Development and characterization of sindbis virus with encoded fluorescent RNA aptamer Spinach2 for imaging of replication and immune-mediated changes in intracellular viral RNA

Voraphoj Nilaratanakul, Debra A. Hauer, Diane E. Griffin

Research output: Contribution to journalArticle

Abstract

Viral RNA studies often rely on in situ hybridization and reverse transcriptase-PCR to provide snapshots of RNA dynamics in infected cells. To facilitate analysis of cellular RNAs, aptamers Spinach and Spinach2 that bind and activate the conditional fluorophore 3, 5-difluoro-4-hydroxybenzylidene imidazolinon have been developed. To determine the feasibility of applying this technology to viral RNA, we have used cDNA clones of the TE strain of Sindbis virus (SINV) to construct multiple viruses containing one or two copies of tRNA-scaffolded Spinach2 after a second subgenomic promoter, TEds-1Sp and TEds-2Sp within the 3′UTR, TE-1UTRSp, or after a second subgenomic promoter and in the 3′UTR, TEds-1Sp+1 UTRSp. TEds-1Sp+1 UTRSp gave the brightest signal and replicated well in cell culture, while TEds-2Sp was the dimmest and replicated poorly. Selection of baby hamster kidney cells infected with TEds-1Sp+1 UTRSp for improved signal intensity identified a virus with a stronger signal and point mutations in the tRNA scaffold. Imaging of SINV in BHK cells showed RNA to be concentrated in filopodia that contacted and transferred RNA to adjacent cells. The effect of treatment with anti-E2 antibody, which effects non-cytolytic clearance of SINV from neurons, on viral RNA was cell-type-dependent. In antibodytreated BHK cells, intracellular viral RNA increased and spread of infection continued. In undifferentiated and differentiated AP7 neuronal cells antibody treatment induced viral RNA clearance. Both viruses with two inserted aptamers were prone to deletion. These studies form the basis for further development of aptamer-labelled viral RNAs that will facilitate functional studies on the dynamics of infection and clearance.

Original languageEnglish (US)
Article number000755
Pages (from-to)992-1003
Number of pages12
JournalJournal of General Virology
Volume98
Issue number5
DOIs
StatePublished - May 1 2017

Fingerprint

Nucleotide Aptamers
Sindbis Virus
Viral RNA
RNA
Viruses
3' Untranslated Regions
Transfer RNA
Infection
Pseudopodia
Spinacia oleracea
Reverse Transcriptase Polymerase Chain Reaction
Point Mutation
Cricetinae
In Situ Hybridization
Anti-Idiotypic Antibodies
Complementary DNA
Clone Cells
Cell Culture Techniques
Technology
Kidney

Keywords

  • Alphavirus
  • Aptamer
  • Fluorescent viral RNA
  • Live cell imaging
  • Neurons
  • Sindbis virus

ASJC Scopus subject areas

  • Virology

Cite this

Nilaratanakul, Voraphoj; Hauer, Debra A.; Griffin, Diane E. / Development and characterization of sindbis virus with encoded fluorescent RNA aptamer Spinach2 for imaging of replication and immune-mediated changes in intracellular viral RNA.

In: Journal of General Virology, Vol. 98, No. 5, 000755, 01.05.2017, p. 992-1003.

Research output: Contribution to journalArticle

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