Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides

Xinying Zong, Lulu Huang, Vidisha Tripathi, Raechel Peralta, Susan M. Freier, Shuling Guo, Kannanganattu V. Prasanth

Research output: Contribution to journalArticle


Long noncoding RNAs (lncRNAs) have recently emerged as important players in diverse cellular processes. Among them, a large fraction of lncRNAs are localized within cell nucleus. And several of these nuclearretained lncRNAs have been found to regulate key nuclear processes, which brings up the requirement of effective genetic tools to explore the functions of this “dark matter” inside the nucleus. While siRNAs and shRNAs are widely used tools in loss-of-function studies, their general efficiency in depleting nuclearretained lncRNAs is limited, due to the fact that the RNAi machinery is located mainly in the cytoplasm of mammalian cells. Here, we describe the usage of chemically modified chimeric DNA antisense oligonucleotides (ASO) in effective knockdown of nuclear-retained lncRNAs, with a focus on the detailed workflow from the design and synthesis of ASOs, to in vitro and in vivo delivery methods.

Original languageEnglish (US)
Pages (from-to)321-331
Number of pages11
JournalMethods in Molecular Biology
StatePublished - Jan 1 2015


  • Chemically modified chimeric DNA antisense oligonucleotides (ASO)
  • Electroporation
  • Free uptake
  • In vivo delivery
  • Knockdown
  • Lipid transfection
  • Long noncoding RNAs (lncRNAs)
  • Nuclear-retained long noncoding RNAs (nr-lncRNAs)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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