1d80
From Proteopedia
(New page: 200px<br /><applet load="1d80" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d80, resolution 2.200Å" /> '''CRYSTAL STRUCTURE O...) |
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| - | [[Image:1d80.gif|left|200px]]<br /><applet load="1d80" size=" | + | [[Image:1d80.gif|left|200px]]<br /><applet load="1d80" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d80, resolution 2.200Å" /> | caption="1d80, resolution 2.200Å" /> | ||
'''CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION'''<br /> | '''CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has | + | The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(anti).G(syn) base pairs--i.e., G-4/G-16(anti).G-21/G-9(syn). The Hoogsteen base pairing involves atoms O-6 and N-7 of the guanine in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G.G base pair has a bifurcated hydrogen bond between G-4(N-1)...G-21(N-7) and G-4(N-1)...G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispairing. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The G.G base pairing induces high-BII phosphate conformations at residues G-9 and T-20 in addition to more normal BII conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of G.G mispairs in DNA. |
==About this Structure== | ==About this Structure== | ||
| - | 1D80 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:// | + | 1D80 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=1D80 OCA]. |
==Reference== | ==Reference== | ||
Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation., Skelly JV, Edwards KJ, Jenkins TC, Neidle S, Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):804-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8430089 8430089] | Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation., Skelly JV, Edwards KJ, Jenkins TC, Neidle S, Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):804-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8430089 8430089] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Edwards, K | + | [[Category: Edwards, K J.]] |
| - | [[Category: Jenkins, T | + | [[Category: Jenkins, T C.]] |
[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
| - | [[Category: Skelly, J | + | [[Category: Skelly, J V.]] |
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: mismatched]] | [[Category: mismatched]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:14:00 2008'' |
Revision as of 10:14, 21 February 2008
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CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION
Overview
The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(anti).G(syn) base pairs--i.e., G-4/G-16(anti).G-21/G-9(syn). The Hoogsteen base pairing involves atoms O-6 and N-7 of the guanine in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G.G base pair has a bifurcated hydrogen bond between G-4(N-1)...G-21(N-7) and G-4(N-1)...G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispairing. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The G.G base pairing induces high-BII phosphate conformations at residues G-9 and T-20 in addition to more normal BII conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of G.G mispairs in DNA.
About this Structure
1D80 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation., Skelly JV, Edwards KJ, Jenkins TC, Neidle S, Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):804-8. PMID:8430089
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