RUI: Comparative Analysis of Small RNA Motifs

Colorado College, Colorado Springs CO

Investigators

Abstract

RNA is made up of four nucleotide bases: adenine (A), guanine (G), uracil (U) and cytosine (C). The order in which these four bases are found in any RNA is called its sequence. These bases interact with each other, A with U (A-U) and G with C (G-C) to form canonical base pairs. Many unique combinations of interactions occur in RNA, for example, G with A (G.A) or G with U (G.U) to form non-canonical base pairs. Other interactions also occur, for example, a few A's can stack on top of each other or an unpaired U can interact with an A-U pair to form U.A-U base triple. Currently, when RNA is folded using the known rules of interactions, many regions of RNA are left in "bulges" and "loops". The rules for structure formation within these regions are not known; however, these sites are known to be involved in interactions with proteins, RNA, and drugs. This project will focus on small bulge structures that are found in many different RNA and are stable in the absence of the large RNA. One such structure is a three-nucleotide bulge that is commonly found in important regions of many RNA, such as ribosomal RNA, AIDS-causing human immunodeficiency virus type 1 (HIV-1), and in small RNA called micro-RNA. There are many questions that need to be answered : are all three-nucleotide bulge RNA forming similar structures? What happens to the structure and stability of RNA if the bulge sequences become slightly bigger or smaller? Do these bulge nucleotides interact with other neighboring portions of RNA? If the presence of a bulge sequence causes RNA to bend, can we predict the bend angle and the energy required to do so? Do the bulge sequences bind to metal ions? Does the metal binding help stabilize or straighten the RNA? To understand the structure and function of short bulged RNA, the energy required to "undo" the structure will be measured; the stronger the structure, the more energy it will take to unfold. The RNA sequence in and around the bulge will be altered to determine the corresponding changes in energy required to unfold the RNA. Since the shape of RNA determines how it moves through a matrix or absorbs certain types of light, these techniques will be used to study bending of RNA. How tightly certain metal ions and other molecules bind to RNA will also be measured. The importance of this study is first and foremost to understand the basic structures that form in RNA. This research will determine general patterns that are to be expected for small bulged sequences. These "rules" can then be included in computer programs that are currently used to predict RNA structures. As these bulge sequences are derived from functionally important RNA, this study will improve the link between the structure and function of these RNA. The nucleotide sequence for DNA and RNA of many organisms is currently available. Thus, improving the ability to link this information to the structure and function of molecules will enhance the usefulness of the genome databases. For example, many new pathogens, including organisms used in bio-terrorism, can now be sequenced quickly. To design RNA-based drugs to neutralize a pathogen will require a very detailed understanding of local and global structures of functionally important RNA for both the pathogen and the host. The broader impact of this research is that it will be done with undergraduate students. Students will start working on independent research projects starting as early as their first year of college. This research will also be incorporated into nucleic acid biochemistry courses. By participating, students interested in the biological sciences will learn quantitative research methods and will improve their mathematical skills. Abstract concepts learned in courses will become more interesting when applied to real life problems. Students will participate in course-linked outreach activities in their local communities and K-12 school system. Students will use their knowledge to provide information on biochemistry of diseases and drugs to their communities, which in turn will make science relevant to their own lives. Students will work with K-12 school system to provide mentoring and to direct science-based activities to keep the younger students curious about science. Students will get an opportunity to work with scientists in three different countries and will experience the international nature of research. These projects will bring the excitement of research into the undergraduate environment. The equipment and expertise will be shared with neighboring schools and it will benefit everyone involved. Student researchers will be encouraged to become members of professional societies, such as the American Society for Biochemistry and Molecular Biology (ASBMB), and will be given opportunities to present their research at regional, national, and international meetings. Towards this end, Undergraduate Affiliate Network (UAN) has been created by ASBMB and students have started a local chapter. The research and outreach experiences will help students to see the relevance of science to real world problems, and to realize that they, as scientists, can make a difference in their communities.