1fv8
From Proteopedia
(New page: 200px<br /><applet load="1fv8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fv8" /> '''NMR STUDY OF AN HETEROCHIRAL HAIRPIN'''<br /...) |
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| - | [[Image:1fv8.gif|left|200px]]<br /><applet load="1fv8" size=" | + | [[Image:1fv8.gif|left|200px]]<br /><applet load="1fv8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1fv8" /> | caption="1fv8" /> | ||
'''NMR STUDY OF AN HETEROCHIRAL HAIRPIN'''<br /> | '''NMR STUDY OF AN HETEROCHIRAL HAIRPIN'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We carried out a structural study of the DNA heterochiral strand d | + | We carried out a structural study of the DNA heterochiral strand d (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine ) replaces T (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs to a strong topoisomerase II DNA cleavage site and which has been shown to resolve into a hairpin structure with a stem formed by eight Waston-Crick base-pairs and a single residue loop closed by an A.C sheared base-pair. Although - AT(L)C-, like its parent -ATC-, folds into a hairpin structure at low and high DNA concentrations it displays a lower stability (Tm of 56 degrees C versus 58.5 degrees C). Several NMR features in -AT(L)C- account for the disruption of the A.C pairing in the loop and a weakening of the C.G base-pair stability at the stem-loop junction. For instance, the exchange of the loop imino protons with solvent is accelerated compared with the natural oligonucleotide -ATC-. The higher flexibility of the heterochiral loop is confirmed by the results of NMR restrained molecular dynamics. In the calculated final structures of -AT(L)C-, the T10(L) residue moves the A9 and C11 residues away, thus preventing the loop closure through a C.A sheared base-pair and the achievement of a good base-base or sugar-base stacking. Actually, most of the stabilizing interactions present in -ATC- are lost in the heterochiral - AT(L)C- explaining its weaker stability. |
==About this Structure== | ==About this Structure== | ||
| - | 1FV8 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:// | + | 1FV8 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=1FV8 OCA]. |
==Reference== | ==Reference== | ||
NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop., El Amri C, Mauffret O, Santamariar F, Tevanian G, Rayner S, Fermandjian S, J Biomol Struct Dyn. 2001 Dec;19(3):459-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11790144 11790144] | NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop., El Amri C, Mauffret O, Santamariar F, Tevanian G, Rayner S, Fermandjian S, J Biomol Struct Dyn. 2001 Dec;19(3):459-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11790144 11790144] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Amri, C | + | [[Category: Amri, C El.]] |
[[Category: Fermandjian, S.]] | [[Category: Fermandjian, S.]] | ||
[[Category: Mauffret, O.]] | [[Category: Mauffret, O.]] | ||
| Line 22: | Line 22: | ||
[[Category: heterochiral loop]] | [[Category: heterochiral loop]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:43:01 2008'' |
Revision as of 10:43, 21 February 2008
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NMR STUDY OF AN HETEROCHIRAL HAIRPIN
Overview
We carried out a structural study of the DNA heterochiral strand d (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine ) replaces T (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs to a strong topoisomerase II DNA cleavage site and which has been shown to resolve into a hairpin structure with a stem formed by eight Waston-Crick base-pairs and a single residue loop closed by an A.C sheared base-pair. Although - AT(L)C-, like its parent -ATC-, folds into a hairpin structure at low and high DNA concentrations it displays a lower stability (Tm of 56 degrees C versus 58.5 degrees C). Several NMR features in -AT(L)C- account for the disruption of the A.C pairing in the loop and a weakening of the C.G base-pair stability at the stem-loop junction. For instance, the exchange of the loop imino protons with solvent is accelerated compared with the natural oligonucleotide -ATC-. The higher flexibility of the heterochiral loop is confirmed by the results of NMR restrained molecular dynamics. In the calculated final structures of -AT(L)C-, the T10(L) residue moves the A9 and C11 residues away, thus preventing the loop closure through a C.A sheared base-pair and the achievement of a good base-base or sugar-base stacking. Actually, most of the stabilizing interactions present in -ATC- are lost in the heterochiral - AT(L)C- explaining its weaker stability.
About this Structure
1FV8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR study of a heterochiral DNA hairpin:impact of L-enantiomery in the loop., El Amri C, Mauffret O, Santamariar F, Tevanian G, Rayner S, Fermandjian S, J Biomol Struct Dyn. 2001 Dec;19(3):459-70. PMID:11790144
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