Dataset Information

SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators.

ABSTRACT: SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device can detect and report the presence of SARS-CoV-2-specific genes. The presence of SARS-CoV-2-related genes triggers the translation of sfGFP mRNAs, resulting in a green fluorescence output. The approach proposed here has the potential of being a game changer in SARS-CoV-2 diagnostics by providing an easy-to-run, low-cost diagnostic capability.

SUBMITTER: Koksaldı IC

PROVIDER: S-EPMC8265535 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators.

Köksaldı İlkay Çisil İÇ Köse Sıla S Ahan Recep Erdem RE Hacıosmanoğlu Nedim N Şahin Kehribar Ebru E Güngen Murat Alp MA Baştuğ Aliye A Dinç Bedia B Bodur Hürrem H Özkul Aykut A Şeker Urartu Özgür Şafak UÖŞ

Analytical chemistry 20210630 28

SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approa ...[more]

PMID: 34192453

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Project description:Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation.

Dataset Information

SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators.

Publications

SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators.

Similar Datasets

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