title: IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations.
abstract: Tridecamers containing a central no-base residue (X) have been synthesized and hybridized to their complementary strands, so as to constitute duplexes consisting of two hexamers separated by central mismatched X-A or X-T pairs. The effect of the introduction of this deoxyribose derivative on duplex stability was investigated by measuring UV absorbance as a function of salt concentration and temperature. As expected, the duplexes containing the abnormal base pairs (X-T and X-A) are less stable when compared to the totally complementary duplexes (A-T and T-A). The X-T mismatched duplex shows the most unstable thermodynamical behaviour. The conformational changes of these duplexes were studied by IR spectroscopy in condensed phase as a function of water content. At high relative humidity, the IR spectra show that these tridecamers form B-type double stranded duplex structures. If the water content is decreased, only the duplexes m5CGm5CGCTXAGCTTC GCGCGAATCGAAG and, to a lesser degree, m5CGm5CGCTXAGCTTC GCGGCATTCGAAG undergo a partial B---Z transition involving the methylated hexamer, the conformation of the second segment remaining of the B type. These results show that only one apurinic residue leads to a flexible junction between B and Z forms in a short duplex containing 5-methyl-2'-deoxycytidines.
authors.affiliation: Laboratoire de Spectroscopie Biomoléculaire Université Paris-Nord, Bobohny, France.
authors.forename: S
authors.initials: S
authors.lastname: Adam
authors.forename: J P
authors.initials: JP
authors.lastname: Ridoux
authors.forename: P
authors.initials: P
authors.lastname: Bourtayre
authors.forename: E
authors.initials: E
authors.lastname: Taillandier
authors.forename: S
authors.initials: S
authors.lastname: Pochet
authors.forename: T
authors.initials: T
authors.lastname: Huynh-Dinh
authors.forename: J
authors.initials: J
authors.lastname: Igolen
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000032:analysis; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D013055:Spectrophotometry, Infrared; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature
chemical_list: D009692:Nucleic Acid Heteroduplexes; D004247:DNA