The objective of this RUI project is to develop models to predict the structure of RNA molecules from their sequence. RNAs are intimately involved in a wide variety of biological activities. During the process of gene expression, they serve as informational molecules and part of the decoding machinery. Biological molecules, including RNA, must fold into the correct three-dimensional shape to acquire their active-functional form. These studies will combine both stability and structural characterization of RNA duplexes to achieve a better understanding of the nature of RNA structure.
Undergraduate students will perform all of the investigations, including the selection of sequences to be investigated, providing them with excellent training and valuable research experience. Students from the PI's laboratory have an excellent track record for attending graduate and professional schools after obtaining their BS degrees. Since 2005, eight of these students are attending graduate school in either chemistry or biochemistry; and, eight are attending professional school. The graduate programs attended by the students include Yale University, University of Rochester, Penn State University, Duke University, Carnegie Mellon University, and University of Illinois Urbana-Champaign. Since 2000, 27 of the PI's students have been co-authors on papers. One of the students won the undergraduate poster competition at the National AAAS meeting in 1995. In addition, a high school chemistry teacher will be recruited to join the research group during the summer. The high school teacher will have the opportunity to engage in authentic research using state-of-the-art techniques, methodology and instrumentation. This will enhance the teacher's abilities and experience base and make for a richer teaching and learning experience in high school science classes.
The research objective of this proposal was to improve methods for predicting the structure of RNA from sequence. Specifically we examine the stability of small model RNA molecules with defined structural characteristics. Changes in the sequence of the RNAs are then correlated to the relative stability of the RNA to develop rules to predict the stability of naturally occurring RNAs from their sequence. The research is done by undergraduate students as part of their senior project and summer research experiences. These experiences increase the students’ interest in graduate school and research in general. Research results summary: The outcomes of this work have resulted in improved methods to predict the folding of RNA. Specifically our results have led to improvements in the prediction of unpaired nucleotides of the RNA duplex which will help in understanding RNA folding and interactions. Additionally, we have developed fluorescent methods for the structural analysis of small RNAs. This procedure allows us to distinguish which of two identical nucleotides is in fact unpaired. This project was primarily done by 18 undergraduate students who gained training in independent research. A high school science teacher also worked on the project gaining insight into independent research. Eight students were coauthors on published manuscripts. In addition, four of these students presented their work at national or regional conferences. Four of the students who have graduated are currently attending professional schools and four are attending graduate school.
