Kinetic Analysis of the Cleavage of the Ribose Phosphodiester Bond within Guanine and Cytosine-Rich Oligonucleotides and Dinucleotides at 65–200 °C and Its Implications Concerning the Chemical Evolution of RNA

Abstract

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 3′,5′-cytidylylguanosine sequence (-C3′pGd-) within oligonucleotides and dinucleotides were determined, where the -C3′pGd- sequence in oligonucleotides is less stable than 2′,5′-cytidylylguanosine (C2′pG) and 3′,5′-cytidylylguanosine (C3′pG). 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 2′-deoxycytidylyl-2′-deoxyguanosine (CdpGd) is much higher than that of a ribose phosphodiester bond at low temperatures, but becomes comparable at 200 °C. During the degradation of C2′pG or C3′pG, interconversion between C2′pG and C3′pG 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 C2′pG and C3′pG 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 C3′pG, and 87 kJ mol−1 for C2′pG, 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 ΔH≠app = 94–105 kJ mol−1 and ΔS≠app = −(36–59) J mol−1 T−1 for five oligonucleotides, ΔH≠app = 86 kJ mol−1 and ΔS≠app = −97 J mol−1 T−1 for C3′pG, ΔH≠app = 84 kJ mol−1, ΔS≠app = −105 J mol−1 T−1 for C2′pG, and ΔH≠app = 135 kJ mol−1, ΔS≠app = +2 J mol−1 T−1 for CdpGd. The activation parameters, ΔH≠app and ΔS≠app, for the oligonucleotides increased with the length of the surrounding sequence of -C3′pGd-; 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.