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1k29

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{{STRUCTURE_1k29| PDB=1k29 | SCENE= }}
{{STRUCTURE_1k29| PDB=1k29 | SCENE= }}
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'''Solution Structure of a DNA Duplex Containing M1G Opposite a 2 Base Pair Deletion'''
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===Solution Structure of a DNA Duplex Containing M1G Opposite a 2 Base Pair Deletion===
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==Overview==
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The pyrimidopurinone adduct M1G [3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]-purin-10(3H)-on e], formed in DNA upon exposure to malondialdehyde or base propenals, was incorporated into 5'-d(ATCGCMCGGCATG)-3'-5'-d(CATGCCGCGAT)-3', where M = M1G. This duplex contained a two-nucleotide bulge in the modified strand, and was named the M1G-2BD oligodeoxynucleotide. It provided a model for -2 bp strand slippage deletions associated with the (CpG)3-iterated repeat hotspot for frameshift mutations from the Salmonella typhimurium hisD3052 gene. M1G was chemically stable in the M1G-2BD duplex at neutral pH. The two-base bulge in the M1G-2BD oligodeoxynucleotide was localized and consisted of M1G and the 3'-neighbor deoxycytosine. The intrahelical orientation of M1G was established from a combination of NOE and chemical shift data. M1G was in the anti conformation about the glycosyl bond. The 3'-neighbor deoxycytosine appeared to be extruded toward the major groove. In contrast, when M1G was placed into the corresponding fully complementary (CpG)3-iterated repeat duplex at neutral pH, spontaneous and quantitative ring-opening to N(2)-(3-oxo-1-propenyl)-dG (the OPG adduct) was facilitated [Mao, H., Reddy, G. R., Marnett, L. J., and Stone, M. P. (1999) Biochemistry 38, 13491-13501]. The structure of the M1G-2BD duplex suggested that the bulged sequence lacked a cytosine amino group properly positioned to facilitate opening of M1G and supports the notion that proper positioning of deoxycytosine complementary to M1G is necessary to promote ring-opening of the exocyclic adduct in duplex DNA. The structure of the M1G-2BD duplex was similar to that of the structural analogue 1,N(2)-propanodeoxyguanosine (PdG) in the corresponding PdG-2BD duplex [Weisenseel, J. P., Moe, J. G., Reddy, G. R., Marnett, L. J., and Stone, M. P. (1995) Biochemistry 34, 50-64]. The fixed position of the bulged bases in both instances suggests that these exocyclic adducts do not facilitate transient bulge migration.
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(as it appears on PubMed at http://www.pubmed.gov), where 11747439 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11747439}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K29 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K29 OCA].
==Reference==
==Reference==
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[[Category: Malondialdehyde]]
[[Category: Malondialdehyde]]
[[Category: Two base deletion]]
[[Category: Two base deletion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:12:40 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 21:25:45 2008''

Revision as of 18:25, 1 July 2008

Image:1k29.png

Template:STRUCTURE 1k29

Solution Structure of a DNA Duplex Containing M1G Opposite a 2 Base Pair Deletion

Template:ABSTRACT PUBMED 11747439

About this Structure

Full experimental information is available from OCA.

Reference

The exocyclic 1,N2-deoxyguanosine pyrimidopurinone M1G is a chemically stable DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene., Schnetz-Boutaud NC, Saleh S, Marnett LJ, Stone MP, Biochemistry. 2001 Dec 25;40(51):15638-49. PMID:11747439

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