1b60: Difference between revisions

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[[Image:1b60.gif|left|200px]]<br /><applet load="1b60" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1b60.gif|left|200px]]<br /><applet load="1b60" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1b60" />

'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS'''<br />

==Overview==

Lipid peroxidation products, as well as the metabolic products of vinyl, chloride, react with cellular DNA producing the mutagenic adduct, 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other, exocyclic derivatives. High-resolution NMR spectroscopy and restrained, molecular dynamics simulations were used to establish the solution, structure of an 11-mer duplex containing an epsilondC.dC base-pair at its, center. The NMR data suggested a regular right-handed helical structure, having all residues in the anti orientation around the glycosydic torsion, angle and Watson-Crick alignments for all canonical base-pairs of the, duplex. Restrained molecular dynamics generated a three-dimensional model, in excellent agreement with the spectroscopic data. The (epsilondC., dC)-duplex structure is a regular right-handed helix with a slight bend at, the lesion site and no severe distortions of the sugar-phosphate backbone., The epsilondC adduct and its partner dC were displaced towards opposite, grooves of the helix, resulting in a lesion-containing base-pair that was, highly sheared but stabilized to some degree by the formation of a single, hydrogen bond. Such a sheared base-pair alignment at the lesion site was, previously observed for epsilondC.dG and epsilondC.T duplexes, and was, also present in the crystal structures of duplexes containing dG.T and dG., U mismatches. These observations suggest the existence of a substrate, structural motif that may be recognized by specific DNA glycosylases, during the process of base excision repair.

Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an epsilondC.dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (epsilondC. dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilondC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for epsilondC.dG and epsilondC.T duplexes, and was also present in the crystal structures of duplexes containing dG.T and dG. U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.

==About this Structure==

1B60 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=1B60 OCA].

1B60 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=1B60 OCA].

==Reference==

Line 14:

[[Category: Cullinan, D.]]

[[Category: Johnson, F.]]

[[Category: Santos, C.De.Los.]]

[[Category: Santos, C De Los.]]

[[Category: edc]]

[[Category: ethenodc]]

[[Category: exocyclic lesion]]

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@@ Line 1: / Line 1: @@
-[[Image:1b60.gif|left|200px]]<br /><applet load="1b60" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1b60.gif|left|200px]]<br /><applet load="1b60" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1b60" />
 '''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS'''<br />
 ==Overview==
-Lipid peroxidation products, as well as the metabolic products of vinyl, chloride, react with cellular DNA producing the mutagenic adduct, 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other, exocyclic derivatives. High-resolution NMR spectroscopy and restrained, molecular dynamics simulations were used to establish the solution, structure of an 11-mer duplex containing an epsilondC.dC base-pair at its, center. The NMR data suggested a regular right-handed helical structure, having all residues in the anti orientation around the glycosydic torsion, angle and Watson-Crick alignments for all canonical base-pairs of the, duplex. Restrained molecular dynamics generated a three-dimensional model, in excellent agreement with the spectroscopic data. The (epsilondC., dC)-duplex structure is a regular right-handed helix with a slight bend at, the lesion site and no severe distortions of the sugar-phosphate backbone., The epsilondC adduct and its partner dC were displaced towards opposite, grooves of the helix, resulting in a lesion-containing base-pair that was, highly sheared but stabilized to some degree by the formation of a single, hydrogen bond. Such a sheared base-pair alignment at the lesion site was, previously observed for epsilondC.dG and epsilondC.T duplexes, and was, also present in the crystal structures of duplexes containing dG.T and dG., U mismatches. These observations suggest the existence of a substrate, structural motif that may be recognized by specific DNA glycosylases, during the process of base excision repair.
+Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an epsilondC.dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (epsilondC. dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilondC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for epsilondC.dG and epsilondC.T duplexes, and was also present in the crystal structures of duplexes containing dG.T and dG. U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.
 ==About this Structure==
-B60 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=1B60 OCA].
+B60 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=1B60 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Cullinan, D.]]
 [[Category: Johnson, F.]]
-[[Category: Santos, C.De.Los.]]
+[[Category: Santos, C De Los.]]
 [[Category: edc]]
 [[Category: ethenodc]]
 [[Category: exocyclic lesion]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:46:18 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:52 2008''