171d: Difference between revisions

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-[[Image:171d.gif|left|200px]]<br /><applet load="171d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:171d.gif|left|200px]]<br /><applet load="171d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="171d" />
 '''SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT'''<br />
 ==Overview==
-The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT), (araC)d(GCG)]2 was examined by comparing its nuclear magnetic resonance, (NMR)-determined solution structure with that of the control duplex, d[(CGCGAATTCGCG)]2. 1H and 31P resonances in both duplexes were assigned, using a combination of 2-D 1H NMR and a 3-D 31P-1H heteroTOCSY-NOESY, experiment. Proton-proton distances (determined from NOESY data) and sugar, dihedral angles (from NOESY and COSY data) were used in restrained, molecular dynamics simulations starting from canonical A- or B-form DNA, models. Both the control and araC sets of simulations converged to B-type, structures. These structures were subjected to full relaxation matrix, refinement to produce final structures which were in excellent agreement, (R1/6 &lt; 0.05) with the observed NOE intensities. A detailed comparison of, the final control and araC structures revealed a global similarity, (overall RMSD approximately 1.3 A), with significant differences localized, at the araC site and neighboring bases. These included changes in sugar, pucker, backbone torsion angles, base stacking, and other helical, parameters. These findings are in general agreement with the previously, published X-ray structure of a decamer duplex containing araC. One, intriguing feature of the NMR solution structure not found in the crystal, structure is the presence of an intramolecular hydrogen bond between the, 2' hydroxyl on the araC sugar and the 3' phosphate group.
+The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT) (araC)d(GCG)]2 was examined by comparing its nuclear magnetic resonance (NMR)-determined solution structure with that of the control duplex d[(CGCGAATTCGCG)]2. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H NMR and a 3-D 31P-1H heteroTOCSY-NOESY experiment. Proton-proton distances (determined from NOESY data) and sugar dihedral angles (from NOESY and COSY data) were used in restrained molecular dynamics simulations starting from canonical A- or B-form DNA models. Both the control and araC sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures which were in excellent agreement (R1/6 &lt; 0.05) with the observed NOE intensities. A detailed comparison of the final control and araC structures revealed a global similarity (overall RMSD approximately 1.3 A), with significant differences localized at the araC site and neighboring bases. These included changes in sugar pucker, backbone torsion angles, base stacking, and other helical parameters. These findings are in general agreement with the previously published X-ray structure of a decamer duplex containing araC. One intriguing feature of the NMR solution structure not found in the crystal structure is the presence of an intramolecular hydrogen bond between the 2' hydroxyl on the araC sugar and the 3' phosphate group.
 ==About this Structure==
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=171D OCA].
+D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=171D OCA].
 ==Reference==
 Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Schweitzer BI, Mikita T, Kellogg GW, Gardner KH, Beardsley GP, Biochemistry. 1994 Sep 27;33(38):11460-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7918360 7918360]
 [[Category: Protein complex]]
-[[Category: Beardsley, G.P.]]
+[[Category: Beardsley, G P.]]
-[[Category: Gardner, K.H.]]
+[[Category: Gardner, K H.]]
-[[Category: Kellogg, G.W.]]
+[[Category: Kellogg, G W.]]
 [[Category: Mikita, T.]]
-[[Category: Schweitzer, B.I.]]
+[[Category: Schweitzer, B I.]]
 [[Category: anti-neoplastic]]
 [[Category: arabinosylcytosine]]
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 [[Category: nmr]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:04:18 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:44 2008''