2hli

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[[Image:2hli.gif|left|200px]]
 
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==Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence==
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The line below this paragraph, containing "STRUCTURE_2hli", creates the "Structure Box" on the page.
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<StructureSection load='2hli' size='340' side='right'caption='[[2hli]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2hli]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HLI FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KAG:2-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE+5-PHOSPHATE'>KAG</scene></td></tr>
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{{STRUCTURE_2hli| PDB=2hli | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hli OCA], [https://pdbe.org/2hli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hli RCSB], [https://www.ebi.ac.uk/pdbsum/2hli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hli ProSAT]</span></td></tr>
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</table>
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'''Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Cho Y-J]]
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The conformation of the crotonaldehyde-derived N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct in the oligodeoxynucleotide 5'-d(G(1)C(2)T(3)A(4)G(5)C(6)X(7)A(8)G(9)T(10)C(11)C(12))-3'.5'-d(G(13)G(1 4)A(15)C(16)T(17)C(18)G(19)C(20)T(21)A(22)G(23)C(2)(4))-3', where X = N(2)-[3-oxo-1(S)-methyl-propyl]-dG, is reported. This adduct arises from opening of the cyclic N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct when placed opposite dC in duplex DNA. This oligodeoxynucleotide contains the 5'-CpG-3' sequence in which the N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG but not the N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct preferentially formed an interstrand carbinolamine cross-link [Kozekov, I. D., Nechev, L. V., Moseley, M. S., Harris, C. M., Rizzo, C. J., Stone, M. P., and Harris, T. M. (2003) J. Am. Chem. Soc. 125, 50-61; Cho, Y.-J., Wang, H., Kozekov, I. D., Kurtz, A. J., Jacob, J., Voehler, M., Smith, J., Harris, T. M., Lloyd, R. S., Rizzo, C. J., and Stone, M. P. (2006) Chem. Res. Toxicol. 19, 195-208]. Analysis of (1)H NOE data, chemical shift perturbations, and deoxyribose pseudorotations and backbone torsion angles suggested the presence of a stable and ordered DNA conformation at pH 9.3 and 30 degrees C, with minimal conformational perturbation. The spectral line widths of the adduct protons were comparable to those of the oligodeoxynucleotide, suggesting that the correlation times of these protons were similar to those of the overall duplex. The crotonaldehydic-derived methyl protons showed NOEs in the 5'-direction to C(18) H1', G(19) H1', and G(19) H4' in the complementary strand of the duplex. The aldehyde proton of the adduct exhibited NOEs in the 3'-direction to A(8) H1' and A(8) H4' in the modified strand. All of these NOEs involved DNA protons facing the minor groove. Molecular dynamics calculations, restrained by distances and torsion angles derived from the NMR data, revealed that within the minor groove, the aldehyde of the N(2)-[3-oxo-1(S)-methyl-propyl]-dG adduct oriented in the 3'-direction, while the 1(S) methyl group oriented in the 5'-direction. This positioned the aldehyde distal to the G(19) exocyclic amine and provided a rationale as to why the N(2)-(S-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct generated interstrand cross-links less efficiently than did the N(2)-(R-alpha-CH(3)-gamma-OH-1,N(2)-propano-2')-dG adduct.
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[[Category: Harris TM]]
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[[Category: Jacob J]]
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==About this Structure==
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[[Category: Kozekov ID]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HLI OCA].
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[[Category: Kurtz AJ]]
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[[Category: Rizzo CJ]]
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==Reference==
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[[Category: Smith J]]
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Orientation of the crotonaldehyde-derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA adduct hinders interstrand cross-link formation in the 5'-CpG-3' sequence., Cho YJ, Wang H, Kozekov ID, Kozekova A, Kurtz AJ, Jacob J, Voehler M, Smith J, Harris TM, Rizzo CJ, Lloyd RS, Stone MP, Chem Res Toxicol. 2006 Aug;19(8):1019-29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16918240 16918240]
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[[Category: Stone MP]]
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[[Category: Cho, Y J.]]
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[[Category: Voehler M]]
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[[Category: Harris, T M.]]
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[[Category: Wang H]]
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[[Category: Jacob, J.]]
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[[Category: Kozekov, I D.]]
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[[Category: Kurtz, A J.]]
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[[Category: Rizzo, C J.]]
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[[Category: Smith, J.]]
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[[Category: Stone, M P.]]
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[[Category: Voehler, M]]
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[[Category: Wang, H.]]
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[[Category: 5'-cpg-3' sequence]]
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[[Category: Interstrand dna cross-link]]
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[[Category: S-crotonaldehyde-dg adduct]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 06:25:49 2008''
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Current revision

Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence

PDB ID 2hli

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