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PDBsum entry 1n8c
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References listed in PDB file
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Key reference
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Title
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Solution structure of a cis-Opened (10r)-N6-Deoxyadenosine adduct of (9s,10r)-9,10-Epoxy-7,8,9,10-Tetrahydrobenzo[a]pyrene in a DNA duplex.
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Authors
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D.E.Volk,
V.Thiviyanathan,
J.S.Rice,
B.A.Luxon,
J.H.Shah,
H.Yagi,
J.M.Sayer,
H.J.Yeh,
D.M.Jerina,
D.G.Gorenstein.
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Ref.
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Biochemistry, 2003,
42,
1410-1420.
[DOI no: ]
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PubMed id
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Abstract
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The solution structure of an 11-mer DNA duplex, d(CGGTCA*CGAGG) x
d(CCTCGTGACCG), containing a 10R adduct at dA* that corresponds to the cis
addition of the N(6)-amino group of dA(6) to
(+)-(9S,10R)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene was studied by 2D NMR
methods. The NOESY cross-peak patterns indicate that the hydrocarbon is
intercalated on the 5'-side of the modified base. This observation is the same
as that observed for other oligonucleotides containing (10R)-dA adducts but
opposite to that observed for the corresponding (10S)-dA adducts which are
intercalated on the 3'-side of the modified base. The hydrocarbon is
intercalated from the major groove without significant disruption of either the
anti glycosidic torsion angle of the modified residue or the base pairing of the
modified residue with the complementary residue on the opposite strand. The
ensemble of 10 structures determined exhibits relatively small variations (6-15
degrees) in the characteristic hydrocarbon-base dihedral angles (alpha' and
beta') as well as the glycosidic torsion angle chi. These angles are similar to
those in a previously determined cis-opened benzo[a]pyrene diol epoxide-(10R)-dA
adduct structure. Comparison of the present structure with the cis-opened diol
epoxide adduct suggests that the absence of the 7- and 8-hydroxyl groups results
in more efficient stacking of the aromatic moiety with the flanking base pairs
and deeper insertion of the hydrocarbon into the helix. Relative to normal
B-DNA, the duplex containing the present tetrahydroepoxide adduct is unwound at
the lesion site, whereas the diol epoxide adduct structure is more tightly wound
than normal B-DNA. Buckling of the adducted base pair as well as the C(5)-G(18)
base pair that lies immediately above the hydrocarbon is much less severe in the
present adducted structure than its cis-opened diol epoxide counterpart.
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Headers
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