Concerning the alkaline hydrolysis of soluble ribonucleic acid

Ion-exchangechrmtography 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.

A study of the alkaline hydrolysis of fractionated reticulocyte ribosomal ribonucleic acid and its relevance to secondary structure

1. RNA isolated from the sub-units of rabbit reticulocyte ribosomes was hydrolysed by 0.4n-potassium hydroxide at 20 degrees . The probability of main-chain scission was calculated from the number-average chain length, which was obtained from S(25,w) in 0.01m-phosphate buffer. 2. The fraction, f, of the original secondary structure that the fragments re-formed at neutral pH in 4m-guanidinium chloride, as well as in 0.01m- and 0.1m-phosphate buffer, was derived from changes in extinction over the range 220-310mmu on thermal denaturation. 3. The secondary structure of RNA is regarded as an assembly of hairpin loops each of 2N+b residues on average, where N is the number of base-paired residues and b is the number of unpaired residues. 4. If chain scission takes place at random then 2N+b=logf/log(1-p). 5. For RNA from the smaller sub-unit 2N+b was estimated as 25+/-5 residues, compared with 30+/-5 residues for the less stable species and 35+/-5 residues for the more stable species of hairpin loop of RNA from the larger sub-unit.

Hydrolysis of polynucleotides and the characterization of their secondary structure. A theoretical study

1. Single-stranded RNA may be regarded as an assembly of L hairpin loops each stabilized by N base pairs and each containing b unpaired residues; one loop is connected to another by c residues. 2. A theory based on the statistics of the random degradation of linear polymers was developed to relate N, b and c with the probability, p, of hydrolysing a diesterified phosphate bond. 3. The number of residues per hairpin loop, which is 2N+b, is related to the fraction, f, of the original loops remaining intact by the equation: 2N+b=logf/log(1-p). 4. The theory was extended to show that the number of residues per loop may be evaluated by fractionating the RNA after hydrolysis and examining the secondary structure of each fraction. Fragments that are shorter than the hairpin loop cannot reproduce the original secondary structure. The probability that a fragment will form an intact loop increases most rapidly for fragments of between 2N+b and 2(2N+b)+c residues. 5. The probability of producing a fragment capable of forming one, and only one, hairpin loop was related to N, b and c.

A study of the hydrolysis of unfractionated reticulocyte ribosomal ribonucleic acid by pancreatic ribonuclease and its relevance to secondary structure

1. Unfractionated RNA from reticulocyte ribosomes was hydrolysed with pancreatic ribonuclease at 25 degrees . The molecular weight decreased rapidly to about 3s when about 6% of the residues were soluble in 0.5n-perchloric acid. In the early stages 60-80% of the hydrolysed linkages were ;hidden'. The denaturation spectrum was affected. Continued hydrolysis led to slow changes in S value, in the electrophoresis pattern in polyacrylamide gels and in the denaturation spectrum. 2. Hydrolysis of RNA with alkali to fragments of between 2.8s and 5.9s led to changes in the denaturation spectrum similar to those observed in the early stages of enzymic hydrolysis. 3. A theory was developed to relate changes in secondary structure with main-chain scission. 4. The results agree with the ;hairpin-loop' model for RNA. The denaturation studies are consistent with the presence of more than one species of hairpin loop that differ in their denaturation spectra. The average length of the hairpin loop was estimated to be 10-20 residues and an upper limit of 35 residues was established. 5. It is inferred, on the basis of studies with model compounds, that the stability of single-stranded stacked structures is hardly dependent on salt concentration. 6. The denaturation spectrum of the fragments obtained on hydrolysis became less dependent on ionic strength, suggesting that double-helical structures revert to a single-stranded stacked form on denaturation.