Differentiation of DNA and RNA on filter paper discs

Differentiation of radioactive DNA and RNA deposited on filter paper discs can be accomplished by a relatively simple procedure. RNA can be efficiently removed by incubating the dises, impaled on pins, with 0.2 ml of 0.5 n NaOH for 90 min at 37°C. DNA can be removed after NaOH hydrolysis by treating the discs with 5% TCA for 30 min at 90°C. A correction is necessary to determine the actual amounts of DNA and RNA in order to account for the loss of DNA (13.8%) during the NaOH hydrolysis procedure.     

A simple multiwell tray for manipulation of radiolabeled nucleic acids on filter disks

This note describes a simple tray in which large numbers of radiolabeled nucleic acid samples mounted on paper or glass-fiber disks can be subjected to various treatments prior to counting by liquid scintillation spectrometry. The tray is useful for analysis of samples from ultracentrifugal fractionation of nucleic acids, for direct sampling of RNA or DNA polymerase assays in vitro, and for analysis of nucleic acid labeling in bacterial cultures.     

Procedure for the base composition of RNA especially suited for samples containing relatively large amounts of DNA and protein

An inexpensive procedure suitable for determining the base composition of RNA in a sample containing large amounts of DNA and protein is presented. The method involves cold acid precipitation, mild alkaline hydrolysis, acid hydrolysis, ion-exchange separation, and spectral analysis. At least 70 μg RNA is required, which for accuracy within 7% should be no less than 4% dry weight in a chromatin sample or 2% dry weight in a ribonucleoprotein sample. Purine-pyrimidine ratios may be obtained on samples with relatively even less RNA. The precision is approximately ±2% for the values of the individual bases, and the over-all RNA recovery is 90%. Despite the multiple steps involved, three samples may be carried through the entire procedure in one day.     

Spectrophotometric analysis of RNA and DNA using cetyltrimethylammonium bromide

A versatile procedure is described for the analysis of RNA and DNA in brain using cetyltrimethylammonium bromide as the initial precipitant. Optimal conditions are described for the precipitation, hydrolysis, and effective separation of the RNA and DNA fractions from contaminating protein. The RNA and DNA fraction can now be accurately estimated by uv absorbance without a two wavelength correction. This method has also been used for the analysis of other mammalian organs and for mammalian cells obtained from tissue culture. The method may also be used for the simultaneous determination of radioactivity in nucleic acids. The orcinol reaction is shown to give high values for brain RNA.     

Quantitative microdetermination of DNA by two-dimensional electron capture gas chromatography of the thymine constituent

A highly sensitive and specific two-dimensional electron-capture gas chromatographic method has been developed for determining small amounts of DNA by measuring its thymine content. The method can also be used to measure RNA based on uracil content. The nucleic acids were hydrolyzed and released constituents were separated and detected as their chloromethyldimethylsilyl ethers. The minimal amount detected was 5 pg of each base. Standard curves were linear from 5 to 200 pg. This method allowed quantitative determination of 2 ng of DNA (routinely detectable quantity) after hydrolysis of biological material in formic acid, even in the presence of large amounts of RNA and/or protein. For example, this method has been shown to be successful in determination of the DNA contents of manually isolated nucleic such as from amphibian oocytes. Besides being accurate, the procedure was rapid: after maximal hydrolysis (usually about 45 min) the derivatization and gas chromatographic analysis was completed in another 15 min. The procedure described represents a direct biochemical alternative to cytophotometric estimation of nuclear contents and has the advantage of providing values for absolute DNA content per nucleus.     

Analysis of the 5'-termini of nascent DNA chains synthesized in permeable cells of Bacillus subtilis

The nascent DNA synthesized by permeable cells of Bacillus subtilis in the presence of 5'-mercurideoxycytidine triphosphate and 2',3'-dideoxyATP has been isolated and characterized. The newly synthesized DNA was isolated free from other cellular nucleic acids by affinity chromatography on thiol-substituted agarose. The number average chain length of the nascent DNA synthesized in one minute at 25 degrees C was 33 nucleotide residues, due to the chain-terminating action of 2',3'-dideoxyATP. Several lines of evidence indicated that at least 90% of the DNA thus isolated carried a terminally phosphorylated RNA moiety at its 5'-end: (1) the nascent DNA was resistant to exonucleolytic degradation by spleen phosphodiesterase unless first hydrolyzed by strong alkali or ribonuclease; (2) the 5'-termini of nascent DNA could not be phosphorylated by polynucleotide kinase unless first treated with alkaline phosphatase or subjected to hydrolysis by strong alkali or ribonuclease; (3) alkaline hydrolysis of nascent DNA labeled with 32P at the 5'-end released unlabeled DNA with a free 5'-terminus and 32P-labeled ribonucleoside 3',5'-bisphosphates; (4) ribonuclease degradation of similarly labeled material produced an unlabeled DNA-containing polynucleotide fraction and 32P-labeled ribo-oligonucleotides; (5) chromatography on dihydroxyboryl cellulose showed that the RNA moiety lacked a 3'-terminal cis-diol grouping (even after treatment with alkaline phosphatase) unless first subjected to the 3'-exonucleolytic action of bacteriophage T4 DNA polymerase. The sequence of the ribonucleotide chains was elucidated by end-group labeling with polynucleotide kinase and digestion with various ribonucleases. The ribonucleotide moiety was primarily three and four residues in length with the predominant sequence (pp)pApG(pC)1-2pDNA. The possibility that it represents a primer for discontinuous DNA synthesis is discussed.     

