This project links two broadly important problems in biomedical science. First, the human immunodeficiency virus (HIV)infects 5 million people annually and causes ~3 million deaths through AIDS. Studies of the structural biology of HIV have contributed significantly to therapeutic drug strategies against the virus. The HIV RNA genome is directly involved in almost every aspect of the retroviral infectivity cycle, but remains the least well understood component of HIV.A comprehensive structural map of the HIV-1 genome will make it easier to identify new targets for antiretroviral drugs and to design siRNA and other antisense approaches. Second, essentially all RNAs function in biology only after they fold into a specific secondary structure. Existing RNA structure mapping technologies are laborious and error prone and yield an incomplete view of RNA structure. Our laboratory has developed a new RNA structure analysis technology that solves the problems associated with traditional approaches and that is supported by extensive successful exploratory work. We will develop RNA structure analysis into a mature technology roughly as straightforward as DNA sequencing is today. We seek to use this technology to analyze the structure of an entire HIV-1 RNA genome. In collaboration with experts in HIV biology and in bioinformatics, we will tackle the following Aims: (1) Create a complete, seamless technology for quantitative analysis of the structure of long RNAs. We will make this technology accessible to all interested biomedical scientists. (2) Use our high throughput RNA structure mapping technology to obtain quantitative structural information for an entire HIV-1RNA genome. (3) Determine differences in the genomic RNA structure at different stages in the viral life cycle. This work is likely to advance significantly our understanding of how the human immunodeficiency virus works and thus how to interfere with HIV functioning. This work accomplishes this goal by creating a tool -- facile RNAstructure analysis - that can be broadly used by biomedical scientists to address diverse biological problems with consequences for human health.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Study Section
AIDS Molecular and Cellular Biology Study Section (AMCB)
Program Officer
Embry, Alan C
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University of North Carolina Chapel Hill
Schools of Arts and Sciences
Chapel Hill
United States
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Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M (2016) Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox. Trends Biochem Sci 41:734-6
Smola, Matthew J; Rice, Greggory M; Busan, Steven et al. (2015) Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc 10:1643-69
Weeks, Kevin M (2015) RNA clubs. RNA 21:760-1
Weeks, Kevin M (2015) Review toward all RNA structures, concisely. Biopolymers 103:438-48
Lavender, Christopher A; Lorenz, Ronny; Zhang, Ge et al. (2015) Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. PLoS Comput Biol 11:e1004126
Lavender, Christopher A; Gorelick, Robert J; Weeks, Kevin M (2015) Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes. PLoS Comput Biol 11:e1004230
Rice, Greggory M; Leonard, Christopher W; Weeks, Kevin M (2014) RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA 20:846-54
Siegfried, Nathan A; Busan, Steven; Rice, Greggory M et al. (2014) RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods 11:959-65
Low, Justin T; Garcia-Miranda, Pablo; Mouzakis, Kathryn D et al. (2014) Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry 53:4282-91
Homan, Philip J; Favorov, Oleg V; Lavender, Christopher A et al. (2014) Single-molecule correlated chemical probing of RNA. Proc Natl Acad Sci U S A 111:13858-63

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