RNA recognition by Tat-derived peptides: interaction in the major groove?

Cell. 1991 Aug 9;66(3):577-88. doi: 10.1016/0092-8674(81)90020-9.


Replication of human immunodeficiency virus requires binding of the viral Tat protein to its RNA target sequence TAR; peptides derived from Tat bind to a TAR "contact site" spanning 5 bp and a trinucleotide pyrimidine bulge. We find that high affinity binding requires a U residue in the bulge loop and 2 specific adjacent base pairs. Other bulged RNAs bind in a lower affinity nonspecific manner; sequence-specific binding requires a bulge loop of more than 1 nucleotide. Reaction with diethyl pyrocarbonate indicates that one effect of the bulge is to make the otherwise deep and narrow RNA major groove accessible. A model consistent with these data involves local distortion of A-form geometry at the bulge, which bends the helix and permits protein binding and interactive access in the RNA major groove.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Carrier Proteins / metabolism*
  • Diethyl Pyrocarbonate / chemistry
  • Gene Products, tat / metabolism*
  • Hydrogen Bonding
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleic Acid Conformation
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism*
  • RNA-Binding Proteins
  • Structure-Activity Relationship
  • Thermodynamics


  • Carrier Proteins
  • Gene Products, tat
  • RNA, Viral
  • RNA-Binding Proteins
  • Diethyl Pyrocarbonate