An aptamer based fluorometric microcystin-LR assay using DNA strand-based competitive displacement

Chinnappan, Raja; AlZabn, Razan; Abu‐Salah, Khalid M.; Zourob, Mohammed

doi:10.1007/s00604-019-3504-8

Cited by 23 publications

(5 citation statements)

References 34 publications

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“…However, the current aptamer-based small molecule sensing platforms are mostly designed using aptamers screened from SELEX, and the original aptamer length is 40–100 nt ( Wang et al, 2022 ). Only a few fractions of bases in aptamer are involved in target binding ( Chinnappan et al, 2019 ). In a tertiary conformation made up of the remaining unbound base, the target material may be interfered with.…”

Section: Introductionmentioning

confidence: 99%

Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology

Qin

Bubiajiaer

et al. 2022

Front. Bioeng. Biotechnol.

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Various biosensors based on aptamers are currently the most popular rapid detection approaches, but the performance of these sensors is closely related to the affinity of aptamers. In this work, a strategy for constructed high-affinity aptamer was proposed. By truncating the bases flanking the 59 nt dexamethasones (DEX) original aptamer sequence to improve the sensitivity of the aptamer to DEX, and then base mutation was introduced to further improve the sensitivity and selectivity of aptamers. Finally, the 33 nt aptamer Apt-M13 with G-quadruplex structures was obtained. The dissociation constant (Kd) was determined to be 200 nM by Graphene oxide (GO)-based fluorometry. As-prepared Apt-M13 was used for a label-free colorimetric aptamer sensor based on gold nanoparticles, the LOD was 3.2-fold lower than the original aptamer described in previous works. The anti-interference ability of DEX analogs is also further improved. It indicates that truncation technology effectively improves the specificity of the aptamer to DEX in this work, and the introduction of mutation further improves the affinity and selectivity of the aptamer to DEX. Therefore, the proposed aptamer optimization method is also expected to become a general strategy for various aptamer sequences.

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Section: Introductionmentioning

confidence: 99%

Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology

Qin

Bubiajiaer

et al. 2022

Front. Bioeng. Biotechnol.

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“…Both fluorescently-labeled and label-free biosensing approaches have been reported with the possibility of on-site detection using portable analyzers [ 56 , 57 , 58 , 59 ]. The target of interest can range from small molecules such as the mycotoxins aflatoxin B1 [ 60 ] and ochratoxin A [ 61 ], bisphenol A [ 62 ], the antibiotic tobramycin [ 54 ] and the marine toxin okadaic acid [ 63 ], to larger entities such as lipopolysaccharides [ 64 ] and the cyclic heptapeptide microcystin-LR (a hepatotoxin produced by cyanobacteria) [ 65 ]. Furthermore, proteins such as tropomyosin (a major shrimp allergen) [ 66 ] and glycated hemoglobin [ 67 ] or even whole bacteria such as Salmonella enteritidis [ 68 ] can be measured using this approach.…”

Section: Strategies For Improving Binding Affinity Through Chemicamentioning

confidence: 99%

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Elskens

Madder

2020

IJMS

103

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Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer’s target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.

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“…Only a small fraction of the total number of nucleotides in an aptamer sequence is involved in target recognition. 20,21,[30][31][32][33][34] Fifteen of the 60 nucleotides composing the α-thrombin parent aptamer, for example, are responsible for binding. 35,36 Considering that E-AB sensors rely on changes in electron transfer rates of the redox reporter that occur within short distances (< 1-2 nm) [37][38][39] from the electrode, shortening sequences could improve their analytical responses.…”

Section: Introductionmentioning

confidence: 99%

Truncations and in silico Docking to Enhance the Analytical Response of Aptamer-Based Biosensors

Nguyen,

Osborne,

Prevot

et al. 2024

Preprint

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Aptamers are short oligonucleotides capable of binding specifically to various targets (i.e., small molecules, proteins, and whole cells) which have been introduced in biosensors such as in the electrochemical aptamer-based (E-AB) sensing platform. E-AB sensors are comprised of a redox-reporter-modified aptamer attached to an electrode that undergoes, upon target addition, a binding-induced change in electron transfer rates. To date, E-AB sensors have faced a limitation in the translatability of aptamers into the sensing platform presumably because sequences obtained from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are typically long (> 80 nucleotides) and that obtaining structural information remains time and resource consuming. In response, we explore the utility of aptamer base truncations and in silico docking to improve their translatability into E-AB sensors. Here, we first apply this to the glucose aptamer, which we characterize in solution using NMR methods to guide design and translate truncated variants in E-AB biosensors. We further investigated applicability of the truncation and computational approaches to five other aptamer systems (vancomycin, cocaine, methotrexate, theophylline, and ochratoxin A) from which we derived functional E-AB sensors. We foresee that our strategy will increase the success rate of translating aptamers into sensing platforms to afford low-cost measurements of molecules directly in undiluted complex matrices.

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An aptamer based fluorometric microcystin-LR assay using DNA strand-based competitive displacement

Cited by 23 publications

References 34 publications

Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology

Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Truncations and in silico Docking to Enhance the Analytical Response of Aptamer-Based Biosensors

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