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Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties.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 cyc...

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Autores principales: Nauwelaerts, Koen, Lescrinier, Eveline, Sclep, Gert, Herdewijn, Piet
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087899/
https://www.ncbi.nlm.nih.gov/pubmed/15863723
http://dx.doi.org/10.1093/nar/gki538
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author Nauwelaerts, Koen
Lescrinier, Eveline
Sclep, Gert
Herdewijn, Piet
author_facet Nauwelaerts, Koen
Lescrinier, Eveline
Sclep, Gert
Herdewijn, Piet
author_sort Nauwelaerts, Koen
collection PubMed
description Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties.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 (2)H(3) (N-type) and (2)H(3) (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 (2)H(3) conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the (2)H(3) 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.
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spelling pubmed-10878992005-05-02 Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides Nauwelaerts, Koen Lescrinier, Eveline Sclep, Gert Herdewijn, Piet Nucleic Acids Res Article 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 (2)H(3) (N-type) and (2)H(3) (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 (2)H(3) conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the (2)H(3) 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. Oxford University Press 2005 2005-04-29 /pmc/articles/PMC1087899/ /pubmed/15863723 http://dx.doi.org/10.1093/nar/gki538 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Nauwelaerts, Koen
Lescrinier, Eveline
Sclep, Gert
Herdewijn, Piet
Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title_full Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title_fullStr Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title_full_unstemmed Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title_short Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
title_sort cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087899/
https://www.ncbi.nlm.nih.gov/pubmed/15863723
http://dx.doi.org/10.1093/nar/gki538
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AT herdewijnpiet cyclohexenylnucleicacidsconformationallyflexibleoligonucleotides