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. Author manuscript; available in PMC: 2012 Oct 15.
Published in final edited form as: Methods. 2009 Aug 3;49(2):148–166. doi: 10.1016/j.ymeth.2009.07.005

Figure 4.

Figure 4

Raman spectroscopic investigation of HDV ribozyme crystals. (A) Raman difference spectra (pH 7.5 – pH 5.0) of crystals of the unmodified HDV ribozyme (top panel) and an HDV ribozyme in which 7-deazaguanosine has replaced the cleavage site G1 (bottom panel). The difference spectrum of the unmodified ribozyme shows peaks at 1489 and 323 cm−1, thought to arise from metal ion coordination of a guanosine N7 and from a single inner sphere Mg2+ hydrate, respectively. Both features are lost when 7-deazaguanosine replaces guanosine at the cleavage site. (B) Stereo model of the HDV ribozyme active site, constructed by combining the Raman spectroscopic results with pre- and post-cleavage crystallographic data. The Mg2+ ion (magenta) directly coordinates the N7 of G1, along with five water molecules (grey spheres). [Taken from (13), with permission.]