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1at4

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{{STRUCTURE_1at4| PDB=1at4 | SCENE= }}
{{STRUCTURE_1at4| PDB=1at4 | SCENE= }}
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'''INTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT-X-CTCTCT), NMR, 7 STRUCTURES'''
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===INTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT-X-CTCTCT), NMR, 7 STRUCTURES===
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==Overview==
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The solution properties of the parallel intramolecular DNA triplex d(GAGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)8-O-PO2-O-(CH2)8-O-PO2-) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV melting and high-resolution nuclear magnetic resonance spectroscopy (NMR). All nucleotides were primarily in the S conformation (i.e. near C2'-endo) in both the duplex and the triplex. However, the sugars of the Hoogsteen pyrimidine strand had a lower fraction of the S state than the Watson-Crick strands. Glycosidic torsion angles derived from nuclear Overhauser effect (NOE) build-up curves were found in the range -103 degrees to -133 degrees, with a clear alternation in magnitude along the GAGAGA strand in the triplex, whereas the glycosidic torsion angles were more similar in the duplex. Internucleotide NOEs were also consistent with an overall B-like geometry, rather than the A family. However, particularly in the Hoogsteen strand, some sequential NOE intensities were intermediate between those of the B and A forms. Distance and torsion constraints derived from NMR experiments were used to generate structures and were refined by restrained molecular dynamics. Extensive chemical shift differences between residues in the triplex and duplex were found for the purine strand, and there were remarkable differences in the pattern of shift differences for the A and G residues that correlated with differences in glycosidic torsion angles. Although there are differences in structure between the free duplex and that in the triplex, they are in important respects similar, indicating that only small conformational adjustments are needed to make parallel triple helices.
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(as it appears on PubMed at http://www.pubmed.gov), where 9398169 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9398169}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AT4 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AT4 OCA].
==Reference==
==Reference==
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[[Category: Dna]]
[[Category: Dna]]
[[Category: Intramolecular triplex]]
[[Category: Intramolecular triplex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:39:54 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:32:52 2008''

Revision as of 14:32, 30 June 2008

Image:1at4.png

Template:STRUCTURE 1at4

INTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT-X-CTCTCT), NMR, 7 STRUCTURES

Template:ABSTRACT PUBMED 9398169

About this Structure

Full experimental information is available from OCA.

Reference

Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex., Bartley JP, Brown T, Lane AN, Biochemistry. 1997 Nov 25;36(47):14502-11. PMID:9398169

Page seeded by OCA on Mon Jun 30 17:32:52 2008

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