Figure 3.
Fig. 3. Distortion of DNA by the BPDE adduct. (A)
Comparison of the crystal and NMR structures. The dA*·dT
and the surrounding base pairs including the replicating base
pair are shown as ball-and-stick models. The crystal structures
are shown with the F[o] - F[c] omit electron density maps
contoured at 1.0 in blue. The carbon,
oxygen, nitrogen, and phosphorus atoms are colored yellow, red,
blue, and purple, respectively. (B) Hydrogen bond formation at
dA*·dT and the adjacent replicating base pair
dT·dATP. Looking down the DNA helical axis, the two
layers of the base pair and the PAH adduct are shown, purple for
the replicating base pair, gold for the dA* adduct, and green
for its partner dT. The incoming nucleotide in BP-1 is in the
syn conformation. In the BP-2 complex, where the PAH is in the
major groove, the adenine base of the dA* is shifted to the
major groove, disrupting the normal hydrogen bonds with its
partner, dT. The location of a normal dA is modeled in gray. (C)
Stereo view of the overlay of the DNA structures from BP-1
(blue) and BP-2 (gold) after superimposition of the Dpo4
structures. With the PAH intercalated, the base pair ladder in
the BP-1 complex is shifted by one register compared with that
in the BP-2 complex.
in blue. The carbon,
oxygen, nitrogen, and phosphorus atoms are colored yellow, red,
blue, and purple, respectively. (B) Hydrogen bond formation at
dA*·dT and the adjacent replicating base pair
dT·dATP. Looking down the DNA helical axis, the two
layers of the base pair and the PAH adduct are shown, purple for
the replicating base pair, gold for the dA* adduct, and green
for its partner dT. The incoming nucleotide in BP-1 is in the
syn conformation. In the BP-2 complex, where the PAH is in the
major groove, the adenine base of the dA* is shifted to the
major groove, disrupting the normal hydrogen bonds with its
partner, dT. The location of a normal dA is modeled in gray. (C)
Stereo view of the overlay of the DNA structures from BP-1
(blue) and BP-2 (gold) after superimposition of the Dpo4
structures. With the PAH intercalated, the base pair ladder in
the BP-1 complex is shifted by one register compared with that
in the BP-2 complex.