This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
179d
From Proteopedia
(New page: 200px<br /><applet load="179d" size="450" color="white" frame="true" align="right" spinBox="true" caption="179d" /> '''SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX ...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:179d.jpg|left|200px]]<br /><applet load="179d" size=" | + | [[Image:179d.jpg|left|200px]]<br /><applet load="179d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="179d" /> | caption="179d" /> | ||
'''SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS'''<br /> | '''SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The solution structure of the d(T-C-G-A) sequence at acidic pH has been | + | The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C+ .C (three hydrogen bonds along Watson-Crick edge), G.G (two symmetry related N2-H.. N3 hydrogen bonds) and A.A (two symmetry related N6-H..N7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C+ .C base-pair. All four residues adopt anti glycosidic torsion angles and C2'-endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex. |
==About this Structure== | ==About this Structure== | ||
| - | 179D 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:// | + | 179D 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=179D OCA]. |
==Reference== | ==Reference== | ||
Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs., Wang Y, Patel DJ, J Mol Biol. 1994 Sep 30;242(4):508-26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7932707 7932707] | Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs., Wang Y, Patel DJ, J Mol Biol. 1994 Sep 30;242(4):508-26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7932707 7932707] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
[[Category: Wang, Y.]] | [[Category: Wang, Y.]] | ||
[[Category: dna]] | [[Category: dna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:54 2008'' |
Revision as of 09:38, 21 February 2008
|
SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS
Overview
The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C+ .C (three hydrogen bonds along Watson-Crick edge), G.G (two symmetry related N2-H.. N3 hydrogen bonds) and A.A (two symmetry related N6-H..N7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C+ .C base-pair. All four residues adopt anti glycosidic torsion angles and C2'-endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex.
About this Structure
179D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs., Wang Y, Patel DJ, J Mol Biol. 1994 Sep 30;242(4):508-26. PMID:7932707
Page seeded by OCA on Thu Feb 21 11:38:54 2008
