1u01: Difference between revisions

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[[Image:1u01.gif|left|200px]]
{{Seed}}
[[Image:1u01.png|left|200px]]


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{{STRUCTURE_1u01|  PDB=1u01  |  SCENE=  }}  
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'''High resolution NMR structure of 5-d(GCGT*GCG)-3/5-d(CGCACGC)-3 (T*represents a cyclohexenyl nucleotide)'''
===High resolution NMR structure of 5-d(GCGT*GCG)-3/5-d(CGCACGC)-3 (T*represents a cyclohexenyl nucleotide)===




==Overview==
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Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4-20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the 2H3 conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the 2H3 conformation when incorporated in a d(5'-GCGT*GCG-3')/d(5'-CGCACGC-3') duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences.
The line below this paragraph, {{ABSTRACT_PUBMED_15863723}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 15863723 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15863723}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U01 OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U01 OCA].  


==Reference==
==Reference==
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[[Category: Nucleic acid]]
[[Category: Nucleic acid]]
[[Category: Rna mimic]]
[[Category: Rna mimic]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 10:34:46 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:34:36 2008''

Revision as of 13:34, 28 July 2008

File:1u01.png

Template:STRUCTURE 1u01

High resolution NMR structure of 5-d(GCGT*GCG)-3/5-d(CGCACGC)-3 (T*represents a cyclohexenyl nucleotide)

Template:ABSTRACT PUBMED 15863723

About this Structure

Full experimental information is available from OCA.

Reference

Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides., Nauwelaerts K, Lescrinier E, Sclep G, Herdewijn P, Nucleic Acids Res. 2005 Apr 29;33(8):2452-63. Print 2005. PMID:15863723

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