title: Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template.
abstract: BACKGROUND
  Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP*RT*P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet*RT*P/T complex).
  
  
  RESULTS
  UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP*RT*P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJ(F). UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet*RT*P/T complex (i.e., in the pre-translocation position).
  
  
  CONCLUSIONS
  For +1 dNTP*RT*P/T and foscarnet*RT*P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, USA.
authors.forename: Wiriya
authors.initials: W
authors.lastname: Rutvisuttinunt
authors.forename: Peter R
authors.initials: PR
authors.lastname: Meyer
authors.forename: Walter A
authors.initials: WA
authors.lastname: Scott
mesh_terms: D001483:Base Sequence; D001973:Bromodeoxyuridine / Q000737:chemistry / Q000494:pharmacology; D003432:Cross-Linking Reagents / Q000494:pharmacology; D017931:DNA Primers / Q000378:metabolism*; D017245:Foscarnet / Q000494:pharmacology; D054303:HIV Reverse Transcriptase / Q000037:antagonists & inhibitors / Q000378:metabolism*; D046911:Macromolecular Substances / Q000378:metabolism; D008954:Models, Biological; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000378:metabolism / Q000502:physiology; D011485:Protein Binding; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology; D012689:Sequence Homology, Nucleic Acid; D013698:Templates, Genetic
chemical_list: D003432:Cross-Linking Reagents; D017931:DNA Primers; D046911:Macromolecular Substances; D009711:Nucleotides; D018894:Reverse Transcriptase Inhibitors; D017245:Foscarnet; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D001973:Bromodeoxyuridine