214d
From Proteopedia
(New page: 200px<br /><applet load="214d" size="350" color="white" frame="true" align="right" spinBox="true" caption="214d" /> '''THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTA...) |
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==Overview== | ==Overview== | ||
| - | Two-dimensional 1H NMR spectroscopy was used to determine the solution | + | Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position. |
==About this Structure== | ==About this Structure== | ||
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Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8950487 8950487] | Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8950487 8950487] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Gotfredsen, C | + | [[Category: Gotfredsen, C H.]] |
| - | [[Category: Jacobsen, J | + | [[Category: Jacobsen, J P.]] |
| - | [[Category: Spielmann, H | + | [[Category: Spielmann, H P.]] |
[[Category: Wengel, J.]] | [[Category: Wengel, J.]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:20:59 2008'' |
Revision as of 14:21, 21 February 2008
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THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT
Overview
Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.
About this Structure
214D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:8950487
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