• RNA / Volume 8 / Issue 02 / February 2002, pp 252-260
  • Copyright © 2002 RNA Society
  • DOI: http://dx.doi.org/ (About DOI), Published online: 13 February 2002

Water counting: Quantitating the hydration level of paramagnetic metal ions bound to nucleotides and nucleic acids

a1 Department of Chemistry, University of California at Davis, Davis, California 95616, USA


Binding of divalent metal ions plays a key role in the structure and function of ribozymes and other RNAs. In turn, the energetics and kinetics of the specific binding process are dominated by the balance between the cost of dehydrating the aqueous ion and the energy gained from inner-sphere interactions with the macromolecule. In this work, we introduce the use of the pulsed EPR technique of 2H Electron Spin-Echo Envelope Modulation (ESEEM) to determine the hydration level of Mn2+ ions bound to nucleotides and nucleic acids. Mn2+ is an excellent structural and functional mimic for Mg2+, the most common divalent ion of physiological interest. Comparison of data in D2O and H2O, with aqueous Mn2+ as a reference standard, allows a robust and precise determination of the number of bound water molecules, and therefore the number of RNA-derived ligands. Examples of applications to the mononucleotide models MnGMP and MnATP, as well as to the paradigmatic RNA system tRNAPhe, are shown.

(Received September 6 2001)
(Revised September 26 2001)
(Accepted November 26 2001)

Key Words: ATP; EPR; ESEEM; GMP; manganese; tRNA.

c1 Reprint requests to: R. David Britt, Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, USA; e-mail: rdbritt@ucdavis.edu