RNA aptamers directed to human immunodeficiency virus type 1 gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production

Dhivya Ramalingam, Sonald Duclair, Siddhartha A K Datta, Andrew Ellington, Alan Rein, Vinayaka R. Prasad

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

Gag orchestrates the assembly and release of human immunodeficiency virus type 1 (HIV-1) particles. We explored here the potential of anti-Gag RNA aptamers to inhibit HIV-1 replication. In vitro, RNA aptamers raised against an HIV-1 Gag protein, lacking the N-terminal myristate and the C-terminal p6 (DP6-Gag), could bind to matrix protein (MA), nucleocapsid protein (NC), or entire DP6-Gag protein. Upon cotransfection with pNL4-3.Luc molecular clone into 293T cells, six of the aptamers caused mild inhibition (2- to 3-fold) in the extracellular capsid levels, and one aptamer displayed 20-fold inhibition. The reduction was not due to a release defect but reflected Gag mRNA levels. We hypothesized that the aptamers influence genomic RNA levels via perturbation of specific Gag-genomic RNA interactions. Binding studies revealed that the "NC-binders" specifically compete with the packaging signal (ψ) of HIV-1 for binding to DP6-Gag. Therefore, we tested the ability of two NC-binders to inhibit viruses containing ψ-region deletions (ΔSL1 or ΔSL3) and found that the NC-binders were no longer able to inhibit Gag synthesis. The inability of these aptamers to inhibit ψ-deleted viruses correlated with the absence of competition with the corresponding ψ transcripts lacking SL1 or SL3 for binding DP6-Gag in vitro. These results indicate that the NC-binding aptamers disrupt Gag-genomic RNA interaction and negatively affect genomic RNA transcription, processing, or stability. Our results reveal an essential interaction between HIV-1 Gag and the ψ-region that may be distinct from that which occurs during the encapsidation of genomic RNA. Thus, anti-Gag aptamers can be an effective tool to perturb Gag-genomic RNA interactions.

Original languageEnglish (US)
Pages (from-to)305-314
Number of pages10
JournalJournal of Virology
Volume85
Issue number1
DOIs
StatePublished - Jan 2011

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Nucleotide Aptamers
gag Gene Products
Nucleocapsid
nucleocapsid
Nucleocapsid Proteins
Human immunodeficiency virus 1
HIV-1
nucleocapsid proteins
RNA
Viruses
viruses
genomics
Human Immunodeficiency Virus gag Gene Products
Virus Attachment
HEK293 Cells
Capsid
Myristic Acid
Product Packaging
Virus Replication
Protein Binding

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

RNA aptamers directed to human immunodeficiency virus type 1 gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production. / Ramalingam, Dhivya; Duclair, Sonald; Datta, Siddhartha A K; Ellington, Andrew; Rein, Alan; Prasad, Vinayaka R.

In: Journal of Virology, Vol. 85, No. 1, 01.2011, p. 305-314.

Research output: Contribution to journalArticle

Ramalingam, Dhivya ; Duclair, Sonald ; Datta, Siddhartha A K ; Ellington, Andrew ; Rein, Alan ; Prasad, Vinayaka R. / RNA aptamers directed to human immunodeficiency virus type 1 gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production. In: Journal of Virology. 2011 ; Vol. 85, No. 1. pp. 305-314.
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