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| | {{STRUCTURE_149d| PDB=149d | SCENE= }} | | {{STRUCTURE_149d| PDB=149d | SCENE= }} |
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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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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_8075980}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 8075980 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_8075980}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=149D OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=149D OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Nmr]] | | [[Category: Nmr]] |
| | [[Category: Triplex]] | | [[Category: Triplex]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:30:30 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:30:43 2008'' |
Revision as of 12:30, 30 June 2008
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
Template:ABSTRACT PUBMED 8075980
About this Structure
Full experimental 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 Mon Jun 30 15:30:43 2008
