Näytä suppeat kuvailutiedot

dc.contributor.authorSaarnio, Ville K.
dc.contributor.authorSalorinne, Kirsi
dc.contributor.authorRuokolainen, Visa P.
dc.contributor.authorNilsson, Jesper R.
dc.contributor.authorTero, Tiia-Riikka
dc.contributor.authorOikarinen, Sami
dc.contributor.authorWilhelmsson, L. Marcus
dc.contributor.authorLahtinen, Tanja M.
dc.contributor.authorMarjomäki, Varpu S.
dc.date.accessioned2021-01-14T09:45:57Z
dc.date.available2021-01-14T09:45:57Z
dc.date.issued2020
dc.identifier.citationSaarnio, V. K., Salorinne, K., Ruokolainen, V. P., Nilsson, J. R., Tero, T.-R., Oikarinen, S., Wilhelmsson, L. M., Lahtinen, T. M., & Marjomäki, V. S. (2020). Development of functionalized SYBR green II related cyanine dyes for viral RNA detection. <i>Dyes and Pigments</i>, <i>177</i>, Article 108282. <a href="https://doi.org/10.1016/j.dyepig.2020.108282" target="_blank">https://doi.org/10.1016/j.dyepig.2020.108282</a>
dc.identifier.otherCONVID_34674105
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/73612
dc.description.abstractFluorescent probes for sensing nucleic acids have found widespread use in the field of cell and molecular biology. However, probes combined with potential for post-synthetic conjugation, e.g. for intra-endosomal measurements of RNA, are unavailable. Herein we developed cyanine dyes that can be conjugated to viral capsid or other targets. First, we solved the crystal structure of SYBR Green II. The structural elucidation of this commonly used RNA probe provided the basis for synthesizing similar molecules with much desired function for post-synthetic conjugation. To address this need, cyanine dyes were prepared using an alternative synthesis protocol. All studied compounds showed considerable brightness upon binding to nucleic acids. However, regardless of the common chromophore on the dyes, the observed fluorescence emission intensities varied significantly, where methyl-substituted dye 1 gave values higher than SYBR Green II, whereas compounds 2–5 containing undecyl spacers had lower values. Studying the structure-activity relationship revealed the longer alkyl chains to induce slight perturbation in dye intercalation, as well as demanding larger binding area on the nucleic acid lattice, explaining these differences. To study the potential biological use of the dyes, the RNA genome of enterovirus echovirus 1 was studied in vitro with the probes. A novel method employing the low binding space requirement of 1 was developed to determine the single-to-double-stranded RNA ratio of a sample, whereas compound 4 was covalently bound to the viral capsid and used successfully to monitor the viral RNA release from within the capsid. The presented results open new possibilities for preparation and use of SYBR Green-based nucleic acid probes to further apply these compounds for increasingly demanding targeting in biological contexts.en
dc.format.mimetypeapplication/pdf
dc.languageeng
dc.language.isoeng
dc.publisherElsevier
dc.relation.ispartofseriesDyes and Pigments
dc.rightsCC BY-NC-ND 4.0
dc.subject.othercyanines
dc.subject.othernucleic acids
dc.subject.otherfluorescent probes
dc.subject.otherRNA recognition
dc.subject.otherhost-guest systems
dc.subject.otherviruses
dc.titleDevelopment of functionalized SYBR green II related cyanine dyes for viral RNA detection
dc.typeresearch article
dc.identifier.urnURN:NBN:fi:jyu-202101141088
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosKemian laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.laitosDepartment of Chemistryen
dc.contributor.oppiaineOrgaaninen kemiafi
dc.contributor.oppiaineNanoscience Centerfi
dc.contributor.oppiaineFysikaalinen kemiafi
dc.contributor.oppiaineSolu- ja molekyylibiologiafi
dc.contributor.oppiaineOrganic Chemistryen
dc.contributor.oppiaineNanoscience Centeren
dc.contributor.oppiainePhysical Chemistryen
dc.contributor.oppiaineCell and Molecular Biologyen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.type.coarhttp://purl.org/coar/resource_type/c_2df8fbb1
dc.description.reviewstatuspeerReviewed
dc.relation.issn0143-7208
dc.relation.volume177
dc.type.versionacceptedVersion
dc.rights.copyright© 2020 Elsevier Ltd. All rights reserved.
dc.rights.accesslevelopenAccessfi
dc.type.publicationarticle
dc.relation.grantnumber266492
dc.relation.grantnumber
dc.subject.ysonukleiinihapot
dc.subject.ysomerkkiaineet
dc.subject.ysofluoresenssi
dc.subject.ysoväriaineet
dc.subject.ysosynteettiset väriaineet
dc.subject.ysoRNA
dc.subject.ysovirukset
dc.format.contentfulltext
jyx.subject.urihttp://www.yso.fi/onto/yso/p10072
jyx.subject.urihttp://www.yso.fi/onto/yso/p17476
jyx.subject.urihttp://www.yso.fi/onto/yso/p3265
jyx.subject.urihttp://www.yso.fi/onto/yso/p2176
jyx.subject.urihttp://www.yso.fi/onto/yso/p27872
jyx.subject.urihttp://www.yso.fi/onto/yso/p7689
jyx.subject.urihttp://www.yso.fi/onto/yso/p1123
dc.rights.urlhttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.relation.doi10.1016/j.dyepig.2020.108282
dc.relation.funderResearch Council of Finlanden
dc.relation.funderJane and Aatos Erkko Foundationen
dc.relation.funderSuomen Akatemiafi
dc.relation.funderJane ja Aatos Erkon säätiöfi
jyx.fundingprogramAcademy Project, AoFen
jyx.fundingprogramFoundationen
jyx.fundingprogramAkatemiahanke, SAfi
jyx.fundingprogramSäätiöfi
jyx.fundinginformationThis work was supported by the Academy of Finland [266492 to T.-R.T and V.S., and 257125 to V.M.]; Jane and Aatos Erkko Foundation [Novel probes for discovering anti-virals to V.S., T.L., and V.M.]; and the Swedish Foundation for Strategic Research [IRC15-0065 for J.R.N., and L.M.W.]. GLP-GPI plasmid was obtained as a kind gift from Lucas Pelkmans from ETH Zurich.
dc.type.okmA1


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