1dk9: Difference between revisions

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[[Image:1dk9.gif|left|200px]]<br /><applet load="1dk9" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1dk9.gif|left|200px]]<br /><applet load="1dk9" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1dk9" />

'''SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)'''<br />

==Overview==

The three-dimensional structures of two DNA duplexes d(CATGAGTAC)., d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high, resolution nuclear magnetic resonance spectroscopy and restrained, molecular dynamics. Good convergence was observed between final structures, derived from A- and B-form starting geometries for both 1 and 2., Structures of 1 and 2 are right-handed duplexes within the B-form, conformational regime. Furthermore, the structures of 1 and 2 are highly, similar, with differences in the structures localized to the vicinity of, residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation, and it is displaced towards the major groove. Furthermore, unlike T14 in, 2, the base of X14 has reduced pi-pi stacking interactions with C13 and, C15 and the nitro group of X14 is pointing out of the major groove. The, structures presented here establish the basis of the thermal data of DNA, duplexes containing X and should be informative during the design of, improved wild card nucleobase analogs.

The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs.

==About this Structure==

1DK9 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=1DK9 OCA].

1DK9 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=1DK9 OCA].

==Reference==

NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control., Klewer DA, Hoskins A, Zhang P, Davisson VJ, Bergstrom DE, LiWang AC, Nucleic Acids Res. 2000 Nov 15;28(22):4514-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11071940 11071940]

[[Category: Protein complex]]

[[Category: Bergstrom, D.E.]]

[[Category: Bergstrom, D E.]]

[[Category: Davisson, V.J.]]

[[Category: Davisson, V J.]]

[[Category: Hoskins, A.]]

[[Category: Klewer, D.A.]]

[[Category: Klewer, D A.]]

[[Category: LiWang, A.C.]]

[[Category: LiWang, A C.]]

[[Category: dna]]

[[Category: duplex]]

Line 22:

[[Category: structure]]

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@@ Line 1: / Line 1: @@
-[[Image:1dk9.gif|left|200px]]<br /><applet load="1dk9" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dk9.gif|left|200px]]<br /><applet load="1dk9" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dk9" />
 '''SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)'''<br />
 ==Overview==
-The three-dimensional structures of two DNA duplexes d(CATGAGTAC)., d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high, resolution nuclear magnetic resonance spectroscopy and restrained, molecular dynamics. Good convergence was observed between final structures, derived from A- and B-form starting geometries for both 1 and 2., Structures of 1 and 2 are right-handed duplexes within the B-form, conformational regime. Furthermore, the structures of 1 and 2 are highly, similar, with differences in the structures localized to the vicinity of, residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation, and it is displaced towards the major groove. Furthermore, unlike T14 in, 2, the base of X14 has reduced pi-pi stacking interactions with C13 and, C15 and the nitro group of X14 is pointing out of the major groove. The, structures presented here establish the basis of the thermal data of DNA, duplexes containing X and should be informative during the design of, improved wild card nucleobase analogs.
+The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs.
 ==About this Structure==
-DK9 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=1DK9 OCA].
+DK9 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=1DK9 OCA].
 ==Reference==
 NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control., Klewer DA, Hoskins A, Zhang P, Davisson VJ, Bergstrom DE, LiWang AC, Nucleic Acids Res. 2000 Nov 15;28(22):4514-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11071940 11071940]
 [[Category: Protein complex]]
-[[Category: Bergstrom, D.E.]]
+[[Category: Bergstrom, D E.]]
-[[Category: Davisson, V.J.]]
+[[Category: Davisson, V J.]]
 [[Category: Hoskins, A.]]
-[[Category: Klewer, D.A.]]
+[[Category: Klewer, D A.]]
-[[Category: LiWang, A.C.]]
+[[Category: LiWang, A C.]]
 [[Category: dna]]
 [[Category: duplex]]
@@ Line 22: / Line 22: @@
 [[Category: structure]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:14:33 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:26 2008''