1wan
From Proteopedia
(New page: 200px<br /><applet load="1wan" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wan" /> '''DNA DTA TRIPLEX, NMR, 7 STRUCTURES'''<br /> ...) |
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| - | [[Image:1wan.gif|left|200px]]<br /><applet load="1wan" size=" | + | [[Image:1wan.gif|left|200px]]<br /><applet load="1wan" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wan" /> | caption="1wan" /> | ||
'''DNA DTA TRIPLEX, NMR, 7 STRUCTURES'''<br /> | '''DNA DTA TRIPLEX, NMR, 7 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have used NMR spectroscopy to study a pyrimidine-purine-pyrimidine DNA | + | We have used NMR spectroscopy to study a pyrimidine-purine-pyrimidine DNA triplex containing a non-natural base, 1-(2-deoxy-beta-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole (D3), in the third strand. The D3 base has been previously shown to specifically recognize T-A and C-G base-pairs via intercalation on the 3' side (with respect to the purine strand) of the target base pair, instead of forming sequence-specific hydrogen bonds. 1H resonance assignments have been made for the D3 base and most of the non-loop portion of the triplex. The solution structure of the triplex was calculated using restrained molecular dynamics and complete relaxation matrix refinement. The duplex portion of the triplex has an over-all helical structure that is more similar to B-DNA than to A-DNA. The three aromatic rings of the D3 base stack on the bases of all three strands and mimic a triplet. The conformation of the D3 base and its sequence specificity are discussed. |
==About this Structure== | ==About this Structure== | ||
| - | 1WAN 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:// | + | 1WAN 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=1WAN OCA]. |
==Reference== | ==Reference== | ||
Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3., Wang E, Koshlap KM, Gillespie P, Dervan PB, Feigon J, J Mol Biol. 1996 Apr 19;257(5):1052-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8632468 8632468] | Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3., Wang E, Koshlap KM, Gillespie P, Dervan PB, Feigon J, J Mol Biol. 1996 Apr 19;257(5):1052-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8632468 8632468] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Dervan, P | + | [[Category: Dervan, P B.]] |
[[Category: Feigon, J.]] | [[Category: Feigon, J.]] | ||
[[Category: Gillespie, P.]] | [[Category: Gillespie, P.]] | ||
| - | [[Category: Koshlap, K | + | [[Category: Koshlap, K M.]] |
[[Category: Wang, E.]] | [[Category: Wang, E.]] | ||
[[Category: deoxyribonucleic acid]] | [[Category: deoxyribonucleic acid]] | ||
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[[Category: triplex]] | [[Category: triplex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:42:13 2008'' |
Revision as of 13:42, 21 February 2008
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DNA DTA TRIPLEX, NMR, 7 STRUCTURES
Overview
We have used NMR spectroscopy to study a pyrimidine-purine-pyrimidine DNA triplex containing a non-natural base, 1-(2-deoxy-beta-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole (D3), in the third strand. The D3 base has been previously shown to specifically recognize T-A and C-G base-pairs via intercalation on the 3' side (with respect to the purine strand) of the target base pair, instead of forming sequence-specific hydrogen bonds. 1H resonance assignments have been made for the D3 base and most of the non-loop portion of the triplex. The solution structure of the triplex was calculated using restrained molecular dynamics and complete relaxation matrix refinement. The duplex portion of the triplex has an over-all helical structure that is more similar to B-DNA than to A-DNA. The three aromatic rings of the D3 base stack on the bases of all three strands and mimic a triplet. The conformation of the D3 base and its sequence specificity are discussed.
About this Structure
1WAN is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3., Wang E, Koshlap KM, Gillespie P, Dervan PB, Feigon J, J Mol Biol. 1996 Apr 19;257(5):1052-69. PMID:8632468
Page seeded by OCA on Thu Feb 21 15:42:13 2008
