RNA Secondary Structure Determination by NMR.
Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes. NAPSS-CS minimally requires input of the order of base pairs as determined from nuclear Overhauser effect spectroscopy (NOESY) of imino protons. The program deduces the 5'-3' direction of the base pairs if certain chemical shifts are also input. Secondary structures predicted by the program provide assignments of input chemical shifts to particular nucleotides in the sequence, thus facilitating an important step for determination of the three dimensional structure by NMR. The method is particularly useful for revealing pseudoknots and an example is provided. The method may also allow determination of secondary structures when a sequence folds into two structures that exchange slowly.
Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627-0216, USA.|Center for RNA Biology, University of Rochester, Rochester, NY, USA.
Jonathan L
JL
Chen
Center for RNA Biology, University of Rochester, Rochester, NY, USA.|Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
Stanislav
S
Bellaousov
Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627-0216, USA. douglas.turner@rochester.edu.|Center for RNA Biology, University of Rochester, Rochester, NY, USA. douglas.turner@rochester.edu.
Douglas H
DH
Turner
D000818:Animals; D019295:Computational Biology / Q000379:methods; D006801:Humans; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D064878:Web Browser
D012313:RNA
Chemical shifts; NAPSS; NMR; RNA secondary structure