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Published on: October 25, 2017
Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides.
Koen Nauwelaerts1, Eveline Lescrinier, Gert Sclep
1Rega Institute for Medical Research, Laboratory for Medicinal Chemistry Minderbroedersstraat 10, B-3000 Leuven, Belgium.
Cyclohexenyl nucleic acid (CeNA) mimics natural DNA sugars, showing similar conformational flexibility. This synthetic nucleoside uniquely adopts varied conformations within different DNA duplexes, revealed by NMR spectroscopy.
Area of Science:
- Biochemistry
- Organic Chemistry
- Molecular Biology
Background:
- Cyclohexenyl nucleic acid (CeNA) is a synthetic nucleic acid mimic.
- It replaces the natural (deoxy)ribose sugar with cyclohexenyl moieties.
- Understanding CeNA conformation is crucial for its application as a DNA mimic.
Purpose of the Study:
- To investigate the conformational properties of cyclohexenyl nucleosides using NMR spectroscopy.
- To develop and apply the HexRot program for calculating CeNA conformations.
- To compare the conformational behavior of CeNA with natural ribose nucleosides.
Main Methods:
- Development of the HexRot program for conformational analysis of cyclohexenyl compounds via NMR.
- Measurement of scalar coupling constants in cyclohexenyl nucleosides and DNA duplexes.
- NMR spectroscopy to determine the conformation of CeNA monomers and incorporated duplexes.
Main Results:
- HexRot program successfully calculated conformations from scalar coupling constants.
- Conformational equilibria and thermodynamic parameters of cyclohexenyl nucleosides closely resemble those of natural ribose nucleosides.
- CeNA demonstrated conformational flexibility, adopting the 2H3 conformation in various DNA duplexes and exhibiting fast equilibrium between states in a monomer.
Conclusions:
- Cyclohexenyl nucleosides exhibit conformational properties analogous to natural nucleosides.
- CeNA is the first synthetic nucleoside shown to adopt distinct conformations when incorporated into different double-stranded DNA sequences.
- NMR spectroscopy is a powerful tool for elucidating the conformational dynamics of synthetic nucleic acids.
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