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. Author manuscript; available in PMC: 2010 Oct 1.
Published in final edited form as: Methods. 2009 May 4;49(2):101–111. doi: 10.1016/j.ymeth.2009.04.016

Table 1.

Summary of chemical information obtainable by Raman crystallography of RNA

Chemical Information Example
Proton-binding: identification of RNA base and determination of pKa pKa of C75 in HDV ribozyme crystal near 6.5
Metal-binding interactions: identification of metal Bound innersphere Mg2+ itself has peak at ~322 cm−1.
Metal-binding: quantification of number of metals and affinity Agreement between metals from Raman and from crystal structure.
Metal-binding interactions: identification of RNA ligands Innersphere Mg2+ -PO2− interaction has a differential near 1100 cm−1. Innersphere Mg2+ N7 of guanine interaction has a differential near 1490 cm−1.
Isotope effects on metal binding Determination of H218O and 2H2O effects on bound innersphere Mg2+ ion.
RNA conformational changes ribose, phosphate backbone
Compare crystal behavior to solution Similar pKa, metal binding found for HDV ribozyme.
Chemical reaction in crystal; identify reaction intermediates and determine optimal conditions for trapping target species for X-ray analysis Not demonstrated for RNA yet, but shown for proteins