title: Inhibition of 5'-UTR RNA conformational switching in HIV-1 using antisense PNAs.
abstract: BACKGROUND
  The genome of retroviruses, including HIV-1, is packaged as two homologous (+) strand RNA molecules, noncovalently associated close to their 5'-end in a region called dimer linkage structure (DLS). Retroviral HIV-1 genomic RNAs dimerize through complex interactions between dimerization initiation sites (DIS) within the (5'-UTR). Dimer formation is prevented by so calledLong Distance Interaction (LDI) conformation, whereas Branched Multiple Hairpin (BMH) conformation leads to spontaneous dimerization.
  
  
  RESULTS
  We evaluated the role of SL1 (DIS), PolyA Hairpin signal and a long distance U5-AUG interaction by in-vitro dimerization, conformer assay and coupled dimerization and template-switching assays using antisense PNAs. Our data suggests evidence that PNAs targeted against SL1 produced severe inhibitory effect on dimerization and template-switching processes while PNAs targeted against U5 region do not show significant effect on dimerization and template switching, while PNAs targeted against AUG region showed strong inhibition of dimerization and template switching processes.
  
  
  CONCLUSIONS
  Our results demonstrate that PNA can be used successfully as an antisense to inhibit dimerization and template switching process in HIV -1 and both of the processes are closely linked to each other. Different PNA oligomers have ability of switching between two thermodynamically stable forms. PNA targeted against DIS and SL1 switch, LDI conformer to more dimerization friendly BMH form. PNAs targeted against PolyA haipin configuration did not show a significant change in dimerization and template switching process. The PNA oligomer directed against the AUG strand of U5-AUG duplex structure also showed a significant reduction in RNA dimerization as well as template- switching efficiency.The antisense PNA oligomers can be used to regulate the shift in the LDI/BMH equilibrium.
authors.affiliation: Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
authors.forename: Braham
authors.initials: B
authors.lastname: Parkash
authors.forename: Atul
authors.initials: A
authors.lastname: Ranjan
authors.forename: Vinod
authors.initials: V
authors.lastname: Tiwari
authors.forename: Sharad Kumar
authors.initials: SK
authors.lastname: Gupta
authors.forename: Navrinder
authors.initials: N
authors.lastname: Kaur
authors.forename: Vibha
authors.initials: V
authors.lastname: Tandon
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D002021:Buffers; D019281:Dimerization; D016679:Genome, Viral / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects / Q000528:radiation effects; D009691:Nucleic Acid Denaturation / Q000187:drug effects / Q000528:radiation effects; D009692:Nucleic Acid Heteroduplexes / Q000187:drug effects / Q000528:radiation effects; D059372:Nucleotide Motifs / Q000235:genetics; D016376:Oligonucleotides, Antisense / Q000494:pharmacology; D020135:Peptide Nucleic Acids / Q000494:pharmacology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D013698:Templates, Genetic; D044366:Transition Temperature; D014466:Ultraviolet Rays
chemical_list: D020121:5' Untranslated Regions; D002021:Buffers; D009692:Nucleic Acid Heteroduplexes; D016376:Oligonucleotides, Antisense; D020135:Peptide Nucleic Acids; D012333:RNA, Messenger; D012367:RNA, Viral