Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using raman crystallography

Bo Gong, Yuanyuan Chen, Eric L. Christian, Jui Hui Chen, Elaine Chase, Durga M. Chadalavada, Rieko Yajima, Barbara L. Golden, Philip C. Bevilacqua, Paul R. Carey

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34 Scopus citations

Abstract

A Raman microscope and Raman difference spectroscopy are used to detect the vibrational signature of RNA-bound magnesium hydrate in crystals of hepatitis delta virus (HDV) ribozyme and to follow the effects of magnesium hydrate binding to the nonbridging phosphate oxygens in the phosphodiester backbone. There is a correlation between the Raman intensity of the innersphere magnesium hydrate signature peak, near 322 cm-1, and the intensity of the PO2- symmetric stretch, near 1100 cm-1, perturbed by magnesium binding, demonstrating direct observation of -PO2-⋯Mg2+(H2O)x innersphere complexes. The complexes may be pentahydrates (x = 5) and tetrahydrates (x = 4). The assignment of the Raman feature near 322 cm-1 to a magnesium hydrate species is confirmed by isotope shifts observed in D2O and H218O that are semiquantitatively reproduced by calculations. The standardized intensity changes in the 1100 cm-1 PO2- feature seen upon magnesium hydrate binding indicates that there are ∼5 innersphere Mg2+-O2P contacts per HDV molecule when the crystal is exposed to a solution containing 20 mM magnesium.

Original languageEnglish (US)
Pages (from-to)9670-9672
Number of pages3
JournalJournal of the American Chemical Society
Volume130
Issue number30
DOIs
StatePublished - Jul 30 2008

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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    Gong, B., Chen, Y., Christian, E. L., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., & Carey, P. R. (2008). Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using raman crystallography. Journal of the American Chemical Society, 130(30), 9670-9672. https://doi.org/10.1021/ja801861s