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PDBsum entry 152d
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DOI no:
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Biochemistry
33:3649-3659
(1994)
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PubMed id:
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Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes.
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L.A.Lipscomb,
M.E.Peek,
F.X.Zhou,
J.A.Bertrand,
D.VanDerveer,
L.D.Williams.
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ABSTRACT
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In crystallographic structures of biological macromolecules, one can observe
many hydration rings that originate at one water molecule, pass via hydrogen
bonds through several others, and return to the original water molecule.
Five-membered water rings have been thought to occur with greater frequency than
other ring sizes. We describe a quantitative assessment of relationships between
water ring size and frequency of occurrence in the vicinity of nucleic acid
interfaces. This report focuses on low-temperature X-ray crystallographic
structures of two anthracyclines, adriamycin (ADRI) and daunomycin (DAUN), bound
to d(CGATCG) and on several DNA structures published previously by others. We
have obtained excellent low-temperature (-160 degrees C, LT) X-ray intensity
data for d(CGATCG)-adriamycin and d(CGATCG)-daunomycin with a multiwire area
detector. The LTX-ray data sets contain 20% (daunomycin, LT-DAUN) and 35%
(adriamycin, LT-ADRI) more reflections than were used to derive the original
room-temperature (15 degrees C) structures [Frederick, C.A., Williams, L.D.,
Ughetto, G., van der Marel, G. A., van Boom, J.H., Rich, A., & Wang, A.H.-J.
(1990) Biochemistry 29, 2538-2549]. The results show that five-membered water
rings are not preferred over other ring sizes. This assessment is consistent
with our observation of broad dispersion W-W-W angles (sigma = 20 degrees). In
addition, we report that the thermal mobility, distinct from the static
disorder, of the amino sugar of daunomycin and adriamycin is significantly
greater than that of the rest of the complex. This mobility implies that if the
central AT base pair is switched to a CG base pair, there should be a low energy
cost in avoiding the guanine amino group. The energy difference (for the
sugar-binding preference) between d(CGTACG) and d(CGCGCG) could be considerably
less than 20 kcal/mol, a value proposed previously from computation.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.Z.Akhter,
A.Sharma,
and
M.R.Rajeswari
(2011).
Interaction of adriamycin with a promoter region of hmga1 and its inhibitory effect on HMGA1 expression in A431 human squamous carcinoma cell line.
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Mol Biosyst,
7,
1336-1346.
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M.Shin,
H.Matsunaga,
and
K.Fujiwara
(2010).
Differences in accumulation of anthracyclines daunorubicin, doxorubicin and epirubicin in rat tissues revealed by immunocytochemistry.
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Histochem Cell Biol,
133,
677-682.
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H.Yu,
J.Ren,
J.B.Chaires,
and
X.Qu
(2008).
Hydration of drug-DNA complexes: greater water uptake for adriamycin compared to daunomycin.
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J Med Chem,
51,
5909-5911.
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X.Li,
D.T.Moore,
and
S.S.Iyengar
(2008).
Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: case study of the proton-bound dimethyl ether dimer.
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J Chem Phys,
128,
184308.
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S.Komorsky-Lovrić
(2006).
Redox kinetics of adriamycin adsorbed on the surface of graphite and mercury electrodes.
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Bioelectrochemistry,
69,
82-87.
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L.M.Tumir,
I.Piantanida,
I.Juranović,
Z.Meić,
S.Tomić,
and
M.Zinić
(2005).
Recognition of homo-polynucleotides containing adenine by a phenanthridinium bis-uracil conjugate in aqueous media.
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Chem Commun (Camb),
(),
2561-2563.
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S.B.Howerton,
A.Nagpal,
and
L.D.Williams
(2003).
Surprising roles of electrostatic interactions in DNA-ligand complexes.
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Biopolymers,
69,
87-99.
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PDB code:
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Y.Razskazovskiy,
M.G.Debije,
and
W.A.Bernhard
(2000).
Direct radiation damage to crystalline DNA: what is the source of unaltered base release?
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Radiat Res,
153,
436-441.
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J.Barciszewski,
J.Jurczak,
S.Porowski,
T.Specht,
and
V.A.Erdmann
(1999).
The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions.
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Eur J Biochem,
260,
293-307.
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X.Shui,
L.McFail-Isom,
G.G.Hu,
and
L.D.Williams
(1998).
The B-DNA dodecamer at high resolution reveals a spine of water on sodium.
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Biochemistry,
37,
8341-8355.
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PDB code:
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G.G.Hu,
X.Shui,
F.Leng,
W.Priebe,
J.B.Chaires,
and
L.D.Williams
(1997).
Structure of a DNA-bisdaunomycin complex.
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Biochemistry,
36,
5940-5946.
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PDB code:
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L.A.Lipscomb,
F.X.Zhou,
and
L.D.Williams
(1996).
Clathrate hydrates are poor models of biomolecule hydration.
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Biopolymers,
38,
177-181.
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M.C.Wahl,
S.T.Rao,
and
M.Sundaralingam
(1996).
Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition.
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Biophys J,
70,
2857-2866.
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PDB code:
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M.C.Wahl,
and
M.Sundaralingam
(1995).
New crystal structures of nucleic acids and their complexes.
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Curr Opin Struct Biol,
5,
282-295.
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M.Kochoyan,
and
J.L.Leroy
(1995).
Hydration and solution structure of nucleic acids.
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Curr Opin Struct Biol,
5,
329-333.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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