1p3x: Difference between revisions

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[[Image:1p3x.gif|left|200px]]
{{Seed}}
[[Image:1p3x.png|left|200px]]


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{{STRUCTURE_1p3x|  PDB=1p3x  |  SCENE=  }}  
{{STRUCTURE_1p3x|  PDB=1p3x  |  SCENE=  }}  


'''INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES'''
===INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES===




==Overview==
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Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-PCPCPCPP) (PDD-EG), which contains 5-(1-propynl)-2'-deoxyuridine (P) in the third strand and hexakis(ethylene glycol) linkers [(EG)6]. The structure was calculated using X-PLOR with distance and dihedral angle restraints obtained from two-dimensional NMR experiments and refined with the direct relaxation matrix method. The structures show that the extended aromatic electron cloud of the propynylU nucleotide stacks well over the 5'-neighboring nucleotides, resulting in increased stabilization. The propynylU nucleotides also affect the overall structure of the triple helix. A comparison of the structure to that of the nonmodified intramolecular DNA triplex of the same sequence, d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT) (DDD-EG), shows that PDD-EG has a more A-DNA like X displacement and inclination than DDD-EG yet still maintains predominantly S-type sugar puckers as found in DDD-EG and other DNA triplexes.
The line below this paragraph, {{ABSTRACT_PUBMED_9558315}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 9558315 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9558315}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3X OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3X OCA].  


==Reference==
==Reference==
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[[Category: Propyne]]
[[Category: Propyne]]
[[Category: Triplex]]
[[Category: Triplex]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 04:39:15 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:55:33 2008''

Revision as of 10:55, 27 July 2008

File:1p3x.png

Template:STRUCTURE 1p3x

INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES

Template:ABSTRACT PUBMED 9558315

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand., Phipps AK, Tarkoy M, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5820-30. PMID:9558315

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