Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modified DNA Antisense Oligonucleotides

  • Xinying Zong
  • Lulu Huang
  • Vidisha Tripathi
  • Raechel Peralta
  • Susan M. Freier
  • Shuling GuoEmail author
  • Kannanganattu V. PrasanthEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1262)


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 nuclear-retained 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 nuclear-retained 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.

Key words

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



Research in the KVP lab is supported by grants from NIH/NIGMS (GM088252) and American Cancer Society (RSG-11-174-01-RMC).


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Xinying Zong
    • 1
  • Lulu Huang
    • 2
  • Vidisha Tripathi
    • 1
  • Raechel Peralta
    • 2
  • Susan M. Freier
    • 2
  • Shuling Guo
    • 2
    Email author
  • Kannanganattu V. Prasanth
    • 1
    Email author
  1. 1.Department of Cell and Developmental BiologyUniversity of Illinois at Urbana-ChampaignUrbana-ChampaignUSA
  2. 2.Isis PharmaceuticalsCarlsbadUSA

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