Purification of DNA for bacterial productivity estimates

[methyl-3H]thymidine-labeled DNA from natural populations of aquatic bacteria was completely separated from RNA and protein by hydroxylapatite chromatography. The procedure was validated by monitoring increases in Escherichia coli cell count, A550, DNA concentration, and thymidine incorporation into DNA isolated by the proposed technique. The procedure can be used in the field and does not rely on the use of acid-base hydrolysis or volatile organic solvents.     

Factors affecting the course of DNA acid hydrolysis in carrying out the Feulgen reaction]

Literature data concerning acid hydrolysis of DNA during the Feulgen procedure are reviewed, with emphasis being made on the dependence of Schiff-apurinic acid binding on the fixation technique, the temperature of hydrolysis and acid concentration, the rate of extraction of depolymerized DNA fragments, the nucleotide composition of DNA, the chromatin state, and on the composition of nucleoprotein. Some practical considerations for optimization of the Feulgen procedure for a precise quantitative determination of DNA amount are given.     

Purification of DNA for bacterial productivity estimates.

[methyl-3H]thymidine-labeled DNA from natural populations of aquatic bacteria was completely separated from RNA and protein by hydroxylapatite chromatography. The procedure was validated by monitoring increases in Escherichia coli cell count, A550, DNA concentration, and thymidine incorporation into DNA isolated by the proposed technique. The procedure can be used in the field and does not rely on the use of acid-base hydrolysis or volatile organic solvents.     

The estimation of the nucleic acids of tissue sections and its use as a unit of comparison for quantitative histochemistry

Summary There are many advantages in using the nucleic acid content of tissue sections as the unit of comparison for quantitative histochemistry. A quick, simple, reliable method for the estimation of DNA and RNA in sections of rat liver is described. The method depends on the differential hydrolysis in IN HCl at 60° C; the RNA is removed after 4 min hydrolysis and the DNA by a further 30 min hydrolysis. The optimum extinction of the hydrolysates is measured in an ultraviolet spectrophotometer. The results show a reproducibility, between serial sections, of better than ±5 %.     

Hydrolysis with lead perchlorate: A new method used to estimate RNA in sugarcane tissues

The precipitation and hydrolysis of RNA by lead perchlorate has been studied and the results have been applied to estimate RNA in three widely different tissues from Saccharum species (sugarcane). This new method makes it possible to estimate RNA in highly lignified tissue for which existing methods using cold perchloric acid or warm alkali are unsuitable. As far as comparisons are possible, lead perchlorate gives the same results as extraction with acid and alkali, except that values are slightly lower in rapidly dividing tissue. Acid-soluble materials are removed by a single extraction with 0.01 m Pb(ClO₄)₂ at pH 2, where RNA and DNA are quantitatively precipitated but not hydrolyzed. Specific hydrolysis of RNA is then carried out at neutral pH with a solution containing 3 m Pb(ClO₄)₂ and 2.5 n NaOH, and the products are extracted at pH 2. DNA and most interfering materials remain insoluble. RNA in the extract is measured by uv absorption versus a combined tissue/reagent blank. The entire procedure can be carried out at room temperature. DNA in the tissue can be estimated as usual (1–3).     

Effect of ecdysterone contact period on development of wing disks of the fleshfly, Sarcophaga peregrina, in vitro

The ecdysterone contact period required for pupal development of Sarcophaga wing disks was studied in vitro. When the disks were cultured in a medium with 1 × 10^?6 M ecdysterone for about 21 hr, evagination of wing disks occurred independent of a later transfer into a hormone-free medium. The contact period required for wing evagination was dependent on the concentration of ecdysterone.When the disks cultured in the ecdysterone-containing medium were subjected to an intervening ecdysterone-free condition, evagination of the wing occurred if the period of the hormone contact before and after the ecdysterone-free period totalled a certain length. The total period required for wing evagination was altered both by the duration of the intervening hormone-free culture and duration of the first culture with ecdysterone.The morphogenetic effect of ecdysterone is discussed in relation to RNA synthesis in vitro.     

