color changes by detection outcomes for pseudoviruses using various aptamers. Reprinted from [ 117 ].…”

Section: Figurementioning

confidence: 99%

“…This sensor exploits the yellow-to-pink transition of phenol due to urease activity enhanced by RCA, achieving an LOD of 3.2 × 10 3 copies/mL for pseudovirus. Reprinted from [117].…”

Section: Optical Sensingmentioning

confidence: 99%

“…Nine aptamers were utilized in sandwich assays to detect pseudoviruses expressing S proteins from the SARS-CoV-2 wild-type (WT), P.1, B.1.617.2, and B.1.1.529 variants. (C) The data show color changes by detection outcomes for pseudoviruses using various aptamers.Reprinted from[117].…”

mentioning

confidence: 99%

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Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

Park,

Lee

et al. 2024

Biosensors

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The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.

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Dimeric DNA Aptamers for the Spike Protein of SARS‐CoV‐2 Derived from a Structured Library with Dual Random Domains

Amini,

Ma,

Zhang

et al. 2024

Small Methods

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Multimeric aptamer strategies are often adopted to improve the binding affinity of an aptamer toward its target molecules. In most cases, multimeric aptamers are constructed by connecting pre‐identified monomeric aptamers derived from in vitro selection. Although multimerization provides an added benefit of enhanced binding avidity, the characterization of different aptamer pairings adds more steps to an already lengthy procedure. Therefore, an aptamer engineering strategy that directly selects for multimeric aptamers is highly desirable. Here, an in vitro selection strategy is reported on using a pre‐structured DNA library that forms dimeric aptamers. Rather than using a library containing a single random region, which is nearly ubiquitous in existing aptamer selections, the library contains two random regions separated by a flexible poly‐thymidine linker. Following sixteen rounds of selection against the SARS‐CoV‐2 spike protein, a relevant model target protein due to the COVID‐19 pandemic, the top aptamers displayed superb affinity with KD values as low as 150 pM. Further analysis reveals that each random region functions as a distinct binding moiety and works together to achieve higher affinity. The demonstrated strategy provides an accelerated method to obtain high‐affinity aptamers, which may prove useful in future aptamer diagnostic and therapeutic applications.

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

Cited by 5 publications

References 80 publications

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications

Dimeric DNA Aptamers for the Spike Protein of SARS‐CoV‐2 Derived from a Structured Library with Dual Random Domains

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