Conformational stability of dinucleotides in solution

Abstract

A variety of 3′ → 5′ and 2′ → 5′ dinucleoside phosphates (at neutral pH) have been studied using circular dichroic and absorption spectra in a range of temperature of −20 to + 80 °C. Two kinds of circular dichroic spectra can be observed at low temperature: one “conservative” represented by a pair of bands of opposite sign, the other “non-conservative” composed of one main positive band, characteristic of guanine and cytosine compounds. Both spectra are consistent with a model of dissymmetrical, single-stranded helical conformation. Thermodynamic parameters for the process order ⇌ disorder in dinucleotides have been estimated by following thermally induced changes in circular dichroic spectra. Values are similar for all the 3′ → 5′ derivatives and are of the order of 6 to 7.5 kcal./mole for ΔH o , about 20 to 25 e.u./mole for ΔS 0 and about 0.5 kcal./mole at 0 °C for ΔF o . This absence of major differences in thermodynamic parameters does not permit one to divide dinucleotides into groups characterized by a stacked or unstacked conformation; for example, 3′ → 5′ uridylyl-uridine (UpU) is appreciably stacked at 20 °C. Examination of corresponding 2′ → 5′ dinucleoside phosphates gave quite different results in the same range of temperature, indicating that stacking is much less marked compared with the 3′ → 5′ compounds. An intramolecular hydrogen bond involving the 2′-hydroxyl group of the ribose is postulated to explain these differences.