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PDBsum entry 1a9h
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References listed in PDB file
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Key reference
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Title
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Structures of apurinic and apyrimidinic sites in duplex dnas.
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Authors
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R.D.Beger,
P.H.Bolton.
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Ref.
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J Biol Chem, 1998,
273,
15565-15573.
[DOI no: ]
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PubMed id
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Abstract
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Natural and exogenous processes can give rise to abasic sites with either a
purine or pyrimidine as the base on the opposing strand. The solution state
structures of the apyrimidinic DNA duplex, with D6 indicating an abasic site,
referred to as AD, and the apurinic DNA duplex with a dC17,
referred to as CD, have been determined. A particularly striking difference is
that the abasic site in CD is predominantly a beta hemiacetal, whereas in AD the
alpha and beta forms are equally present. Hydrogen bonding with water by the
abasic site and the base on the opposite strand appears to play a large role in
determining the structure near the damaged site. Comparison of these structures
with that of a duplex DNA containing a thymine glycol at the same position as
the abasic site and with that of a duplex DNA containing an abasic site in the
middle of a curved DNA sequence offers some insight into the common and distinct
structural features of damaged DNA sites.
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Figure 7.
Fig. 7. The percentage of the accessible surface area of
residues dT[18] and dC[19] as a function of probe molecule
radius is shown. The percentage accessible surface area is shown
for both forms of AD and both forms of CD.
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Figure 9.
Fig. 9. The structures shown at the top are those of the
 and  forms of AD
with that of the DNA duplex of d(C[1]G[2]
C[3]G[4]A[5]Tg[6]A[7]C[8]G[9]C[10]C[11]) paired with
d(G[12]G[13]C[14]G[15]T[16]A[17]T[18]C[19]G[20]C[21]G[22]), with
Tg indicating thymine glycol shown in the middle. At the bottom
the and structures
of AD are compared along with those of the duplex of d(C[1]G[2]
C[3]A[4]A[5]A[6]A[7]A[8]T[9]G[10]C[11]G[12]) paired with
d(C[13]G[14]C[15]A[16]T[17]T[18]D[19]T[20]T[21]C[22]C[23]G[24]).
Only the central 5 residues of each strand are shown.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
15565-15573)
copyright 1998.
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Headers
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