A spectrophotometric study of the secondary structure of ribonucleic acid based on a method for diminishing single-stranded base-‘stacking’ without affecting multi-helical structures

Self Cite

1. The thermal denaturation of DNA from rat liver was studied spectrophotometrically. In sodium phosphate buffers denaturation led to a single-stranded form having, at 25 degrees , about 25% of the hypochromism of the intact double helix. 2. The hypochromism of the denatured form was the same in 1mm- as in 10mm-sodium phosphate buffer and was scarcely affected by reaction with formaldehyde. The hypochromism was decreased by about 40% in the presence of 8m-urea. 3. The hypochromism of denatured DNA at low ionic strengths was about the same as that of fragments of reticulocyte ribosomal RNA that were too short to form double-helical secondary structure and about the same as that of RNA after reaction with formaldehyde. 4. The spectrum of DNA was slightly affected by the presence of 8m-urea or 4m-guanidinium chloride. The differences in the spectrum of the native and denatured forms of DNA in 0.1m-sodium phosphate buffer, in 8m-urea-10mm-sodium phosphate buffer and in 4m-guanidinium chloride-10mm-sodium phosphate buffer, pH7.6, were similar but not identical. 5. Denatured rat liver DNA appears to have no double-helical character at 25 degrees in 10mm-sodium phosphate buffer, pH7.6; increasing the buffer concentration to 0.1m leads to a more compact form in which about 40% of the residues form base pairs.

Section: P0csupporting

confidence: 68%

mentioning

confidence: 99%

mentioning

confidence: 99%

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A spectrophotometric study of the denaturation of deoxyribonucleic acid in the presence of urea or formaldehyde and its relevance to the secondary structure of single-stranded polynucleotides

Cox

Kanagalingam

1968

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“…The fraction of hairpin loops re-formed on neutralization was obtained from the denaturation spectrum. In solutions such as 4m-guanidinium chloride the tendency of base residues to stack along a single strand is decreased, but the stability of double-helical structures is scarcely affected (Cox & Kanagalingam, 1967b). Provided that the novel species of hairpin loop do not interfere:…”

Section: ' F = Il-p);mentioning

confidence: 99%

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

Cox

Gould

Kanagalingam

1968

Self Cite

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.

“…Molar residue absorption coefficients of the rRNA species investigated were determined in sodium phosphate buffer (pH 7.0) and 4.0 M-guanidinium chloride/ 10mM-sodium phosphate buffer (pH 7.0). As Table 1 shows, in 4.0M-guanidinium chloride the E values (25 IC) are generally higher than in phosphate buffer, as expected if in the former solvent the hypochromism arising fromn the fraction, f.8, of residues that are stacked in single-stranded parts is largely diminished at room temperature (Cox & Kanagalingam, 1967;Cox, 1970). Thus, when 4.0M-guanidinium chloride is used, changes in absorption on heating are mostly accounted for by the 'unstacking' of bases that are located in bihelical portions of rRNA; since f,, is small, ES tends to sam and eqn.…”

Section: Vol 189mentioning

confidence: 71%

Physicochemical characterization of the ribosomal RNA species of the Mollusca. Molecular weight, integrity and secondary-structure features of the RNA of the large and small ribosomal subunits

Cammarano¹,

Londei²,

Mazzei³

et al. 1980

1. The rRNA species of the Cephalopoda Octopus vulgaris and Loligo vulgaris were found to have unexpectedly high sedimentation coefficients and molecular weights. In 0.1 M-NaCI the L-rRNA (RNA from large ribosomal subunit) has the same s2O value as the L-rRNA of the mammals (30.7 S), whereas the S-rRNA (RNA from small ribosomal subunit) sediments at a faster rate (20.1 S) than the S-rRNA of both the mammals and the fungi (Neurospora crassa) (17.5 S). The molecular weights of the L-rRNA were determined by gel electrophoresis in formamide and found to be 1.66 x 106 (Octopus) and 1.89 x 106 (Loligo); the mol.wt. of the S-rRNA of both species is 0.96 x 106, i.e. much larger than that of the mammals (0.65 x 106) and almost coincident with that of the '23S' RNA of the prokaryotes. 2. By contrast, the less evolved Gastropoda and Lamellibranchiata (Murex trunculus and Macrocallista chione) have S-rRNA and L-rRNA species with mol.wts. of 0.65 x 106 and approx.