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Synthesis and hybridization properties of modified oligodeoxynucleotides carrying non-natural bases

AutorAviñó, Anna; Pérez-Rentero, Sonia; Garibotti, Alejandra V.; Siddiqui, Maqbool Arshad Q; Márquez, Víctor E.; Eritja Casadellà, Ramón
Palabras claveBase Pairing
Base Sequence
Cytidine
DNA
Nucleic Acid Conformation
Nucleic Acid Denaturation
Nucleic Acid Hybridization
Oligodeoxyribonucleotides
Thermodynamics
unclassified drug
zebularine
Fecha de publicación2009
EditorJohn Wiley & Sons
CitaciónChemistry and Biodiversity
ResumenThe 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 DNAmelting 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.
Versión del editorDOI: 10.1002/cbdv.200800239
URIhttp://hdl.handle.net/10261/125042
DOI10.1002/cbdv.200800239
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