Harsha Venkatesh
New York University
Temperature-Dependent Transition Pathways of the HIV-1 Rev Response Element
RNA structural ensembles enable a mechanism of hierarchical regulatory control, where primary sequence dictates secondary structure, which ultimately determines tertiary folding and intermolecular interactions. Mutations in RNA sequences can lead to alternatively folded structured states that may be involved in the progression of disease. While it is known that RNA can transition between these states, an efficient approach that models the making and breaking of base pairs during this process is missing. Here, we build on existing RNA folding tools from the ViennaRNA suite, such as RNAsubopt, Barriers, and Pathfinder, to construct free energy landscapes for the human immunodeficiency virus 1 (HIV-1) Rev response element (RRE) RNA, which is known to sample two major states in solution. Further, we deconvolute structural ensembles from chemical probing experiments at varying temperatures to experimentally bias these landscapes, generating high-accuracy transition paths with single-molecule resolution. This approach not only sheds light on the pathways between the two major states adopted by the HIV-RRE, but also presents an approach that can be used to understand the impact that single-nucleotide polymorphisms (SNPs) and other RNA modifications have on the energetic barriers between structured states. Further investigation into 2D and 3D structural transitions will elucidate a method for identifying intermediates between healthy and disease states, a crucial tool for developing and testing therapeutic agents that promote or prevent certain structures from being sampled.
RNA structural ensembles enable a mechanism of hierarchical regulatory control, where primary sequence dictates secondary structure, which ultimately determines tertiary folding and intermolecular interactions. Mutations in RNA sequences can lead to alternatively folded structured states that may be involved in the progression of disease. While it is known that RNA can transition between these states, an efficient approach that models the making and breaking of base pairs during this process is missing. Here, we build on existing RNA folding tools from the ViennaRNA suite, such as RNAsubopt, Barriers, and Pathfinder, to construct free energy landscapes for the human immunodeficiency virus 1 (HIV-1) Rev response element (RRE) RNA, which is known to sample two major states in solution. Further, we deconvolute structural ensembles from chemical probing experiments at varying temperatures to experimentally bias these landscapes, generating high-accuracy transition paths with single-molecule resolution. This approach not only sheds light on the pathways between the two major states adopted by the HIV-RRE, but also presents an approach that can be used to understand the impact that single-nucleotide polymorphisms (SNPs) and other RNA modifications have on the energetic barriers between structured states. Further investigation into 2D and 3D structural transitions will elucidate a method for identifying intermediates between healthy and disease states, a crucial tool for developing and testing therapeutic agents that promote or prevent certain structures from being sampled.
