Nucleic acid interactions with partners: ions and proteins

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Nucleic acids are essential to life, yet a detailed understanding of how these diverse and complex macromolecules function remains beyond reach. DNA stores and enables propagation of genetic information from within highly structured chromatin. In the last thirty years, unanticipated and often surprising biological roles have been discovered for RNA. RNA's active roles in the cell range from regulating genes through protecting against infection. The rapid pace of discoveries involving RNA far exceeds current knowledge of how these remarkable molecules function. Many of the most important roles of nucleic acids (NAs) rely on folding to compact structures, despite the large negative charge of the backbone, which favors extended structures due to repulsive forces between charges. In chromatin, DNA is packaged by proteins into small units known as nucleosome core particles (NCPs). RNA folding to functional structures results from interactions with positively charged partners. The goal of this program is to understand how biologically essential partners interact with and affect/control the structures of DNA and RNA. Much is known about the double stranded duplex regions of both DNA and RNA structures. Therefore, our studies of DNA will focus on how protein partners compact (release) long duplexes into (from) NCPs. In contrast, for RNA, which is essential single stranded, much less information is available about the flexible connectors that link short, rigid duplexes and enable folding, sensing or protein binding. Innovative experimental tools will be applied to measure NA conformation as well as the effect on conformation of both protein and ionic partners. Systems of interest range from short, single stranded regions, through independently folding RNA motifs, to large protein-DNA complexes. Multiple collaborations with well-established investigators, often grounded in years of shared NIH funding, enable the breadth of this program. Proposed collaborative studies include: optimizing force fields to describe highly flexible NA structures, all atom molecular dynamics (MD) simulations of RNA folding or RNA-protein interactions, testing and refining implicit solvent models of the solution and ion environment of NA elements, and finally biologically oriented studies that focus on the role of proteins in dynamic motions of chromatin.