title: High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.
abstract: The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method (FDM) is a numerically efficient algorithm that fits the entire multi-dimensional time-domain data to a set of multi-dimensional oscillators. Selective 4D constant-time HCCH-COSY experiments that correlate the H5-C5-C6-H6 base spin systems of pyrimidines or the H1'-C1'-C2'-H2' spin systems of ribose sugars were acquired on the (13)C-labeled iron responsive element (IRE) RNA. FDM-processing of these 4D experiments recorded with only 8 complex points in the indirect dimensions showed superior spectral resolution than FT-processed spectra. Practical aspects of obtaining optimal FDM-processed spectra are discussed. The results here demonstrate that FDM-processing can be used to obtain high-resolution 4D spectra on a medium sized RNA in a fraction of the acquisition time normally required for high-resolution, high-dimensional spectra.
authors.affiliation: Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309-0215, USA.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Douglas
authors.forename: Michael P
authors.initials: MP
authors.lastname: Latham
authors.forename: Geoffrey S
authors.initials: GS
authors.lastname: Armstrong
authors.forename: Brad
authors.initials: B
authors.lastname: Bendiak
authors.forename: Arthur
authors.initials: A
authors.lastname: Pardi
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008954:Models, Biological; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011743:Pyrimidines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry*; D012815:Signal Processing, Computer-Assisted
chemical_list: D011743:Pyrimidines; D012313:RNA; D012266:Ribose; C030986:pyrimidine