Matrix Background Screening of an ssDNA Aptamer and Its Identification Against Lactopontin

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(21), P. 11832 - 11832

Published: Nov. 4, 2024

Lactopontin (LPN) is a highly phosphorylated O-glycosylated acidic protein closely associated with infant gut, brain, and immune development, its recognition urgent due to rising application in fortified dairy products formula. In this study, an ssDNA aptamer against LPN was obtained, among which two kinds of matrix-background-assisted systematic evolution ligands via exponential enrichment (SELEX) approaches were performed compared. The direct approach utilize the sample matrix as mixing-incubation background between library that can theoretically increase screening pressure simulate practical scenarios. indirect PBS buffer include counter-screening steps adopt “sample matrix” whole target. Their evolutions monitored through qPCR assays from sequence diversity convergences each sub-library based on change proportion hetero- homo-duplexes dissociation curve melting temperature, also verified statistics high-throughput sequencing. common Seq.I1II3 finally fished out multiple analyses combining frequency, secondary structures, homology, binding assessments, demonstrated good specificity low-nanomolar affinity by assay (KD, 5.9 nM). addition, molecular docking dynamics simulation for their site prediction confirmation. This study provides potential identifying element basis accelerating development methods detection products.

Language: Английский

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Ramachandran-like Conformational Space for DNA

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(21), P. 8339 - 8348

Published: Oct. 18, 2024

DNA's ability to exist in a wide variety of structural forms, subforms, and secondary motifs is fundamental numerous biological processes has driven the development biotechnological applications. Major determinants DNA flexibility are multiple torsional degrees freedom around phosphodiester backbone. This high complexity can be rationalized by using two pseudotorsional angles linking atoms P C4′, from which Ramachandran-like plots built. In this contribution, we explore distribution η (eta: C4′i–1-Pi-C4′i-Pi+1) θ (theta: Pi-C4′i-Pi+1-C4′i+1) known experimental structures retrieved Protein Data Bank (PDB), subdividing conformational space into different datasets. After removal canonical/helical conformations typical B-form, find existence map with clearly permitted forbidden regions. Some these regions populated specific like Z- or A-DNA, motifs, G-quadruplexes junctions. We evaluated sequence dependency energy relationship among high-density identified η–θ space. Furthermore, analyzed effect produced proteins cations when bound DNA, finding that produce some nonhelical conformations, while other appear stabilized divalent cations.

Language: Английский

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Pattern recognition-based aptasensor array for discrimination of matrix effect

Microchemical Journal, Journal Year: 2024, Volume and Issue: unknown, P. 111995 - 111995

Published: Oct. 1, 2024

Language: Английский

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Biosensors for the detection of flaviviruses: A review

Synthetic and Systems Biotechnology, Journal Year: 2024, Volume and Issue: 10(1), P. 194 - 206

Published: Oct. 28, 2024

Language: Английский

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