Ion-exchange chromatography of a dinucleotide preparation from controlled alkaline hydrolysis of ribonucleic acids

With the aim of preparing the 16 possible ribodinucleotides derived from the four principal ribonucleotides, we made a kinetic study to determine the optimum conditions for a partial alkaline hydrolysis of RNA. Satisfactory results were obtained when the hydrolysis of RNA (1g.) in 0.2m-sodium hydroxide (100ml.) at 37 degrees was ceased approx. 10min. after the start of the reaction. The relative yields of the monomer, dimer and trimer fractions were approx. 41:30:15 in E(260) units, indicating that the reaction conditions were reasonably close to those required from kinetic considerations. The partial alkaline hydrolysate was chromatographed on a column of DEAE-Sephadex A-25 in the presence of 7m-urea. The dinucleotide fraction thus obtained was subjected to a subsequent chromatography on Dowex 1 (X2) under acidic conditions to separate the mixture according to base composition and base sequence. The results were satisfactory, and most of the 32 dinucleotides [i.e. 16 XpYp(3') plus 16 XpYp(2')] were fractionated by this single chromatographic procedure. The present method should be useful for further study of oligonucleotides as a time-saving method for the simultaneous preparation of a variety of dinucleotides. Further, examination of the present chromatographic pattern has provided several empirical criteria useful for the identification of oligonucleotides other than dimers appearing in the elution profile of Dowex 1 (X2) column chromatography under similar conditions.