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. Author manuscript; available in PMC: 2011 Oct 19.
Published in final edited form as: Biochemistry. 2010 Oct 19;49(41):8978–8987. doi: 10.1021/bi101021e

Figure 3.

Figure 3

Contour plot of expanded phase-sensitive NOESY spectra (260ms mixing time) recorded in D2O buffer containing 50mM NaCl, 10mM phosphate and 1mM EDTA at pH 6.8 at 25° C. Cross peak connectivity between base protons (7.0–8.4 ppm) and sugar H2’/2” protons (3.0-1.8 ppm) are plotted for the (AP)2−3 duplex (Figure 3) and (AP)2+3 duplex (Figure 3). (Figure 3) Peaks A/A’-P/P’ in the (AP)2−3 duplex are discussed in the text and are assigned as follows: A/A’, A24(H8)-A24(H2”)/A24(H2’); B/B’ A24(H8)-F23(H2”)/F23(H2’); C/C’, A22(H8)-A22(H2’)/A22(H2”); D/D’, G8(H8)-G8(H2’)/G8(H2”); E, G10(H6)-F9(H2”/H2’); F/F’, G10(H8)-G10(H2”)/G10(H2’); G/G’, T5(H6)-T5(H2”)/T5(H2’); H/H’, A6(H8)-T5(H2”)/T5(H2’); I/I’, A6(H8)-A6(H2”)/A6(H2’); J/J’, T7(H8)- A6(H2”)/A6(H2’); K/K’, C19(H6)-C19(H2”)/C19(H2’); L/L’, A20(H8)-C19(H2”)C19(H2’); M/M’, A20(H8)-A20(H2”)/A20(H2’); N/N’, C21(H6)-A20(H2”)/A20(H2’); O, F9(H3’)-F9(H2’/2”) and P/P’, F23(H3’)-F23(H2’)/F23(H2”). These peaks together confirm that both AP residues of the (AP)2−3 duplex are inside the helix at the lesion site. (Figure 3) Peaks A/A’-P in the (AP)2+3 duplex are discussed in the text and are assigned as follows: A/A’, A21(H8)-A21(H2”)/A18(H2’); B/B’, A19(H8)-A19(H2”)/A19(H2’); C, A21(H8)-F20(H2’/2”); D/D’, G7(H8)-G7(H2”)/G7(H2’); E/E’, G5(H8)-G5(H2”)/G5(H2’); F, G7(H8)-F6(H2’/2”); G/G’; A23(H8)-A23(H2”)/A23(H2’); H/H’, A23(H8)-C22(H2”)/C22(H2’); I/I’, C22(H6)-C22(H2”)/C22(H2’); J/J’, C24(H6)-A23(H2”)/A23(H2’); K/K’, A9(H8)-A9(H2”)/A9(H2’); L/L’, A9(H8)-T8(H2”)/T8(H2’); M/M’, T8(H6)-T8(H2”)/T8(H2’); N/N’, T10(H6)-A9(H2”)/A9(H2’); O, F6(H3’)-F6(H2’/2”) and P, F20(H3’)-F20(H2’/2”). The presence of these cross peaks indicate that the AP residues in the (AP)2+3 duplex are also inside the helix at the lesion site.