Photophysics of DFHBI bound to RNA aptamer Baby Spinach

Abstract The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity...

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Autores principales:	Nguyen Thuan Dao, Reinhard Haselsberger, Mai Thu Khuc, Anh Tuân Phan, Alexander A. Voityuk, Maria-Elisabeth Michel-Beyerle
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8cecded680a541a5be6f1e05540797ef
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spelling	oai:doaj.org-article:8cecded680a541a5be6f1e05540797ef2021-12-02T13:26:42ZPhotophysics of DFHBI bound to RNA aptamer Baby Spinach10.1038/s41598-021-85091-y2045-2322https://doaj.org/article/8cecded680a541a5be6f1e05540797ef2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85091-yhttps://doaj.org/toc/2045-2322Abstract The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.Nguyen Thuan DaoReinhard HaselsbergerMai Thu KhucAnh Tuân PhanAlexander A. VoityukMaria-Elisabeth Michel-BeyerleNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nguyen Thuan Dao Reinhard Haselsberger Mai Thu Khuc Anh Tuân Phan Alexander A. Voityuk Maria-Elisabeth Michel-Beyerle Photophysics of DFHBI bound to RNA aptamer Baby Spinach
description	Abstract The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.
format	article
author	Nguyen Thuan Dao Reinhard Haselsberger Mai Thu Khuc Anh Tuân Phan Alexander A. Voityuk Maria-Elisabeth Michel-Beyerle
author_facet	Nguyen Thuan Dao Reinhard Haselsberger Mai Thu Khuc Anh Tuân Phan Alexander A. Voityuk Maria-Elisabeth Michel-Beyerle
author_sort	Nguyen Thuan Dao
title	Photophysics of DFHBI bound to RNA aptamer Baby Spinach
title_short	Photophysics of DFHBI bound to RNA aptamer Baby Spinach
title_full	Photophysics of DFHBI bound to RNA aptamer Baby Spinach
title_fullStr	Photophysics of DFHBI bound to RNA aptamer Baby Spinach
title_full_unstemmed	Photophysics of DFHBI bound to RNA aptamer Baby Spinach
title_sort	photophysics of dfhbi bound to rna aptamer baby spinach
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8cecded680a541a5be6f1e05540797ef
work_keys_str_mv	AT nguyenthuandao photophysicsofdfhbiboundtornaaptamerbabyspinach AT reinhardhaselsberger photophysicsofdfhbiboundtornaaptamerbabyspinach AT maithukhuc photophysicsofdfhbiboundtornaaptamerbabyspinach AT anhtuanphan photophysicsofdfhbiboundtornaaptamerbabyspinach AT alexanderavoityuk photophysicsofdfhbiboundtornaaptamerbabyspinach AT mariaelisabethmichelbeyerle photophysicsofdfhbiboundtornaaptamerbabyspinach
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Photophysics of DFHBI bound to RNA aptamer Baby Spinach

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