title: Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription.
abstract: HIV-1 reverse transcription requires several nucleic acid rearrangement steps that are "chaperoned" by the nucleocapsid protein (NC), including minus-strand transfer, in which the DNA transactivation response element (TAR) is annealed to the complementary TAR RNA region of the viral genome. These various rearrangement processes occur in NC bound complexes of specific RNA and DNA structures. A major barrier to the investigation of these processes in vitro has been the diversity and heterogeneity of the observed nucleic acid/protein assemblies, ranging from small complexes of only one or two nucleic acid molecules all the way up to large-scale aggregates comprised of thousands of NC and nucleic acid molecules. Herein, we use a flow chamber approach involving rapid NC/nucleic acid mixing to substantially control aggregation for the NC chaperoned irreversible annealing kinetics of a model TAR DNA hairpin sequence to the complementary TAR RNA hairpin, i.e., to form an extended duplex. By combining the flow chamber approach with a broad array of fluorescence single-molecule spectroscopy (SMS) tools (FRET, molecule counting, and correlation spectroscopy), we have unraveled the complex, heterogeneous kinetics that occur during the course of annealing. The SMS results demonstrate that the TAR hairpin reactant is predominantly a single hairpin coated by multiple NCs with a dynamic secondary structure, involving equilibrium between a "Y" shaped conformation and a closed one. The data further indicate that the nucleation of annealing occurs in an encounter complex that is formed by two hairpins with one or both of the hairpins in the "Y" conformation.
authors: Center for Nano and Molecular Science and Technology, University of Texas, Austin, TX 78712, USA.
authors: Hsiao-Wei
authors: HW
authors: Liu
authors: Yining
authors: Y
authors: Zeng
authors: Christy F
authors: CF
authors: Landes
authors: Yoen Joo
authors: YJ
authors: Kim
authors: Yongjin
authors: Y
authors: Zhu
authors: Xiaojing
authors: X
authors: Ma
authors: My-Nuong
authors: MN
authors: Vo
authors: Karin
authors: K
authors: Musier-Forsyth
authors: Paul F
authors: PF
authors: Barbara
mesh_terms: D001483:Base Sequence; D031541:Fluorescence Resonance Energy Transfer; D015497:HIV-1 / Q000378:metabolism*; D007700:Kinetics; D018832:Molecular Chaperones; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D019251:Nucleocapsid / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D013696:Temperature; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D018832:Molecular Chaperones; D009696:Nucleic Acids; D009841:Oligonucleotides