1gj0
From Proteopedia
(New page: 200px<br /><applet load="1gj0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gj0" /> '''NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINI...) |
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- | [[Image:1gj0.gif|left|200px]]<br /><applet load="1gj0" size=" | + | [[Image:1gj0.gif|left|200px]]<br /><applet load="1gj0" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1gj0" /> | caption="1gj0" /> | ||
'''NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER'''<br /> | '''NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER'''<br /> | ||
==Overview== | ==Overview== | ||
- | The antitumor antibiotic bleomycin causes two major lesions in the | + | The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo. |
==About this Structure== | ==About this Structure== | ||
- | 1GJ0 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:// | + | 1GJ0 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=1GJ0 OCA]. |
==Reference== | ==Reference== | ||
Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation., Hoehn ST, Turner CJ, Stubbe J, Nucleic Acids Res. 2001 Aug 15;29(16):3413-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11504879 11504879] | Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation., Hoehn ST, Turner CJ, Stubbe J, Nucleic Acids Res. 2001 Aug 15;29(16):3413-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11504879 11504879] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
- | [[Category: Hoehn, S | + | [[Category: Hoehn, S T.]] |
[[Category: Stubbe, J.]] | [[Category: Stubbe, J.]] | ||
- | [[Category: Turner, C | + | [[Category: Turner, C J.]] |
[[Category: apyrimidinic site]] | [[Category: apyrimidinic site]] | ||
[[Category: damaged dna]] | [[Category: damaged dna]] | ||
- | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:50:34 2008'' |
Revision as of 10:50, 21 February 2008
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NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER
Overview
The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.
About this Structure
1GJ0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation., Hoehn ST, Turner CJ, Stubbe J, Nucleic Acids Res. 2001 Aug 15;29(16):3413-23. PMID:11504879
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