Journal of Biomolecular NMR

, Volume 41, Issue 4, pp 209–219 | Cite as

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method

  • Justin T. Douglas
  • Michael P. Latham
  • Geoffrey S. Armstrong
  • Brad Bendiak
  • Arthur Pardi


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 13C-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.


Filter diagonalization method Multi-dimensional NMR RNA HCCH-COSY High dimensionality 



This work was supported in part by NIH grants AI33098 (Arthur Pardi), GM68928 (Geoffrey S. Armstrong), NSF MCB-0236103 (Brad Bendiak) and Michael P. Latham was supported in part by an NIH Training Grant T32 GM65103.

Supplementary material


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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Justin T. Douglas
    • 1
  • Michael P. Latham
    • 1
  • Geoffrey S. Armstrong
    • 1
  • Brad Bendiak
    • 2
  • Arthur Pardi
    • 1
  1. 1.Department of Chemistry and Biochemistry, 215 UCBUniversity of ColoradoBoulderUSA
  2. 2.Department of Cell and Developmental Biology and Biomolecular Structure ProgramUniversity of Colorado Health Sciences CenterAuroraUSA

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