Environmental mutagens are strong inducers of carcinogenesis and can cause DNA damage including single- and double strand breaks, DNA cross-links and DNA-adduct formation. DNA adducts formed by aromatic amines including 2-aminofluorene (AF) and 4-aminobiphenyl (ABP) can adopt one or two out of three distinct conformations: B-type (B), stacked (S) or wedge (W), related to the extent of opening of the base out of the DNA duplex. Notably, AF and ABP can assume either S or B conformations and the sampling of these states is dependent on sequence context. To obtain structural insight into this sequence-dependent phenomena, we have conducted potential of mean force calculations using molecular dynamics simulations of 11-mer 5’-CCATCG∗CXACC-3’ duplexes with varying sequences, where X=A, T, C or G and G∗=fluorine labeled-ABP or -AF. The analyses of the 15ns trajectories indicate that the stacking of adduct is greater in G∗CT than G∗CA. Calculated free energy of G∗ base flipping shows the presence of the second minima of the pseudo-dihedral angle at ∼120°, which corresponds to the S conformer, though the ratio of S/B conformation is less than experimentally detected. Additional analyses are underway to try to better understand the mechanism of S/B conformational equilibrium and the impact of adduct-induced conformational heterogeneity on the stability of S/B conformations.