title: A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures.
abstract: A 5'-C-allylthymidine derivative was prepared from thymidine by the application of a stereoselective allylation procedure and its 5'(S)-configuration was confirmed. From this nucleoside derivative, appropriately protected building blocks were prepared and coupled using standard phosphoramidite chemistry to afford a dinucleotide with two 5'-C-allylgroups. This molecule was used as a substrate for a ring-closing metathesis (RCM) reaction and after deprotection, a 1 : 1 mixture of E- and Z-isomers of a cyclic dinucleotide with an unsaturated 5'-C-to-5'-C connection was obtained. Alternatively, a hydrogenation of the double bond and deprotection afforded a saturated cyclic dinucleotide. An advanced NMR-examination confirmed the constitution of this molecule and indicated a restriction in its overall conformational freedom. After variation of the protecting group strategy, a phosphoramidite building block of the saturated cyclic dinucleotide with the 5'-O-position protected as a pixyl ether and the phosphate protected as a methyl phosphotriester was obtained. This building block was used in the preparation of two 14-mer oligonucleotides with a central artificial bend due to the cyclic dinucleotide moiety. These were found to destabilise duplexes, slightly destabilise bulged duplexes but, to some extent, stabilise a three-way junction in high Mg(2+)-concentrations.
authors.affiliation: Nucleic Acid Center, Department of Chemistry, University of Southern Denmark.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Sharma
authors.forename: Birgitte H
authors.initials: BH
authors.lastname: Mikkelsen
authors.forename: Mikkel S
authors.initials: MS
authors.lastname: Christensen
authors.forename: Katrine E
authors.initials: KE
authors.lastname: Nielsen
authors.forename: Claus
authors.initials: C
authors.lastname: Kirchhoff
authors.forename: Søren L
authors.initials: SL
authors.lastname: Pedersen
authors.forename: Anders M
authors.initials: AM
authors.lastname: Sørensen
authors.forename: Kirsten
authors.initials: K
authors.lastname: Ostergaard
authors.forename: Michael
authors.initials: M
authors.lastname: Petersen
authors.forename: Poul
authors.initials: P
authors.lastname: Nielsen
mesh_terms: D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D013816:Thermodynamics; D013936:Thymidine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D013936:Thymidine