A possible method for characterizing the secondary structure of ribonucleic acids

The E(280)/E(260) ratio was found to be suitable for following the ionization of cytosine residues of polynucleotides on the basis of studies with model compounds such as oligoguanylic acid, oligocytidylic acid, a complex formed between polyadenylic acid and polyuridylic acid, and a copolymer of guanylic acid and cytidylic acid, provided that changes in secondary structure were taken into account. The pK of cytosine residues of a polynucleotide in the amorphous form was found to be 4.70 at 25 degrees in 0.1m-sodium phosphate on the basis of titration at 75-85 degrees and on the assumption that the heat of ionization was the same as the value (5.2kcal./mole) found for CMP. In contrast, the pK of cytosine residues in the double-helical form of DNA was found to be about 3.25. These observations were utilized in estimating the fraction of cytosine residues in helical segments of ribosomal RNA, a copolymer of guanylic acid and cytidylic acid, and a copolymer of adenylic acid, guanylic acid, uridylic acid and cytidylic acid. The ionization of guanine and uracil residues was estimated from changes in the E(270)/E(260) ratio and E(230)/E(260) ratio respectively. In the amorphous form of RNA both residues had the same pK, whereas in the double-helical form ionization was suppressed. The fraction of guanine and uracil residues in amorphous segments may be estimated from the titration curves. The difference in the denaturation spectrum of adenine--uracil and guanine--cytosine base pairs at 280mmu was enhanced in acidic solutions whereas E(260) was hardly affected. Hence a comparison of the increments in E(280) and E(260) obtained on increasing the temperature at constant pH may be used to distinguish the melting ranges of helical domains differing in nucleotide composition. In alkaline solutions comparison of the increments in E(260) and E(270) yields similar information. In acidic solutions the fraction of cytosine residues involved in helical secondary structure, the degree of ionization of cytosine residues and the fraction of adenine--uracil base pairs denatured may be estimated from DeltaE(265) and DeltaE(280). In alkaline solutions the fractions of guanine and uracil residues involved in secondary structure and the degrees of ionization of these residues may be estimated from DeltaE(230), DeltaE(245), DeltaE(260) and DeltaE(280).     

A parallel algorithm for estimating the secondary structure in ribonucleic acids

A parallel algorithm for estimating the secondary structure of an RNA molecule is presented in this paper. The mathematical problem to compute an optimal folding based on free-energy minimization is mapped onto a graph planarization problem. In the planarization problem we want to maximize the number of edges in a plane with no two edges crossing each other. To solve a sequence of n bases, n(n — 1)/2 processing elements are used in our algorithm.     

Studies on the secondary structure of ribosomal ribonucleic acid components of rabbit reticulocytes

The conformation in solution of fractionated 30 S and 19 S ribosomal RNA from rabbit reticulocytes has been studied by optical rotatory dispersion, analysis of thermal melting profiles and their derivatives, and spectrophotometric acid-base titration. From a consideration of the limitations of these methods, it has been possible to set limiting values on the degree of base-pairing and the lengths of the double helices: between 60 and 80% of the bases in 19 S and 30 S RNA are estimated to be paired. The paired segments are not shorter than 4 base pairs, and evidence from other sources is available which indicates that they are not longer than 8–16 base pairs. The spread of helix lengths is greater in the 30 S than in 19 S RNA; and other differences are noted. Several distinct populations of double helices, differing in their thermal stability, are present. Estimates are presented from spectrophotometric and titration data for the base compositions of the paired and unpaired regions.     

Studies on the ribonucleic acids of fresh and processed tea leaves

1. A marked decrease in the total RNA content during the withering process of tea leaves was found. During the fermentation process, there was a small but significant decrease in the total RNA content. 2. During isolation of RNA from tea leaf tissues, the action of leaf ribonuclease was minimized by the addition of sodium dodecyl sulphate during extraction; 1% (w/v) sodium dodecyl sulphate in 0.2m-tris-hydrochloric acid buffer, pH8.0, containing 0.005% EDTA was found to be most efficient for the extraction and gave about 93% yield. 3. The total RNA preparations isolated from fresh, withered and fermented tea leaves were compared with regard to nucleotide composition and spectral characteristics. The total RNA preparations from all three sources contained more purines than pyrimidines (purine/pyrimidine ratio 1.47-1.52).     

A model for the tertiary structure of transfer ribonucleic acids

In view of the possible changes of the structure of DNA at different relative humidities, a similar model for tRNA is proposed. In the native form, the sugar phosphate backbone folds repeatedly on itself resulting in a circular rod structure of about 50 Å in length and about 25 Å in diameter. Both the amino-acyl end and the anticodon site are surrounded by segments of base sequences common to different tRNA’s.