Expression of long anti-HIV-1 hairpin RNAs for the generation of multiple siRNAs: advantages and limitations

Mol Ther. 2008 Jan;16(1):170-7. doi: 10.1038/ Epub 2007 Aug 28.


Promoter expressed long-hairpin RNAs (lhRNAs) that can be processed into multiple small interfering RNA (siRNAs) are being considered as effective agents for treating rapidly mutating viruses such as human immunodeficiency virus (HIV). In the present study, we have generated human U6 promoter-driven lhRNAs of 50, 53, and 80 base pairs (bp) targeting contiguous sequences within the tat and rev genes of HIV-1 and evaluated the efficacy of these lhRNAs as well as their processing in cells. By using multiple G:U mismatches in the stems, we have been able to readily incorporate the long-hairpin structures into a lentiviral vector transduction system. Here we show that such long hairpins can be stably and functionally expressed for a long term in HIV-1 susceptible T cells, where they provide potent inhibition of HIV replication against both non-mutant and mutant variants of HIV-1. Our studies provide strong support for the use of the G:U wobble pair containing lhRNAs to generate multiple siRNAs from a single transcript, but we also show that lhRNAs of 80 bp may be the upper size limit for effectively producing multiple, functional siRNAs.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Anti-HIV Agents / metabolism*
  • Base Sequence
  • Cell Line
  • Down-Regulation / genetics
  • Gene Expression Regulation, Viral / genetics
  • HIV-1 / genetics*
  • Humans
  • Molecular Sequence Data
  • RNA Interference / physiology*
  • RNA, Small Interfering / biosynthesis*
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / physiology
  • RNA, Viral / antagonists & inhibitors
  • RNA, Viral / biosynthesis
  • RNA, Viral / genetics
  • RNA, Viral / physiology
  • Virus Replication / genetics


  • Anti-HIV Agents
  • RNA, Small Interfering
  • RNA, Viral