title: Synthesis and hybridization properties of modified oligodeoxynucleotides carrying non-natural bases.
abstract: The impact of the presence of nonnatural bases on the properties of oligodeoxynucleotides has been studied. First, oligodeoxynucleotides carrying 2'-deoxyzebularine were prepared, and the stability of duplexes carrying this analogue was determined by DNA melting experiments. Melting temperatures and thermodynamic data indicated the preference of 2'-deoxyzebularine for 2'-deoxyguanosine, which behaves as a 2'-deoxycytidine analogue, forming a less stable base pair due to the absence of the amino group at position 4. Moreover, the duplex-hairpin equilibrium of a self-complementary oligodeoxynucleotide carrying several natural and nonnatural bases including 2'-deoxyzebularine as a central mispair, was studied. Depending on the base present in the middle of the sequence, it is possible to affect the stability of the bimolecular duplex modulating the duplex-hairpin equilibrium. Magnesium ions were shown to stabilize preferentially the bimolecular duplex form. The results indicate the importance of the modifications and the role of cations in shifting the structural equilibrium.
authors.affiliation: Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Center on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, E-08028 Barcelona.
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Sónia
authors.initials: S
authors.lastname: Pérez-Rentero
authors.forename: Alejandra V
authors.initials: AV
authors.lastname: Garibotti
authors.forename: Maqbool A
authors.initials: MA
authors.lastname: Siddiqui
authors.forename: Victor E
authors.initials: VE
authors.lastname: Márquez
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003562:Cytidine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics; D013696:Temperature; D013816:Thermodynamics
chemical_list: C540597:2'-deoxyzebularine; D009838:Oligodeoxyribonucleotides; D003562:Cytidine; D004247:DNA