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1u6n

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Solution Structure of an Oligodeoxynucleotide Containing a Butadiene Derived N1 b-Hydroxyalkyl Adduct on Deoxyinosine in the Human N-ras Codon 61 Sequence

Structural highlights

1u6n is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The solution structure of the N1-(1-hydroxy-3-buten-2(S)-yl)-2'-deoxyinosine adduct arising from the alkylation of adenine N1 by butadiene epoxide (BDO), followed by deamination to deoxyinosine, was determined, in the oligodeoxynucleotide d(CGGACXAGAAG).d(CTTCTCGTCCG). This oligodeoxynucleotide contained the BDO adduct at the second position of codon 61 of the human N-ras protooncogene, and was named the ras61 S-N1-BDO-(61,2) adduct. (1)H NMR revealed a weak C(5) H1' to X(6) H8 NOE, followed by an intense X(6) H8 to X(6) H1' NOE. Simultaneously, the X(6) H8 to X(6) H3' NOE was weak. The resonance arising from the T(17) imino proton was not observed. (1)H NOEs between the butadiene moiety and the DNA positioned the adduct in the major groove. Structural refinement based upon a total of 364 NOE-derived distance restraints yielded a structure in which the modified deoxyinosine was in the high syn conformation about the glycosyl bond, and T(17), the complementary nucleotide, was stacked into the helix, but not hydrogen bonded with the adducted inosine. The refined structure provided a plausible hypothesis as to why this N1 deoxyinosine adduct strongly coded for the incorporation of dCTP during trans lesion DNA replication, both in Escherichia coli [Rodriguez, D. A., Kowalczyk, A., Ward, J. B. J., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2001) Environ. Mol. Mutagen. 38, 292-296], and in mammalian cells [Kanuri, M., Nechev, L. N., Tamura, P. J., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2002) Chem. Res. Toxicol. 15, 1572-1580]. Rotation of the N1 deoxyinosine adduct into the high syn conformation may facilitate incorporation of dCTP via Hoogsteen-type templating with deoxyinosine, thus generating A-to-G mutations.

Structure of an oligodeoxynucleotide containing a butadiene oxide-derived N1 beta-hydroxyalkyl deoxyinosine adduct in the human N-ras codon 61 sequence.,Scholdberg TA, Merritt WK, Dean SM, Kowalcyzk A, Harris CM, Harris TM, Rizzo CJ, Lloyd RS, Stone MP Biochemistry. 2005 Mar 8;44(9):3327-37. PMID:15736943^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Scholdberg TA, Merritt WK, Dean SM, Kowalcyzk A, Harris CM, Harris TM, Rizzo CJ, Lloyd RS, Stone MP. Structure of an oligodeoxynucleotide containing a butadiene oxide-derived N1 beta-hydroxyalkyl deoxyinosine adduct in the human N-ras codon 61 sequence. Biochemistry. 2005 Mar 8;44(9):3327-37. PMID:15736943 doi:http://dx.doi.org/10.1021/bi0482452

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1u6n"

@@ Line 1: / Line 1: @@
 ==Solution Structure of an Oligodeoxynucleotide Containing a Butadiene Derived N1 b-Hydroxyalkyl Adduct on Deoxyinosine in the Human N-ras Codon 61 Sequence==
-<StructureSection load='1u6n' size='340' side='right' caption='[[1u6n]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1u6n' size='340' side='right'caption='[[1u6n]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1u6n]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U6N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U6N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1u6n]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U6N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U6N FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BD:N1-(1-HYDROXY-3-BUTEN-2(S)-YL)-2-DEOXYINOSINE+MONO+PHOSPHORIC+ACID'>2BD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u6o|1u6o]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2BD:N1-(1-HYDROXY-3-BUTEN-2(S)-YL)-2-DEOXYINOSINE+MONO+PHOSPHORIC+ACID'>2BD</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u6n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u6n RCSB], [http://www.ebi.ac.uk/pdbsum/1u6n PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u6n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u6n OCA], [https://pdbe.org/1u6n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u6n RCSB], [https://www.ebi.ac.uk/pdbsum/1u6n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u6n ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 15: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1u6n" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Dean, S M]]
+[[Category: Large Structures]]
-[[Category: Harris, C M]]
+[[Category: Dean SM]]
-[[Category: Harris, T M]]
+[[Category: Harris CM]]
-[[Category: Kowalcyzk, A]]
+[[Category: Harris TM]]
-[[Category: Lloyd, R S]]
+[[Category: Kowalcyzk A]]
-[[Category: Merritt, W K]]
+[[Category: Lloyd RS]]
-[[Category: Scholdberg, T A]]
+[[Category: Merritt WK]]
-[[Category: Stone, M P]]
+[[Category: Scholdberg TA]]
-[[Category: Butadiene]]
+[[Category: Stone MP]]
-[[Category: Deoxyinosine]]
-[[Category: Dna]]
-[[Category: Ras61]]

1u6n

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Current revision

Solution Structure of an Oligodeoxynucleotide Containing a Butadiene Derived N1 b-Hydroxyalkyl Adduct on Deoxyinosine in the Human N-ras Codon 61 Sequence

Structural highlights

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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