A spectrophotometric study of the secondary structure of ribonucleic acid based on a method for diminishing single-stranded base-`stacking'' without affecting multihelical structures

1. On the basis of studies with model compounds it was concluded that in 8m-urea-m-potassium chloride (or 4m-guanidinium chloride) in 0.01m-potassium phosphate buffer, pH7.0, multi-helical structures have about the same stability as in 0.1m-potassium phosphate buffer, pH7.0, whereas the tendency of base residues to ;stack' along a single polynucleotide chain is much decreased. 2. Base-pairing was eliminated whereas base-;stacking' persisted after RNA in 1% formaldehyde-0.1m-potassium phosphate buffer, pH7.0, was heated to 95 degrees . 3. From a study of the thermal denaturation of unfractionated transfer RNA from Escherichia coli and of RNA from the fractionated sub-units of rabbit reticulocyte ribosomes in 8m-urea-m-potassium chloride (or 4m-guanidinium chloride) in 0.01m-potassium phosphate buffer, pH7.0, it was inferred that ;stacked' residues may account for up to 25% of the increase in E(260) found on heating RNA in solvents such as 0.1m-potassium phosphate buffer, pH7.0. 4. Changes in the spectrum with temperature were analysed on the basis of the assumptions that (a) the polynucleotide chain is amorphous on denaturation (which is probable in 8m-urea-m-potassium chloride-0.01m-potassium phosphate buffer, pH7.0) and that (b) the polynucleotide chain adopts a single-stranded ;stacked' conformation on denaturation (which is probable when ordinary solvents such as 0.1m-potassium phosphate buffer, pH7.0, are used).     

Chromosomal DNA denaturation and reassociation in situ.

The degree of chromosomal DNA (cDNA) denaturation and renaturation on polytene chromosomes has been measured by UV microspectrophotometry. Also DNA losses occurring upon denaturation have been quantified by Feulgen, gallocyanin-chromalum and UV. It has been observed that denaturation in alkali (0.07 N NaOH at room temperature) and formamide (90% formamide; 0.1 SSC, pH 7.2) at 65 °C removes about 30% of the DNA. Low DNA loss occurs upon denaturation in HCl (0.24 M) at room temperature and 60% formamide: 2 × 10^?4 M EDTA (pH 8) at 55 °C. The presence of 4% formaldehyde in the denaturation buffer prevents DNA loss. After denaturation of chromosomes in 0.1 × SSC containing 4% formaldehyde at 100 °C for 30 sec, an hyperchromicity of 39 °C is observed. The denaturation efficiency varies with the denaturation treatment. The percentage reassociation was measured from the difference in the UV absorption of renatured chromosomes and that of denatured chromosomes from the same set. It seems that in our conditions DNA:DNA reassociation does not occur. The efficiency of hybridization is proportional to the denaturation extent of the DNA. However, the entire fraction of DNA which has been denatured is not available for hybridization.     

Secondary structure of RNA secreted by Ehrlich ascites carcinoma cells]

The RNA, secreted by the cells of Ehrlich ascite carcinoma stimulates the inoculability and growth of the tumour. It contains double-helical regions, is resistable to the effects of pancreatic RNAse, has a melting point at 74 degrees and is eluted from the hydroxylapatite column by 0,25 M phosphate buffer. During its interaction with ethidium bromide the RNA increases the fluorescence of the dye. The amount of double-helical regions in the RNA makes up to 60%. These double-helical regions are formed in the carcinoma-secreted RNA due to RNA self-supercoiling. This was demonstrated by fluorescence studies of the RNA-ethidium bromide complex under various RNA denaturation and renaturation conditions.     

Electron microscopy of simian virus 40 DNA configuration under denaturation conditions.

