Journal of Biomolecular NMR

, Volume 35, Issue 2, pp 103–115 | Cite as

Prediction of molecular alignment of nucleic acids in aligned media

  • Bin Wu
  • Michael Petersen
  • Frederic Girard
  • Marco Tessari
  • Sybren S. Wijmenga


We demonstrate – using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined – that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye–Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye–Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye–Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it’s functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request.


alignment tensor prediction electrostatic alignment NMR nucleic acids RNA residual dipolar couplings 


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This research was supported by grants from the Dutch Science Foundation (SW) and the Danish National Research Council (MP). We thank Prof. C.W. Hilbers for encouraging comments. We also thank the anonymous reviewers for their constructive suggestions.

Supplementary material


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Bin Wu
    • 1
  • Michael Petersen
    • 2
  • Frederic Girard
    • 1
  • Marco Tessari
    • 1
  • Sybren S. Wijmenga
    • 1
  1. 1.Laboratory of Physical Chemistry-Biophysical Chemistry, Institute of Molecules and MaterialsRadboud University NijmegenNijmegenThe Netherlands
  2. 2.Nucleic Acid Center, Department of ChemistryUniversity of Southern DenmarkOdense MDenmark

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