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149d

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[[Image:149d.gif|left|200px]]
[[Image:149d.gif|left|200px]]
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{{Structure
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|PDB= 149d |SIZE=350|CAPTION= <scene name='initialview01'>149d</scene>
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The line below this paragraph, containing "STRUCTURE_149d", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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|GENE=
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|DOMAIN=
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{{STRUCTURE_149d| PDB=149d | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=149d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=149d OCA], [http://www.ebi.ac.uk/pdbsum/149d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=149d RCSB]</span>
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'''SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES'''
'''SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES'''
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==About this Structure==
==About this Structure==
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149D is a [[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=149D OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=149D OCA].
==Reference==
==Reference==
Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples., Radhakrishnan I, Patel DJ, Structure. 1994 Jan 15;2(1):17-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8075980 8075980]
Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples., Radhakrishnan I, Patel DJ, Structure. 1994 Jan 15;2(1):17-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8075980 8075980]
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[[Category: Protein complex]]
 
[[Category: Patel, D J.]]
[[Category: Patel, D J.]]
[[Category: Radhakrishnan, I.]]
[[Category: Radhakrishnan, I.]]
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[[Category: dna]]
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[[Category: Dna]]
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[[Category: nmr]]
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[[Category: Nmr]]
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[[Category: triplex]]
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[[Category: Triplex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:30:30 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:15 2008''
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Revision as of 06:30, 2 May 2008

Image:149d.gif

Template:STRUCTURE 149d

SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES


Overview

BACKGROUND: Under certain conditions, homopyrimidine oligonucleotides can bind to complementary homopurine sequences in homopurine-homopyrimidine segments of duplex DNA to form triple helical structures. Besides having biological implications in vivo, this property has been exploited in molecular biology applications. This approach is limited by a lack of knowledge about the recognition by the third strand of pyrimidine residues in Watson-Crick base pairs. RESULTS: We have therefore determined the solution structure of a pyrimidine.purine.pyrimidine (Y.RY) DNA triple helix containing a guanine residue in the third strand which was postulated to specifically recognize a thymine residue in a Watson-Crick TA base pair. The structure was solved by combining NMR-derived restraints with molecular dynamics simulations conducted in the presence of explicit solvent and counter ions. The guanine of the G-TA triple is tilted out of the plane of its target TA base pair towards the 3'-direction, to avoid a steric clash with the thymine methyl group. This allows the guanine amino protons to participate in hydrogen bonds with separate carbonyls, forming one strong bond within the G-TA triple and a weak bond to an adjacent T.AT triple. Dramatic variations in helical twist around the guanine residue lead to a novel stacking interaction. At the global level, the Y.RY DNA triplex shares several structural features with the recently solved solution structure of the R.RY DNA triplex. CONCLUSIONS: The formation of a G.TA triple within an otherwise pyrimidine.purine.pyrimidine DNA triplex causes conformational realignments in and around the G.TA triple. These highlight new aspects of molecular recognition that could be useful in triplex-based approaches to inhibition of gene expression and site-specific cleavage of genomic DNA.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples., Radhakrishnan I, Patel DJ, Structure. 1994 Jan 15;2(1):17-32. PMID:8075980 Page seeded by OCA on Fri May 2 09:30:30 2008

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