1 Manuscript # 2004-07-21763A Supplementary Figure Legends Figure captions Figure S1 Structural validation of the trapping strategy and crosslinking biochemistry. a, Close-up view of the intrahelical region surrounding the site of crosslink introduction. The extrahelical active site lies outside this view, to the middle right of each panel. Top left, the original lesion-recognition complex1 used in design of the trapping strategy, with the hydrogen bond highlighted between Asn149 and N4 of the estranged C (refer also to Fig. 1c, left); top right, the trapped complex of hOGG1-QC (this work) with oxoG-containing DNA; and bottom, the trapped complex of N149C-hOGG1 with undamaged DNA (this work). Shown in dark blue in the crosslinked structures is a A-weighted2 Fo-Fc map contoured at 3, leaving out the atoms of the thiol-bearing tether attached to the estranged C (-CH2-CH2S-). The weak density for the hydrocarbon portion of the crosslink is indicative of high local conformational mobility. b, Nonreducing SDS-PAGE gel monitoring progress of disulfide crosslink formation between hOGG1-QC (see text) and DNA presenting oxoG or G to the active site, as a function of time. c, Selectivity in formation of crosslinked complex between N149C hOGG1 and G-containing DNA, as a function of tether length (See Fig. 1c for a structural representation of n). Fig. S2. A weighted2 2Fo-Fc electron density maps contoured at 1 shown around selected atoms of the G-complex in the regions of (a) the extrahelical G and (b) estranged C. The DNA backbone is in gold, G in red, estranged C in magenta, and key residues of the protein in cyan. Density for the His270 side chain at the lower left hand corner of (a) was weak. 2 Fig. S3. Structural representation of the expected interactions between the main-chain carbonyl Gly42 and nucleobases examined in this study. Whereas oxoG is known to hydrogen bond with Gly42, the lone pair of electrons on G engender a repulsive interaction with the lone pairs on Gly42. Neither repulsive nor attractive interactions occur with 7-deazaG or 7-deaza-8-aza-G. Fig. S4. A weighted2 2Fo-Fc maps contoured at 1 around selected atoms of the lesion-recognition pocket in the structures of the (a) 7-deaza-8-azaGcomplex and (b) 7-deazaG-complex (region shown and view similar to righthand panels in Fig. 5). 1. 2. Bruner, S. D., Norman, D. P. & Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 85966 (2000). Read, R. J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 104-149 (1986).