After isolation, the DNA of simian virus 40 appeared as a negative supertwist (form I) or as an open circle with at least one single-strand scission (form II). Under the denaturation conditions usually applied, such as heating in the presence of formaldehyde or application of alkali, form I molecules could appear as "relaxed" circles without single-strand scissions (form I') containing denatured sites not visible under the electron microscope. Form II molecules, under these denaturation conditions, showed partial or complete strand separations allowing the construction of denaturation maps. By using a modified denaturation procedure, i.e., heating of isolated SV40 DNA in the presence of dimethyl sulfoxide and formaldehyde followed by keeping the DNA in this denaturation solution at room temperature for periods up to 3 weeks, partially denatured relaxed circles without single-strand scissions were produced (form I'D) in addition to completely denatured form II molecules. The absence of single-strand scissions in form I'D molecules was demonstrated by a second heat treatment, which did not change the configuration of this molecular form. Form I'D molecules, in contrast to form I', contained denatured sites clearly discerible under the electron microscope. This combined application of two subsequent denaturation steps (denaturation by heating followed by denaturation at room temperature and neutral pH) showed that the molecular configuration I'D originated in two steps. The heating procedure produced molecules not distinquishable by electron microscopy from form I. In contrast to form I, these molecules were assumed to possess "preformed" denaturation sites (form I). Further treatment of form I molecules with denaturation solution at room temperature finally transformed them into convalently closed, relaxed, partially denatured circles exhibiting strand separations easily measurable on electron micrographs (form I'D). Denaturation maps of form I'D molecules were constructed by computer and compared with denaturation maps derived from partially denatured form II molecules. From these denaturation maps it can be concluded that the melting of base pairs occurring during the transition of simian virus 40 DNA form I into form I'D also preferentially happened at sites rich in the bases adenosine and thymine.     

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).     

Conformational changes in the extracellular β-lactamase I from Bacillus cereus 569/H/9

1. The thermal denaturation and precipitation of beta-lactamase I from Bacillus cereus 569/H/9 at 60 degrees C are reversible, a soluble and almost fully active enzyme being obtained after solution of the precipitate in 5m-guanidinium chloride or 8m-urea and subsequent removal of the denaturing agent. 2. Inactivation of beta-lactamase I occurs rapidly between 50 degrees and 55 degrees C and is shown by circular-dichroism spectra to be accompanied by an extensive conformational change. 3. A change to a different conformation occurs in 6m-urea. This change is also reversible; refolding with almost complete recovery of enzymic activity occurs within 5min of dilution of the denaturing agent. 4. Inactivation of beta-lactamase I at pH3.0 and 11.0 is also associated with conformational changes, since a proportion of the lost activity is recovered within 5min of adjustment of the pH to 7.0.     

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.     

Detection by electron microscopy of photo-induced denaturation in lambda DNA.

We have used an electron microscope to study localized denatured regions in ultraviolet-irradiated DNA. DNA from bacteriophage lambda was UV-irradiated and then prepared for electron microscopy after fixing in buffered (pH 9.5) formaldehyde solutions at 25 degrees C. The denatured regions observed corresponded to those described by Inman and Schnös (1) who used alkaline denaturation to preferentially destroy thymine-adenine base pairing. In UV-irradiated DNA, pairs of neighboring thymine residues are converted into photodimers; hence, loss of hydrogen bonding most likely occurs in thymine-rich regions and denaturation results. Conceivably, photo-induced denaturation may under some circumstances represent a more convenient method than alkaline denaturation for mapping thymine-rich regions in DNA.     

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.     

Effect of formaldehyde on the efficiency of hybridization of DNA immobilized on nitrocellulose filters.

We report in this study that under certain conditions formaldehyde interacts with DNA and makes it more efficient for hybridization on nitrocellulose filters. Hybridization signals of formaldehyde-treated DNA are stronger (up to 10 fold) as compared with that of the heat- or alkali-denatured DNA. Various parameters of the DNA-formaldehyde reaction are optimized as follows: (a) 6 x SSC, 10% formaldehyde, 60 degrees C, 20-30 min, reaction volume 10-200 microliters or (b) 6 x SSC, 5% formaldehyde, 98 degrees C, 15 min, reaction volume 10-200 microliters. Treatment of agarose gels after electrophoresis with formaldehyde improved both the transfer of DNA and the efficiency of hybridization. The following conditions are recommended for gel treatment: denaturation in 0.3 N NaOH, 1 M NaCl followed by neutralization with 0.5 M phosphate buffer, pH 7.0, containing 10% formaldehyde at 60 degrees C for 20 min.     

The subunits of thyroglobulin

1. Pig thyroglobulin was reduced with dithiothreitol in the presence of sodium dodecyl sulphate, 8m-urea or 6m-guanidinium chloride. 2. The molecular weights of the reduction products were about 165000. 3. Two stable subunits with molecular weights as low as 35000 and 20000 were separated by Sephadex chromatography after prolonged exposure of the reduction products to sodium dodecyl sulphate at pH8.7. Although a hydrolytic reaction is probably implicated, the nature of the chemical linkages broken was not established.     

