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Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1 |
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| Authors: | Wang Hui Ma Xiaojing Yeh Yu-Shan Zhu Yongjin Daugherty Matthew D Frankel Alan D Musier-Forsyth Karin Barbara Paul F |
| Institution: | † Center for Nano and Molecular Science and Technology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas ‡ Department of Biochemistry and Biophysics, University of California, San Francisco, California § Department of Chemistry, Ohio State University, Columbus, Ohio ¶ Department of Biochemistry, Ohio State University, Columbus, Ohio ‖ Center for RNA Biology, Ohio State University, Columbus, Ohio †† Center for Retrovirus Research, Ohio State University, Columbus, Ohio |
| Abstract: | We report a comparative study in which a single-molecule fluorescence resonance energy transfer approach was used to examine how the binding of two families of HIV-1 viral proteins to viral RNA hairpins locally changes the RNA secondary structures. The single-molecule fluorescence resonance energy transfer results indicate that the zinc finger protein (nucleocapsid) locally melts the TAR RNA and RRE-IIB RNA hairpins, whereas arginine-rich motif proteins (Tat and Rev) may strengthen the hairpin structures through specific binding interactions. Competition experiments show that Tat and Rev can effectively inhibit the nucleocapsid-chaperoned annealing of complementary DNA oligonucleotides to the TAR and RRE-IIB RNA hairpins, respectively. The competition binding data presented here suggest that the specific nucleic acid binding interactions of Tat and Rev can effectively compete with the general nucleic acid binding/chaperone functions of the nucleocapsid protein, and thus may in principle help regulate critical events during the HIV life cycle. |
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