Steric Block High Affinity Oligonucleotide Analogues: A New Tool for Mapping RNA-Protein Binding Sites
- Resource Type
- Authors
- Jane Greatorex; Douglas Brown; Michael J. Gait; Andrew M. L. Lever; Emily Joy
- Source
- Nucleosides, Nucleotides and Nucleic Acids. 27:196-212
- Subject
- Binding Sites
Oligoribonucleotides
Chemistry
Oligonucleotide
Virus Assembly
Binding protein
RNA Conformation
Gene Products, gag
RNA-Binding Proteins
RNA
RNA Probes
General Medicine
Plasma protein binding
Biochemistry
Molecular biology
Conserved sequence
A-site
HIV-1
Genetics
Nucleic Acid Conformation
RNA, Viral
Molecular Medicine
Binding site
Protein Binding
- Language
- ISSN
- 1532-2335
1525-7770
Steric-block ON analogues are efficient inhibitors of RNA-protein interaction and therefore have potential to probe RNA sequences for putative protein binding sites and to investigate mechanisms of protein binding. The packaging process of HIV-1 is highly specific involving an interaction between the Gag protein and a conserved sequence that is only present on genomic viral RNA. Using oligonucleotide probes we have confirmed that the terminal purine loop is the major Gag binding site on SL3 and that a secondary Gag binding site exists at an internal purine bulge. We also demonstrate direct binding of oligonucleotide to their binding sites and confirm this interaction does not alter global RNA conformation, making them highly specific, nondisruptive probes of RNA protein interactions.