Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>

Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnos...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Taeyang Heo, Hansol Kang, Seungdo Choi, Jongmin Kim
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	RNA synthetic biology toehold switch pathogenicity island <i>pks</i> island molecular diagnostics Science Q
Acceso en línea:	https://doaj.org/article/23a5c4d2143b496fbf613d2d2414ff47
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:23a5c4d2143b496fbf613d2d2414ff47
record_format	dspace
spelling	oai:doaj.org-article:23a5c4d2143b496fbf613d2d2414ff472021-11-25T18:11:49ZDetection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>10.3390/life111112802075-1729https://doaj.org/article/23a5c4d2143b496fbf613d2d2414ff472021-11-01T00:00:00Zhttps://www.mdpi.com/2075-1729/11/11/1280https://doaj.org/toc/2075-1729Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnostics. As an example, a de-novo-designed riboregulator called toehold switch, with its programmability and compatibility with field-deployable devices showed promising in vitro applications for viral RNA detection such as Zika and Corona viruses. However, the in vivo application of high-performance RNA sensors remains challenging due to the secondary structure of long mRNA species. Here, we introduced ‘Helper RNAs’ that can enhance the functionality of toehold switch sensors by mitigating the effect of secondary structures around a target site. By employing the helper RNAs, previously reported <i>mCherry</i> mRNA sensor showed improved fold-changes in vivo. To further generalize the Helper RNA approaches, we employed automatic design pipeline for toehold sensors that target the essential genes within the <i>pks</i> island, an important target of biomedical research in connection with colorectal cancer. The toehold switch sensors showed fold-changes upon the expression of full-length mRNAs that apparently depended sensitively on the identity of the gene as well as the predicted local structure within the target region of the mRNA. Still, the helper RNAs could improve the performance of toehold switch sensors in many instances, with up to 10-fold improvement over no helper cases. These results suggest that the helper RNA approaches can further assist the design of functional RNA devices in vivo with the aid of the streamlined automatic design software developed here. Further, our solutions for screening and stabilizing single-stranded region of mRNA may find use in other in vivo mRNA-sensing applications such as cas13 crRNA design, transcriptome engineering, and trans-cleaving ribozymes.Taeyang HeoHansol KangSeungdo ChoiJongmin KimMDPI AGarticleRNA synthetic biologytoehold switchpathogenicity island<i>pks</i> islandmolecular diagnosticsScienceQENLife, Vol 11, Iss 1280, p 1280 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA synthetic biology toehold switch pathogenicity island <i>pks</i> island molecular diagnostics Science Q
spellingShingle	RNA synthetic biology toehold switch pathogenicity island <i>pks</i> island molecular diagnostics Science Q Taeyang Heo Hansol Kang Seungdo Choi Jongmin Kim Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
description	Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnostics. As an example, a de-novo-designed riboregulator called toehold switch, with its programmability and compatibility with field-deployable devices showed promising in vitro applications for viral RNA detection such as Zika and Corona viruses. However, the in vivo application of high-performance RNA sensors remains challenging due to the secondary structure of long mRNA species. Here, we introduced ‘Helper RNAs’ that can enhance the functionality of toehold switch sensors by mitigating the effect of secondary structures around a target site. By employing the helper RNAs, previously reported <i>mCherry</i> mRNA sensor showed improved fold-changes in vivo. To further generalize the Helper RNA approaches, we employed automatic design pipeline for toehold sensors that target the essential genes within the <i>pks</i> island, an important target of biomedical research in connection with colorectal cancer. The toehold switch sensors showed fold-changes upon the expression of full-length mRNAs that apparently depended sensitively on the identity of the gene as well as the predicted local structure within the target region of the mRNA. Still, the helper RNAs could improve the performance of toehold switch sensors in many instances, with up to 10-fold improvement over no helper cases. These results suggest that the helper RNA approaches can further assist the design of functional RNA devices in vivo with the aid of the streamlined automatic design software developed here. Further, our solutions for screening and stabilizing single-stranded region of mRNA may find use in other in vivo mRNA-sensing applications such as cas13 crRNA design, transcriptome engineering, and trans-cleaving ribozymes.
format	article
author	Taeyang Heo Hansol Kang Seungdo Choi Jongmin Kim
author_facet	Taeyang Heo Hansol Kang Seungdo Choi Jongmin Kim
author_sort	Taeyang Heo
title	Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
title_short	Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
title_full	Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
title_fullStr	Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
title_full_unstemmed	Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>
title_sort	detection of <i>pks</i> island mrnas using toehold sensors in <i>escherichia coli</i>
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/23a5c4d2143b496fbf613d2d2414ff47
work_keys_str_mv	AT taeyangheo detectionofipksiislandmrnasusingtoeholdsensorsiniescherichiacolii AT hansolkang detectionofipksiislandmrnasusingtoeholdsensorsiniescherichiacolii AT seungdochoi detectionofipksiislandmrnasusingtoeholdsensorsiniescherichiacolii AT jongminkim detectionofipksiislandmrnasusingtoeholdsensorsiniescherichiacolii
_version_	1718411485785358336

Detection of <i>pks</i> Island mRNAs Using Toehold Sensors in <i>Escherichia coli</i>

Ejemplares similares