RNA plays important roles in many areas of Biology. Functional RNA sequences that work at the level of RNA, i.e. not as an mRNA coding region, are called non-coding RNA (ncRNA). ncRNA sequences serve diverse roles from sequence recognition, such as hybridization in RNA interference, to catalyzing reactions, such as peptide bond formation by ribosomal RNA. To understand RNA function and to harness the power of RNA, with RNA interference, therapeutic RNA enzymes, or RNA nanostructures, an understanding of RNA structure is required. RNAstructure is a software package for RNA secondary structure prediction and analysis. It has been downloaded by over 17,000 different users and is available at the Mathews lab website http://rna.urmc.rochester.edu. It provides state-of-the-art algorithms for RNA structure prediction using the most current understanding of RNA folding thermodynamics. It also provides algorithms for finding the optimal secondary structure shared by two sequences, which is, on average, much more accurate than predicting a structure for a single sequence. Furthermore, it provides methods to predict the affinity of structured oligonucleotides (DNA or RNA) annealing to a structured RNA target. These predictions are important for the selection of effective small interfering RNA (siRNA) for gene silencing. RNAstructure is provided with user-friendly graphical user interfaces in C++ for Microsoft Windows and in JAVA for Linux or Mac OS-X. Text interfaces are provided for scripting or command line use. These can be compiled on Unix/Linux/Mac OS-X and executables are provided for Windows. Finally, a shared C++ class library is available for programmers to include algorithms in new programs. The proposal is to extend and maintain RNAstructure. Four formal aims are proposed for the next period of support.
Aim 1 is to provide a new wizard mode for RNAstructure to guide users through the analysis of their sequence(s).
Aim 2 is to update the nearest neighbor parameters for predicting conformational stability using the most recent experimental data.
Aim 3 is to provide all the RNAstructure components via web interfaces.
Aim 4 is to provide fast and accurate prediction of secondary structures that include pseudoknots, which are currently not predicted by most algorithms.

Public Health Relevance

This proposal has direct public health relevance. We provide software tools for predicting, understanding, and targeting RNA structure. These can be applied to understanding the biology of infectious diseases because some viruses, including influenza and HIV, are RNA viruses. Furthermore, they can be used to design novel therapeutics, such as antisense oligonucleotides or small interfering RNA that both target RNA. This RNA-targeting therapeutics could be used for diseases such as cancer or inherited diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM076485-05
Application #
7936497
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Remington, Karin A
Project Start
2005-12-01
Project End
2014-08-31
Budget Start
2010-09-10
Budget End
2011-08-31
Support Year
5
Fiscal Year
2010
Total Cost
$267,627
Indirect Cost
Name
University of Rochester
Department
Biochemistry
Type
Schools of Dentistry
DUNS #
041294109
City
Rochester
State
NY
Country
United States
Zip Code
14627
Spasic, Aleksandar; Kennedy, Scott D; Needham, Laura et al. (2018) Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation. RNA 24:656-672
Berger, Kyle D; Kennedy, Scott D; Schroeder, Susan J et al. (2018) Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops. Biochemistry 57:2121-2131
Spasic, Aleksandar; Berger, Kyle D; Chen, Jonathan L et al. (2018) Improving RNA nearest neighbor parameters for helices by going beyond the two-state model. Nucleic Acids Res 46:4883-4892
Lai, Wan-Jung C; Kayedkhordeh, Mohammad; Cornell, Erica V et al. (2018) mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances. Nat Commun 9:4328
Payea, Matthew J; Sloma, Michael F; Kon, Yoshiko et al. (2018) Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. RNA 24:410-422
Bellaousov, Stanislav; Kayedkhordeh, Mohammad; Peterson, Raymond J et al. (2018) Accelerated RNA secondary structure design using preselected sequences for helices and loops. RNA 24:1555-1567
Belashov, Ivan A; Crawford, David W; Cavender, Chapin E et al. (2018) Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucleic Acids Res 46:6401-6415
Smith, Louis G; Zhao, Jianbo; Mathews, David H et al. (2017) Physics-based all-atom modeling of RNA energetics and structure. Wiley Interdiscip Rev RNA 8:
Sloma, Michael F; Mathews, David H (2017) Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PLoS Comput Biol 13:e1005827
Ward, Max; Datta, Amitava; Wise, Michael et al. (2017) Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic Acids Res 45:8541-8550

Showing the most recent 10 out of 58 publications