Volume 84, Issue 4, Pages 2137-2148 (April 2003) Simulating Structural and Thermodynamic Properties of Carcinogen-Damaged DNA  Shixiang Yan, Min Wu, Dinshaw J. Patel, Nicholas E. Geacintov, Suse Broyde  Biophysical Journal  Volume 84, Issue 4, Pages 2137-2148 (April 2003) DOI: 10.1016/S0006-3495(03)75020-6 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 Structures of (A) (+)- and (−)-anti-BPDE and (B) 10S (+)- and 10R (−)-trans-anti -[BP]-N2-dG adducts. Torsion angles α′ and β′ are defined as: α′, N1–C2–N2–C10(BP); β′, C2–N2–C10(BP)–C9(BP). (C) Sequence context in the NMR solution structures (Cosman et al., 1992; de los Santos et al., 1992), where G*6 is the modified guanine. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 2 Root-mean-square deviations (RMSDs) for the 10S (+)-trans-anti-dG adduct (red), 10R (−)-trans-anti-dG adduct (blue), and the unmodified control duplex (green) over the 3-ns production MD simulation. The RMSDs were calculated relative to the starting structures for the 10S (+)- and 10R (−)-trans-anti-dG adducts and the unmodified control duplex, respectively. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 3 Stereo views of the MD average structures for (A) 10S (+)-trans-anti-dG adduct, (B) 10R (−)-trans-anti-dG adduct, and (C) unmodified control duplex over 1.5–3ns. BP is red, G*6 (G6 in the unmodified control) is green, T17 is light green, C5 and C7 are blue, A16 and A18 are light blue, and other residues are gray. The backbone, sugar atoms from C1 to C11 are gray, and those from G12 to G22 are light magenta. All structures are aligned to have 5′-OH at the top left. All stereo images are constructed for viewing with a stereo viewer. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 Differential hydration of BP aromatic moiety in the 10S (+)- and 10R (−)-trans-anti-dG adducts. Stereo views of (A) the d(ATCG*CT)·d(AGCGAT) region of the 10S (+)-trans-anti-dG adduct and (B) the d(TCG*CTA)·d(TAGCGA) region of the 10R (−)-trans-anti-dG adduct with solvent-accessible surfaces of BP. BP is red, G*6 is green, T17 is light green, residues from A3 to A9 are blue, and residues from T14 to T20 are light blue. The backbone and sugar atoms from A3 to A9 are gray, and those from T14 to T20 are light magenta. The solvent-accessible surface of BP is transparent and in light blue. The structures are aligned to have the 5′ residue of the modified strand at top left. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 Key van der Waals contacts between BP aromatic ring system and DNA residues. Stereo views of (A) the d(ATCG*CT)·d(AGCGAT) region of the 10S (+)-trans-anti-dG adduct and (B) the d(TCG*CTA)·d(TAGCGA) region of the 10R (−)-trans-anti-dG adduct with transparent van der Waals surfaces of relevant residues. The color scheme is given in the caption to Fig. 4. The structures are aligned to have the 5′ residue of the modified strand at top left. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 Stereo views of (A) the d(ATCG*CT)·d(AGCGAT) region of the 10S (+)-trans-anti-dG adduct and (B) the d(TCG*CTA)·d(TAGCGA) region of the 10R (−)-trans-anti-dG adduct from the minor groove side. All atoms are in CPK, and the color scheme is given in the caption to Fig. 4. The structures are aligned to have the 5′ residue of the modified strand at top right. Biophysical Journal 2003 84, 2137-2148DOI: (10.1016/S0006-3495(03)75020-6) Copyright © 2003 The Biophysical Society Terms and Conditions