The HIV pandemic is the fourth leading cause of death worldwide. The RNA genome is arguably the most important component of HIV, yet only around 10% has been structurally characterized. Furthermore, almost all structural studies have been performed on in vitro transcripts of this RNA. The objective of this project is to determine, at single nucleotide resolution, the secondary structure the entire HIV-1 genomic RNA of ~9,200 nucleotides. This challenging goal has recently become feasible due to a high-throughput technology, termed 'SHAPE', developed by the Weeks group at UNC. This project will use SHAPE technology to obtain structural constraints for every nucleotide in the ~9,200 nucleotide HIV-1 genome. Constraints will be used to generate a very accurate secondary structural map of the entire HIV-1 genome using advanced structure predicting algorithms. This approach will be used to obtain structures for both RNA gently extracted from HIV-1 and for the authentic HIV-1 genomic RNA in virio. ? ?
Therefore, the specific aims of this project are: (1) Mapping the Secondary Structure of the HIV-1 Genomic RNA extracted from virions, and (2) Structural comparison of HIV-1 extracted genomic RNA and the genomic RNA in active HIV virions. ? ? ?
