Using Immunoprecipitation Followed by Dot Blotting to Identify Oligonucleotide-Protein Interactions in Cells.

Antisense oligonucleotides (ASOs) are synthetic, short-stranded DNA or RNA oligonucleotides that can inhibit the expression of specific genes via sequence-specific hybridization to their RNA transcripts. Despite their widespread use, much evidence has shown that ASOs are susceptible to nonspecific protein binding in the intracellular environment, hampering the efficacy for gene expression regulation. We have previously described an oligonucleotide-immunoprecipitation (Oligo-IP)-based strategy to investigate ASO and protein interactions in cells. This chapter describes the use of Oligo-IP to investigate the interactions between ASOs and HIV-1 Gag, the major structural protein of the virus.