The temperature dependence of pseudo-first-order rate constants (kcyc) of the cyclization of hexanucleotides 5'-d(pGCGCG)rC and 5'-d(pGCCCG)rG was investigated in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) and imidazole at 0 - 75 ℃. Although the association between the elongating oligomer and the activated monomer is necessary for the success of the formation of oligonucleotides on a polynucleotide template or a clay catalyst, the phosphodiester bond formation in the case of cyclization readily occurs without these catalysts. Thus, the cyclization is regarded as a simple model of the formation of phosphodiester bond. The rate constants (kcyc) were compared with those of the cleavage of the ribose phosphodiester bond, in which the cyclization was more than 50 times faster than the cleavage at 75 ℃. On the basis of this fact, it is deduced that the prebiotic formations of RNA oligomers such as the template-directed reaction and the mineral catalyzed oligomerization would be possible at high temperatures if the association between elongating oligomer and activated monomer (or activated oligomer) is sufficiently strong.
The duplex structure of several heterochiral dodecadeoxynucleotides containing an unnatural L-enantiomer of D-deoxyribose was investigated by using nuclear magnetic resonance, ultraviolet, circular dichroism spectroscopy and restriction endonuclease Eco RI digestion. The UV melting study suggested that the L-nucleotide residue of the heterochiral 12mers retains the base pairing with the complementary natural D-counterpart. This was also supported by 1H NMR analysis of L-4, which also revealed the molecular mechanisms for the L-nucleotide to form the Watson-Crick base pairing. The CD experiments suggested that the duplex structure of the heterochiral 12mers is not significantly different from that of the parental one, and some of the 12mers were recognized by restriction endonuclease EcoRI. These results suggested that the breaking homochirality of the 12mer does not induce significant conformational changes or helical distortion, although the duplex stability is somewhat decreased. The destabilization of the duplex structure for heterochiral DNA might have been advantageous for natural selection of homochiral DNA in the processes of the chemical evolution of DNA.
Life was generated about four billion years ago in the primitive sea as a result of the chemical evolution. The proto-cell was a prokaryotic monad that was formed from a certain aggregate of primitive proteins, nucleic acids, and other macromolecules and wrapped with (phospho)lipid membrane. That membrane served a very important role in the proto-cell born in the primitive sea. This communication addresses the evolutionary process of eukaryotic cell genesis. Eukaryotic cells developed membrane systems remarkably compared to prokaryotic cells. The nucleus, mitochondria, chloroplasts (in plant), endoplasmic reticulum, Golgi apparatus, and other organelles are constructed of lipid membranes inside of which specific enzymes and proteins are positioned. We infer that the eukaryotic organelles were not engendered in an accidental event of symbiotic phenomena, but by evolutionary inevitability of the surviving world.