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 HvH/delta Hcal = 1.04 suggests all-or-none behaviour for the transition of the 2'-deoxyribose oligonucleotide. The analogous parameters of (A) are: delta Hcal = 310 +/- 30 kJ . mol-1, delta HvH = 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 are delta Hcal = 330 +/- 30 kJ.mol-1; delta HvH = 180 +/- 15 kJ.(mol of cooperative unit)-1 delta HvH/ delta Hcal = 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).