1bce: Difference between revisions

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


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{{STRUCTURE_1bce|  PDB=1bce  |  SCENE=  }}  
{{STRUCTURE_1bce|  PDB=1bce  |  SCENE=  }}  


'''INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES'''
===INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES===




==Overview==
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The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with &gt;19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.
The line below this paragraph, {{ABSTRACT_PUBMED_9685482}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 9685482 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9685482}}


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


==Reference==
==Reference==
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[[Category: Deoxyribonucleic acid]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna triplex]]
[[Category: Dna triplex]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:20:11 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:49:36 2008''

Revision as of 15:49, 30 June 2008

File:1bce.png

Template:STRUCTURE 1bce

INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES

Template:ABSTRACT PUBMED 9685482

About this Structure

Full experimental information is available from OCA.

Reference

Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets., Asensio JL, Brown T, Lane AN, Nucleic Acids Res. 1998 Aug 15;26(16):3677-86. PMID:9685482

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