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. Author manuscript; available in PMC: 2010 Feb 25.
Published in final edited form as: J Am Chem Soc. 2009 Feb 25;131(7):2541–2546. doi: 10.1021/ja805460e

Figure 1. Analysis of RNA tertiary structure using a sequence-encoded cleavage agent.

Figure 1

(A). Intercalation of MPE in a bulged, three base-pair helix to replace four canonical base pairs (gray dashed square) in a helix (red square). MPE preferentially intercalates (solid gray box) such that the Fe(II)-EDTA moiety (dashed circle) is oriented towards the bulged A nucleotide. (B). tRNAAsp secondary structure and MPE binding sites. MPE binding sites are shown using the scheme from panel A. Mutants are numbered by the site nearest to the tethered Fe(II)-EDTA group.