1fzs
From Proteopedia
(New page: 200px<br /><applet load="1fzs" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fzs" /> '''DNA WITH PYRENE PAIRED AT ABASIC SITE'''<br ...) |
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| - | [[Image:1fzs.gif|left|200px]]<br /><applet load="1fzs" size=" | + | [[Image:1fzs.gif|left|200px]]<br /><applet load="1fzs" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1fzs" /> | caption="1fzs" /> | ||
'''DNA WITH PYRENE PAIRED AT ABASIC SITE'''<br /> | '''DNA WITH PYRENE PAIRED AT ABASIC SITE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide | + | DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F), an stable abasic site analog, and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support the hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (P.F pair) at the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site. Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs. The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand, sheltering the hydrophobic pyrene moiety from water exposure. The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson-Crick structure. |
==About this Structure== | ==About this Structure== | ||
| - | 1FZS 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:// | + | 1FZS 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=1FZS OCA]. |
==Reference== | ==Reference== | ||
Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites., Smirnov S, Matray TJ, Kool ET, de los Santos C, Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12490724 12490724] | Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites., Smirnov S, Matray TJ, Kool ET, de los Santos C, Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12490724 12490724] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Kool, E | + | [[Category: Kool, E T.]] |
| - | [[Category: Matray, T | + | [[Category: Matray, T J.]] |
| - | [[Category: Santos, C | + | [[Category: Santos, C de los.]] |
[[Category: Smirnov, S.]] | [[Category: Smirnov, S.]] | ||
[[Category: furan]] | [[Category: furan]] | ||
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[[Category: pyrene]] | [[Category: pyrene]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:44:26 2008'' |
Revision as of 10:44, 21 February 2008
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DNA WITH PYRENE PAIRED AT ABASIC SITE
Overview
DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F), an stable abasic site analog, and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support the hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (P.F pair) at the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site. Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs. The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand, sheltering the hydrophobic pyrene moiety from water exposure. The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson-Crick structure.
About this Structure
1FZS is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites., Smirnov S, Matray TJ, Kool ET, de los Santos C, Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:12490724
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