214d: Difference between revisions

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==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.

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==

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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]

[[Category: Protein complex]]

[[Category: Gotfredsen, C.H.]]

[[Category: Gotfredsen, C H.]]

[[Category: Jacobsen, J.P.]]

[[Category: Jacobsen, J P.]]

[[Category: Spielmann, H.P.]]

[[Category: Spielmann, H P.]]

[[Category: Wengel, J.]]

[[Category: dna]]

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[[Category: nmr]]

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@@ Line 4: / Line 4: @@
 ==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.
+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==
@@ Line 12: / Line 12: @@
 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: Gotfredsen, C.H.]]
+[[Category: Gotfredsen, C H.]]
-[[Category: Jacobsen, J.P.]]
+[[Category: Jacobsen, J P.]]
-[[Category: Spielmann, H.P.]]
+[[Category: Spielmann, H P.]]
 [[Category: Wengel, J.]]
 [[Category: dna]]
@@ Line 20: / Line 20: @@
 [[Category: nmr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:47:21 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:20:59 2008''