Helix-destabilization of deoxyribonucleic acid and poly[d(A-T).d(A-T)] by bovine seminal ribonuclease

A ribonuclease isolated earlier from bovine seminal plasma by DNA-affinity chromatography (Ramakrishnamurti, T. and Pandit, M.W. (1983) J. Chromatogr. 260, 216-222) has now been shown by thermal denaturation studies to destabilize the double-helical structure of DNA and poly[d(A-T).d(A-T)]. Thermal denaturation profiles of DNA in the presence of the protein are much more complicated due to the denaturation of protein itself in the temperature range over which DNA predominantly melts. The protein shows relatively stronger affinity towards denatured DNA as compared to native DNA. The action of micrococcal nuclease on DNA and its complexes with ribonuclease A and bovine seminal ribonuclease indicates that both of these proteins destabilize the double-helical structure of native DNA and thereby render the DNA more sensitive to the micrococcal nuclease.     

Thermal denaturation in acidic solutions of double-helical ribonucleic acid from virus-like particles found in Penicillium chrysogenum. A spectrophotometric study

1. Two species of double-helical RNA isolated from mycelium of Penicillium chrysogenum were titrated with acid at 25°C and 95°C (solvent 0.1m-sodium phosphate buffer). At 25°C denaturation occurred at about pH3. At 95°C in the denatured form cytosine residues titrated as a simple monobasic acid of pK3.9 compared with pK2.5 for the native form at 25°C. 2. On thermal denaturation in neutral and acidic solutions one species of RNA (38% rG·rC) `melted' in three distinct stages, equivalent to a mixture of three species, namely one of about 25% rG·rC, another of about 33% rG·rC and a third of about 46% rG·rC: the relative proportions were 0.25:0.35:0.40. 3. On thermal denaturation in acidic solutions the increase in the fraction of ionized cytosine residues concomitant with the `melting' of rG·rC base pair also affects the spectrum especially at 280nm and serves to enhance the contribution of rG·rC base pairs at this wavelength. The increment in ε_(P) at 280nm on `melting' an rG·rC base pair approaches 53501·mol<sup>−1</sup>·cm<sup>−1</sup> depending on pH, compared with 33501·mol<sup>−1</sup>·cm<sup>−1</sup> at pH7. In contrast ε<sub>(P)</sub> at 280nm is scarcely affected by `melting' rA·rU base pairs or by the protonization of adenine residues. 4. Changes in the spectrum of Escherichia coli rRNA on denaturation in acidic solutions were studied to yield the mole fractions of rA·rU and rG·rC base pairs `melting' at particular pH values.     

Size and structure of the genome of infectious pancreatic necrosis virus.

The genome of infectious pancreatic necrosis virus consists of two segments of dsRNA, in equimolar amounts, with molecular weights of 2.5 X 10(6) and 2.3 X 10(6) daltons, as determined by polyacrylamide gel electrophoresis and autoradiography. The viral RNA was resistant to ribonuclease, and in sucrose gradient it co-sedimented at 14S with RNase resistant RNA from virus infected cells. Upon denaturation in 98% formamide, the viral genome sedi-mented at 24S in formamide sucrose gradient and became sensitive to RNase. Denatured 24S viral RNA did revert to its undenatured 14S form upon recentrifugation in aquaeous sucrose gradient (0.1 M NaCL), but co-sedimented with the denatured large size class of reovirus 25S RNA. The same results were obtained if the native viral RNA was pre-treated with ribonuclease before denaturation, indicating the absence of exposed single strainded regions in the viral genome. Since infectious pancreatic necrosis virus contains only two dsRNA segments it does not belong to the family Reoviridae and may represent a new group of viruses.     

Denaturation of deoxyribonucleic acid in situ effect of formaldehyde.

In situ denaturation of nuclear deoxyribonucleic acid (DNA) is studied by use of acridine orange to differentially stain native versus denatured DNA, and a flow-through cytofluorometer for measurements of cell fluorescence. Thermal- or acid-induced DNA denaturation is markedly influenced by formaldehyde. Two mechanisms of the formaldehyde action are distinguished. If cells are exposed to the agent during heating, DNA denaturation is facilitated, most likely by the direct action of formaldehyde as a "passive" denaturing agent on DNA. If cells are pretreated with formaldehyde which is then removed, DNA resistance to denaturation increases, presumably due to chromatin cross-linking. It is believed that both effects occur simultaneously in conventional techniques employing formaldehyde to study DNA in situ, and that the extent of each varies with the temperature and cell type (chromatin condensation). Thus, profiles of DNA denaturation of cells heated with formaldehyde do not represent characteristics of DNA denaturation in situ; DNA denaturation under these conditions is modulated by the reactivity of chromatin components with formaldehyde rather than by DNA interactions with the macromolecules of nuclear mileu.     

