title: Trapping HIV-1 reverse transcriptase before and after translocation on DNA.
abstract: A disulfide cross-linking strategy was used to covalently trap as a stable complex (complex N) a short-lived, kinetic intermediate in DNA polymerization. This intermediate corresponds to the product of polymerization prior to translocation. We also prepared the trapped complex that corresponds to the product of polymerization after translocation (complex P). The cross-linking method that we used is a variation of a technique developed by the Verdine and Harrison laboratories. It involves disulfide interchange between an engineered sulfhydryl group of the protein (Q258C mutation) and a disulfide-containing tether attached at the N(2) amino group of a modified dG in either the template or the primer strand of the nucleic acid. We report here a highly efficient synthesis of the precursor, bis(3-aminopropyl)disulfide dihydrochloride, used to introduce this substituent into the oligonucleotide. Efficient cross-linking takes place when the base pair containing the substituent is positioned seven registers from the dNTP-binding site (N site) and the N site is occupied. Complex N, but not complex P, is a substrate for the ATP-based excision reaction that unblocks nucleoside reverse transcriptase inhibitor (NRTI)-terminated primers and causes resistance to several NRTIs, confirming predictions that the excision reaction takes place only when the 3'-end of the primer is bound at the N site. These techniques can be used for biochemical and structural studies of the mechanism of DNA polymerization, translocation, and excision-based resistance of RT to NRTIs. They may also be useful in studying other DNA or RNA polymerases or other enzymes.
authors.affiliation: Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-5638, USA.
authors.forename: Stefan G
authors.initials: SG
authors.lastname: Sarafianos
authors.forename: Arthur D
authors.initials: AD
authors.lastname: Clark
authors.forename: Steve
authors.initials: S
authors.lastname: Tuske
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Squire
authors.forename: Kalyan
authors.initials: K
authors.lastname: Das
authors.forename: Dequan
authors.initials: D
authors.lastname: Sheng
authors.forename: Palanichamy
authors.initials: P
authors.lastname: Ilankumaran
authors.forename: Andagar R
authors.initials: AR
authors.lastname: Ramesha
authors.forename: Heiko
authors.initials: H
authors.lastname: Kroth
authors.forename: Jane M
authors.initials: JM
authors.lastname: Sayer
authors.forename: Donald M
authors.initials: DM
authors.lastname: Jerina
authors.forename: Paul L
authors.initials: PL
authors.lastname: Boyer
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Hughes
authors.forename: Eddy
authors.initials: E
authors.lastname: Arnold
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001692:Biological Transport; D003460:Crystallization; D004247:DNA / Q000378:metabolism*; D054303:HIV Reverse Transcriptase / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000255:Adenosine Triphosphate; D004247:DNA; D054303:HIV Reverse Transcriptase