Abstract :
A monitoring method of rapid hydrothermal reactions was successfully applied to a kinetic analysis of the cleavage of a ribose phosphodiester bond within oligonucleotides and dinucleotides at 150-200 °C. The apparent rate constants (kapp) of degradation of the ribose 3ʹ,5ʹ-cytidylylguanosine sequence (-C3ʹpGd-) within oligonucleotides and dinucleotides were determined, where the -C3ʹpGd- sequence in oligonucleotides is less stable than 2ʹ,5ʹ-cytidylylguanosine (C2ʹpG) and 3ʹ,5ʹ-cytidylylguanosine (C3ʹpG). It was unexpected that the stability of the target sequence would be dependent on the surrounding sequences of the oligonucleotides, although the temperatures used in the study were extremely higher than the melting points. The stability of a phosphodiester bond of 2ʹ-deoxycytidylyl-2ʹdeoxyguanosine (CdpGd) is much higher than that of a ribose phosphodiester bond at low temperatures, but becomes comparable at 200 °C. During the degradation of C2ʹpG or C3ʹpG, interconversion between C2ʹpG and C3ʹpG was observed along with cleavage of the phosphodiester bond. Based on an analysis of the extent of interconversion, the apparent rate constants of the disappearance of C2ʹpG and C3ʹpG were dissected into the rate constants of hydrolysis (khy) and interconversion (kint), where the values of khy were greater than those of kint. The apparent activation energy of the degradation of the target sequence was 100-109 kJ mol^-1 for oligonucleotides, 90 kJ mol^-1 for C3ʹpG, and 87 kJ mol^-1 for C2ʹpG, and 139 kJ mol^-1 for CdpGd. The apparent activation enthalpy and entropy changes of the degradation of the target sequence were also determined; the values of the activation parameter were (delta)H(not equal)app = 94-105 kJ mol^-1 and (delta)S(not equal)app = -(36-59) J mol^-1 T^-1 for five oligonucleotides, (delta)H(not equal)app = 86 kJ mol^-1 and (delta)S(not equal)app = -97 J mol^-1 T-1 for C3ʹpG, (delta)H(not equal)app = 84 kJ mol^-1, (delta)S(not equal)app = -105 J mol^-1 T^-1 for C2ʹpG, and (delta)H(not equal)app = 135 kJ mol^-1, (delta)S(not equal)app = +2 J mol^-1 T-1 for CdpGd. The activation parameters, (delta)H(not equal)app and (delta)S(not equal)app, for the oligonucleotides increased with the length of the surrounding sequence of -C3ʹpGd-; this fact clearly demonstrates the existence of the influence of the surrounding sequence for the stability of the target ribose phosphodiester bond. Based on a kinetic analysis, the reaction mechanism of the degradation of the ribose phosphodiester bond at high temperatures is discussed. Furthermore, possible pathways of the chemical evolution of RNA are discussed from the viewpoint of the hydrothermal origin of life.
