Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
30 06 2023
30 06 2023
Historique:
received:
04
11
2022
accepted:
22
06
2023
medline:
3
7
2023
pubmed:
1
7
2023
entrez:
30
6
2023
Statut:
epublish
Résumé
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we design a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.
Identifiants
pubmed: 37391423
doi: 10.1038/s41467-023-39611-1
pii: 10.1038/s41467-023-39611-1
pmc: PMC10313827
doi:
Substances chimiques
Rhodamines
0
Fluorescent Dyes
0
Ionophores
0
Oligonucleotides
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3879Informations de copyright
© 2023. The Author(s).
Références
Genes Dev. 2015 Apr 15;29(8):876-86
pubmed: 25877922
Trends Biotechnol. 2012 Jan;30(1):8-16
pubmed: 21924508
Nat Chem. 2014 Aug;6(8):681-9
pubmed: 25054937
Nat Protoc. 2017 Jun;12(6):1198-1228
pubmed: 28518172
Annu Rev Biochem. 2017 Jun 20;86:825-843
pubmed: 28399656
Nat Chem Biol. 2020 Jan;16(1):69-76
pubmed: 31636432
Nat Biotechnol. 2021 Jun;39(6):686-690
pubmed: 33574610
J Am Chem Soc. 2021 Sep 15;143(36):14592-14600
pubmed: 34460256
Nat Biotechnol. 2019 Jun;37(6):667-675
pubmed: 30962542
J Am Chem Soc. 2019 Sep 18;141(37):14491-14495
pubmed: 31487156
Chem Soc Rev. 2014 Feb 21;43(4):1088-106
pubmed: 24056711
J Mol Biol. 2016 Jan 29;428(2 Pt A):308-322
pubmed: 26743847
J Am Chem Soc. 2014 Nov 19;136(46):16299-308
pubmed: 25337688
J Am Chem Soc. 2016 Aug 3;138(30):9365-8
pubmed: 27420907
Nat Chem. 2013 Feb;5(2):132-9
pubmed: 23344448
Cell Chem Biol. 2020 Aug 20;27(8):891-903
pubmed: 32640188
Am J Hum Genet. 2000 Jan;66(1):6-15
pubmed: 10631132
Angew Chem Int Ed Engl. 2013 Dec 9;52(50):13401-4
pubmed: 24133044
Nat Chem. 2020 Feb;12(2):165-172
pubmed: 31792385
Chembiochem. 2019 Sep 2;20(17):2248-2254
pubmed: 31050112
Nano Lett. 2020 Sep 9;20(9):6732-6737
pubmed: 32787168
Nat Chem Biol. 2018 Oct;14(10):964-971
pubmed: 30061719
Chemistry. 2010 Apr 19;16(15):4477-88
pubmed: 20309973
EMBO J. 2010 Apr 7;29(7):1248-61
pubmed: 20186122
Nat Biotechnol. 2019 Nov;37(11):1287-1293
pubmed: 31548726
Org Biomol Chem. 2013 Mar 21;11(11):1805-9
pubmed: 23381503
Cell. 2013 Dec 19;155(7):1479-91
pubmed: 24360272
J Am Chem Soc. 2019 May 8;141(18):7562-7571
pubmed: 30986047
Nat Methods. 2013 Dec;10(12):1219-24
pubmed: 24162923
J Fluoresc. 2004 Jul;14(4):465-72
pubmed: 15617389
Nucleic Acids Res. 2018 Oct 12;46(18):e110
pubmed: 29931157
Nat Rev Neurol. 2016 Jul;12(7):403-12
pubmed: 27340021
Nat Methods. 2015 Mar;12(3):244-50, 3 p following 250
pubmed: 25599551
ACS Nano. 2013 Jun 25;7(6):5207-14
pubmed: 23647371
J Am Chem Soc. 2008 Dec 31;130(52):17652-3
pubmed: 19108696
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Nat Methods. 2018 Mar;15(3):173-182
pubmed: 29377014
Science. 2011 Jul 29;333(6042):642-6
pubmed: 21798953
RNA. 2007 Apr;13(4):555-62
pubmed: 17283214
Nat Rev Mol Cell Biol. 2017 Nov;18(11):685-701
pubmed: 28875992
Nat Chem Biol. 2023 Apr;19(4):478-487
pubmed: 36658339
Nat Methods. 2017 Oct;14(10):987-994
pubmed: 28869757
Nat Biotechnol. 2016 May;34(5):528-30
pubmed: 27088723
Angew Chem Int Ed Engl. 2019 Jan 28;58(5):1266-1279
pubmed: 30102012
Angew Chem Int Ed Engl. 2023 Jan 23;62(4):e202216231
pubmed: 36412996
Mol Cell. 1998 Oct;2(4):437-45
pubmed: 9809065
Hum Mol Genet. 2001 Jul 1;10(14):1449-54
pubmed: 11448936
Hum Mol Genet. 2011 Oct 1;20(19):3811-21
pubmed: 21729883
Nano Lett. 2019 Jan 9;19(1):500-505
pubmed: 30525682
J Am Chem Soc. 2019 Feb 20;141(7):2770-2781
pubmed: 30550714
Nucleic Acids Res. 2015 Dec 2;43(21):e144
pubmed: 26175046
Angew Chem Int Ed Engl. 2016 Mar 1;55(10):3290-4
pubmed: 26844929
ACS Cent Sci. 2019 Sep 25;5(9):1602-1613
pubmed: 31572787