title: Synthesis of functionalized carbocyclic locked nucleic acid analogues by ring-closing diene and enyne metathesis and their influence on nucleic acid stability and structure.
abstract: A series of bicylic 2'-deoxynucleosides that are locked in the N-type conformation due to three-carbon linkages between the 2'- and 4'-positions have been prepared by ring-closing diene or enyne metathesis. The alkene or 1,3-diene hereby introduced in the bicyclic system is further derivatized, the latter showing the expected potential for Diels-Alder reactions. Four derivatives that are saturated or unsaturated as well as functionalized at the 2'-4'-linkage are incorporated into oligodeoxynucleotides, and the affinity of these for complementary RNA and DNA is studied. Substantially increased affinity for complementary RNA is observed, especially with additional hydroxyl groups attached to the bicyclic system. On the other hand, decreased affinity for complementary single-stranded DNA is obtained, whereas only a very small influence on a triplex-forming oligonucleotide sequence is found. Hence, a strong RNA-selective nucleic acid recognition is seen, and it can be concluded that the 2'-oxygen atom is less important for the formation of DNA:RNA duplexes than for the formation of DNA:DNA duplexes. However, the lack of a 2'-oxygen in the duplex formation can be partly compensated by other hydrophilic moieties around the 2'-4'-linkages indicating structural water binding to be of significant importance.
authors.affiliation: Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark.
authors.forename: Surender
authors.initials: S
authors.lastname: Kumar
authors.forename: Marianne H
authors.initials: MH
authors.lastname: Hansen
authors.forename: Nanna
authors.initials: N
authors.lastname: Albaek
authors.forename: Signe I
authors.initials: SI
authors.lastname: Steffansen
authors.forename: Michael
authors.initials: M
authors.lastname: Petersen
authors.forename: Poul
authors.initials: P
authors.lastname: Nielsen
mesh_terms: D002244:Carbon / Q000737:chemistry*; D002625:Chemistry, Organic / Q000379:methods*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry; D017665:Hydroxyl Radical; D007700:Kinetics; D008956:Models, Chemical; D008968:Molecular Conformation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009696:Nucleic Acids; D009841:Oligonucleotides; D017665:Hydroxyl Radical; D012313:RNA; D002244:Carbon; D004247:DNA