1d69
From Proteopedia
(New page: 200px<br /><applet load="1d69" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d69" /> '''SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJ...) |
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caption="1d69" /> | caption="1d69" /> | ||
'''SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJACENT G:A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND BII PHOSPHATE GROUPS'''<br /> | '''SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJACENT G:A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND BII PHOSPHATE GROUPS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The solution structure of a rather unusual B-form duplex [d(ATGAGCGAATA)]2 | + | The solution structure of a rather unusual B-form duplex [d(ATGAGCGAATA)]2 has been determined using two-dimensional nuclear magnetic resonance (2D-NMR) and distance geometry methods. This sequence forms a stable ten base-pair B-form duplex with 3' overhangs and two pairs of adjacent G:A mismatches paired via a sheared hydrogen-bonding scheme. All non-exchangeable protons, including the stereo-specific H-5'S/H-5'R of the 3G and 7G residues, were assigned by 2D-NMR. The phosphorus spectrum was assigned using heteronuclear correlation with H-3' and H-4' reasonances. The complete assignments reveal several unusual nuclear Overhauser enhancements (NOEs) and unusual chemical shifts for the neighboring G:A mismatch pairs and their adjacent nucleotides. Inter-proton distances were derived from time-dependent NOEs and used to generate initial structures, which were further refined by iterative back-calculation of the two-dimensional nuclear Overhauser enhancement spectra; 22 final structures were calculated from the refined distance bounds. All these final structures exhibit fully wound helical structures with small penalty values against the refined distance bounds and small pair-wise root-mean-square deviation values (typically 0.5 A to 0.9 A). The two helical strands exchange base stacking at both of the two G:A mismatch sites, resulting in base stacking down each side rather than down each strand of the twisted duplex. Very large twist angles (77 degrees) were found at the G:A mismatch steps. All the final structures were found to have BII phosphate conformations at the adjacent G:A mismatch sites, consistent with observed downfield 31P chemical shifts and Monte-Carlo conformational search results. Our results support the hypothesis that 31P chemical shifts are related to backbone torsion angles. These BII phosphate conformations in the adjacent G:A mismatch step suggest that hydrogen bonding of the G:A pair G-NH2 to a nearby phosphate oxygen atom is unlikely. The unusual structure of the duplex may be stabilized by strong interstrand base stacking as well as intrastrand stacking, as indicated by excellent base overlap within the mismatch stacks. |
==About this Structure== | ==About this Structure== | ||
| - | 1D69 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:// | + | 1D69 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=1D69 OCA]. |
==Reference== | ==Reference== | ||
Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups., Chou SH, Cheng JW, Reid BR, J Mol Biol. 1992 Nov 5;228(1):138-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1447778 1447778] | Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups., Chou SH, Cheng JW, Reid BR, J Mol Biol. 1992 Nov 5;228(1):138-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1447778 1447778] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Cheng, J | + | [[Category: Cheng, J W.]] |
| - | [[Category: Chou, S | + | [[Category: Chou, S H.]] |
| - | [[Category: Reid, B | + | [[Category: Reid, B R.]] |
[[Category: dna]] | [[Category: dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
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[[Category: sheared hydrogen bonding]] | [[Category: sheared hydrogen bonding]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:13:30 2008'' |
Revision as of 10:13, 21 February 2008
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SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJACENT G:A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND BII PHOSPHATE GROUPS
Overview
The solution structure of a rather unusual B-form duplex [d(ATGAGCGAATA)]2 has been determined using two-dimensional nuclear magnetic resonance (2D-NMR) and distance geometry methods. This sequence forms a stable ten base-pair B-form duplex with 3' overhangs and two pairs of adjacent G:A mismatches paired via a sheared hydrogen-bonding scheme. All non-exchangeable protons, including the stereo-specific H-5'S/H-5'R of the 3G and 7G residues, were assigned by 2D-NMR. The phosphorus spectrum was assigned using heteronuclear correlation with H-3' and H-4' reasonances. The complete assignments reveal several unusual nuclear Overhauser enhancements (NOEs) and unusual chemical shifts for the neighboring G:A mismatch pairs and their adjacent nucleotides. Inter-proton distances were derived from time-dependent NOEs and used to generate initial structures, which were further refined by iterative back-calculation of the two-dimensional nuclear Overhauser enhancement spectra; 22 final structures were calculated from the refined distance bounds. All these final structures exhibit fully wound helical structures with small penalty values against the refined distance bounds and small pair-wise root-mean-square deviation values (typically 0.5 A to 0.9 A). The two helical strands exchange base stacking at both of the two G:A mismatch sites, resulting in base stacking down each side rather than down each strand of the twisted duplex. Very large twist angles (77 degrees) were found at the G:A mismatch steps. All the final structures were found to have BII phosphate conformations at the adjacent G:A mismatch sites, consistent with observed downfield 31P chemical shifts and Monte-Carlo conformational search results. Our results support the hypothesis that 31P chemical shifts are related to backbone torsion angles. These BII phosphate conformations in the adjacent G:A mismatch step suggest that hydrogen bonding of the G:A pair G-NH2 to a nearby phosphate oxygen atom is unlikely. The unusual structure of the duplex may be stabilized by strong interstrand base stacking as well as intrastrand stacking, as indicated by excellent base overlap within the mismatch stacks.
About this Structure
1D69 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups., Chou SH, Cheng JW, Reid BR, J Mol Biol. 1992 Nov 5;228(1):138-55. PMID:1447778
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