IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations.
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.
Adam
S
S
Laboratoire de Spectroscopie Biomoléculaire Université Paris-Nord, Bobohny, France.
Ridoux
J P
JP
Bourtayre
P
P
Taillandier
E
E
Pochet
S
S
Huynh-Dinh
T
T
Igolen
J
J
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
D009692:Nucleic Acid Heteroduplexes; D004247:DNA