Conformation of nucleic acids and the analysis of the hypochromic effect

The spectra of two double-helical RNA species isolated from virus-like particles found in the mycelium of Penicillium chrysogenum were measured at about 25 degrees C, and at 95 degrees C after denaturation to a single-stranded form, and compared with the spectrum of the equivalent mixture of nucleotides. For both species the difference spectrum (epsilon(95 degrees C)-epsilon(25 degrees C)) when increased by 33% was very similar to the difference spectrum (epsilon(nucleotides)-epsilon(25 degrees C)). In contrast it was found for rat liver DNA that there was no simple relation between (epsilon(95 degrees C)-epsilon(25 degrees C)) and (epsilon(nucleotides)-epsilon(25 degrees C)). These observations were accounted for on the basis of the difference spectra for rA.rU, rG.rC, dA.dT and dG.dC base-pairs derived from model polyribonucleotides and polydeoxyribonucleotides. The difference spectra (epsilon(95 degrees C)-epsilon(25 degrees C)) found for rRNA and those calculated from a combination of the difference spectra for rA.rU and rG.rC base-pairs were in good agreement.     

Gamma-ray induced double-strand breaks in DNA resulting from randomly-inflicted single-strand breaks: temporal local denaturation, a new radiation phenomenon?

The induction of single- and double-strand breaks in DNA by gamma-rays has been measured. The maximum number of nucleotide pairs (a) between two independently induced single-strand breaks in opposite strands of the DNA which cannot prevent the occurrence of a double-strand break was found to amount to about 16. This value did not differ significantly for the four types of bacteriophage DNA investigated (T4, T7 and PM2 DNA, and replicative form DNA of phage phiX174) and was the same in 10(-2) M phosphate buffer containing 0, 0.5 or 1 M NaCl. In 10(-3) M phosphate buffer a was 34 nucleotide pairs. Evidence is presented that the relatively large value of a has to be ascribed at least partly to a temporal local denaturation accompanying the induction of a single-strand scission. A contribution of base damage that labilizes the DNA-helix, between two single-strand breaks to the high value of a can not be excluded.     

Instability of F-actin in the absence of ATP: a small amount of myosin destabilizes F-actin.

The effects of the neutral salt concentration, pH, and coexistence of myosin on the denaturation of F-actin without ATP at low temperature were studied using the DNase I inhibition assay. The percent denaturation of F-actin gradually increased with a decrease in pH from 8.0 to 5.2, on incubation for 2 weeks in the presence of 50 mM KCl at 0 degrees C. This change was much faster in 0.5 M KCl and more than 75% of the F-actin became denatured on incubation for 1 week at pH 5.2. The buffer composition was found to exert a strong influence on the denaturation of F-actin. That is, there was a tendency for the denaturation of F-actin at pH 6.0 to be faster in MES[2-(N-morpholino)ethanesulfonic acid]-NaOH buffer than in sodium phosphate buffer, the critical concentrations of actin in 0.5 M KCl being 0.31 mg/ml for MES-NaOH buffer and 0.15 mg/ml for sodium phosphate buffer. A sigmoidal relationship was found between the percent denaturation of F-actin and the KCl concentration added, the greatest change occurring at KCl concentrations between 0.25 and 0.75 M. The time courses of the denaturation of F-actin showed that the percent denaturation rose at first and that in time the rate of the increase decreased. In the case of pH 8.0 and 0.5 M KCl, it took about 1 week for the denaturation rate to begin to drop. The pH of 6.0 further promoted the instability of F-actin exposed to high KCl concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparative effect of microwaves and boiling on the denaturation of DNA

The effect of heat and microwave denaturation of small volumes of double-stranded plasmid DNA has been compared. Samples of intact plasmid DNA had plasmid DNA linearized by digestion with EcoRI were conventionally denatured in a boiling water bath or denatured by 2450 MHz of microwave energy for 0-300 s. Heat denaturation for periods longer than 120 s caused breakdown of linearized plasmid DNA; however, microwave denaturation for 10-300 s caused no apparent degradation of linearized DNA. Breakdown of DNA forms II and III was noted in plasmid DNA subjected to 300 s of either heat or microwave denaturation but breakdown of forms II and III occurred more quickly with heat than with microwave treatment. Microwave treatment was also found to be better than heat to denature 32P-labeled DNA probes subsequently used to detect homologous DNA samples immobilized on nitrocellulose filters. A microwave-treated 32P-labeled DNA probe was able to hybridize to DNA samples 20 times more dilute than a heat-treated 32P-labeled DNA probe. Depending on the form of DNA to be analyzed, these results indicate that small volumes of DNA solutions and radiolabeled DNA probes can be effectively denatured in a conventional microwave oven.