Xylose-DNA: Comparison of the thermodynamic stability of oligo(2'-deoxyxylonucleotide) and oligo(2'-deoxyribonucleotide) duplexes

Abstract

Measurements of differential scanning calorimetry, ultraviolet absorption and circular dichroism have been performed on two synthetic oligo(2'-deoxyxylonucleotides): (A) d[(xA)(3)-(xT)(3)-(xA)(3)-(xT)(3)-T] and (B) d[(xA-xT)(6)-T], and on the oligo(2'-deoxyribonucleotide) (C) d[(A)(3)-(T)(3)-(A)3-(T)(3)]. Oligonucleotides having 2'-deoxyxylose instead of 2'-deoxyribose exhibit unusual thermodynamic, optical and structural features. At identical concentrations the transition temperatures of the oligo(2'-deoxyxylooligomers) are higher than those of the oligo(2'-deoxyribooligomers) indicating higher stability. The calorimetric transition enthalpy of (C) is 270 /- 15 kJ . mol(-1), the corresponding van't Hoff value is 280 /- 15 kJ .(mol of cooperative unit)(-1). The ratio of Delta H-vH/Delta H-cal = 1.04 suggests all-or-none behaviour for the transition of the 2'-deoxyribose oligonucleotide. The analogous parameters of (A) are: Delta H-cal = 310 /- 30 kJ . mol(-1), Delta H-vH = 220 /- 30 kJ .(mol of cooperative unit)(-1). The ratio of 0.71 indicates multistate melting for this compound. The sequence dependence of the thermodynamic quantities becomes apparent when the parameters of the alternating oligo(2'-deoxyxylonucleotide) d[(xA-xT)(6)-T] are compared to those of d[(xA)(3)-(xT)(3)-(xA)(3)-(xT)(3)-T]. The values of (B) are Delta H-cal = 330 /- 30 kJ . mol(-1); Delta H-vH = 180 /- 15 kJ .(mol of cooperative unit)(-1) Delta H-vH/Delta H-cal = 0.55. The transition enthalpy of the alternating oligo(2'-deoxyxylonucleotide) (B) is the highest but the cooperativity of transition is the lowest of the oligonucleotides studied. The circular dichroic spectra of the two oligo(2'deoxyxylonucleotides) show unusual features in that d[(xA)(3)-(xT)(3)-(xA)(3)-(xT)(3)-T] exhibits a spectrum that is suggestive of a left-handed double helix, while the spectrum of the alternating oligo(2'-deoxyxylonucleotide) (B) resembles neither that of (C) nor that of (A).