Isolation of Endogenously Assembled RNA-Protein Complexes Using Affinity Purification Based on Streptavidin Aptamer S1

Int J Mol Sci. 2015 Sep 16;16(9):22456-72. doi: 10.3390/ijms160922456.


Efficient isolation of endogenously assembled viral RNA-protein complexes is essential for understanding virus replication mechanisms. We have developed an affinity purification strategy based on an RNA affinity tag that allows large-scale preparation of native viral RNA-binding proteins (RBPs). The streptavidin-binding aptamer S1 sequence was inserted into the 3' end of dengue virus (DENV) 5'-3' UTR RNA, and the DENV RNA UTR fused to the S1 RNA aptamer was expressed in living mammalian cells. This allowed endogenous viral ribonucleoprotein (RNP) assembly and isolation of RNPs from whole cell extract, through binding the S1 aptamer to streptavidin magnetic beads. Several novel host DENV RBPs were subsequently identified by liquid chromatography with tandem mass spectrometry (LC-MS/MS), including RPS8, which we further implicate in DENV replication. We proposed efficient S1 aptamer-based isolation of viral assembled RNPs from living mammalian cells will be generally applicable to the purification of high- and low-affinity RBPs and RNPs under endogenous conditions.

Keywords: 40S ribosomal protein S8; DENV; RNA binding protein; affinity purification; living mammalian cells; streptavidin aptamer S1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / genetics
  • Aptamers, Nucleotide / metabolism
  • Cell Line, Tumor
  • Chemical Fractionation / methods
  • Cricetinae
  • Dengue Virus / metabolism
  • HEK293 Cells
  • Humans
  • Protein Binding
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / genetics
  • Ribonucleoproteins / metabolism*
  • Streptavidin / chemistry
  • Viral Proteins / chemistry
  • Viral Proteins / genetics
  • Viral Proteins / metabolism*


  • Aptamers, Nucleotide
  • RNA, Viral
  • Ribonucleoproteins
  • Viral Proteins
  • Streptavidin