Rapid purification of bacterial plasmids and coliphage M13 RF without CsCl centrifugation

A simple and rapid procedure for the purification of plasmids from Escherichia coli K12 has been developed. Bacterial cells are subjected to the boiling procedure [D. S. Holmes, and M. Quigley Anal. Biochem.114, 193–197 (1981)] followed by removal of contaminating RNA by chromatography on Sepharose 2B and of genomic DNA by acid-phenol extraction. Plasmids are recovered with good yield. They can be restricted and ligated and will transform host cells. A simple modification of the procedure allows it to be used for the isolation of coliphage M13 RF DNA.     

The sequential enzymatic determination of DNA and RNA

Enzymatically small quantities of native DNA and RNA in crude tissue homogenates can readily be specifically determined using ethidium bromide as a fluorescent indicator. The ethidium bromide-polynucleotide complexes of DNA and RNA serve as effective substrates for deoxyribonuclease and ribonuclease, respectively. Optimal divalent metal cation requirements were determined for a common reaction medium that is compatible for both the DNase and RNase reactions. To a single reaction mixture, that contains a biological sample, sequential addition of DNase and RNase produces a specific and rapid decrease in fluorescence that is proportional to the respective amounts of DNA and RNA present. Levels of DNA and RNA found in six different tissues of the rat were determined enzymatically by this method and compared to that obtained by alternate techniques. Enzymatically determined values were highly reproducible and correlate well with those values obtained by more time-consuming, conventional methods. Most enzymatically determined RNA levels in tissues, however, were significantly greater than those levels obtained spectrophotometrically. Advantages of the enzymatic procedure for analysis of tissue polynucleotide content are: (1) rapid determination of both DNA and RNA within a single sample aliquot allowing maximum use of available sample; (2) extensive fractionation and extraction of the tissue are not required; (3) it is especially useful when quantities of tissue are limited; and (4) sensitivity to 0.05 and 0.25 μg of DNA and RNA, respectively. Reaction conditions developed for the assay also provide for a highly sensitive means to continuously monitor DNA hydrolysis; DNase activity is directly proportional to the amount of enzyme added.     

The Protease Domain Increases the Translocation Stepping Efficiency of the Hepatitis C Virus NS3-4A Helicase

Hepatitis C virus (HCV) NS3 protein has two enzymatic activities of helicase and protease that are essential for viral replication. The helicase separates the strands of DNA and RNA duplexes using the energy from ATP hydrolysis. To understand how ATP hydrolysis is coupled to helicase movement, we measured the single turnover helicase translocation-dissociation kinetics and the pre-steady-state P_i release kinetics on single-stranded RNA and DNA substrates of different lengths. The parameters of stepping were determined from global fitting of the two types of kinetic measurements into a computational model that describes translocation as a sequence of coupled hydrolysis-stepping reactions. Our results show that the HCV helicase moves with a faster rate on single stranded RNA than on DNA. The HCV helicase steps on the RNA or DNA one nucleotide at a time, and due to imperfect coupling, not every ATP hydrolysis event produces a successful step. Comparison of the helicase domain (NS3h) with the protease-helicase (NS3-4A) shows that the most significant contribution of the protease domain is to improve the translocation stepping efficiency of the helicase. Whereas for NS3h, only 20% of the hydrolysis events result in translocation, the coupling for NS3-4A is near-perfect 93%. The presence of the protease domain also significantly reduces the stepping rate, but it doubles the processivity. These effects of the protease domain on the helicase can be explained by an improved allosteric cross-talk between the ATP- and nucleic acid-binding sites achieved by the overall stabilization of the helicase domain structure.     

Multiple forms of DNA-dependent RNA polymerases in Xenopus laevis. Rapid purification and structural and immunological properties

DNA-dependent RNA polymerases I, II, and III (EC 2.7.7.6) were isolated from Xenopus laevis ovaries. The soluble enzymes were precipitated with polyethyleneimine and subjected to chromatography on heparin-Sepharose, DEAE-Sephadex, and phosphocellulose. RNA polymerase I was subjected to an additional chromatographic step on CM-Sephadex. The procedure required 40 h and produced purified RNA polymerase forms IA, IIA, and III in yields of 5 to 40%. The specific activities of RNA polymerases IIA and III (on native DNA) were comparable to those reported from other eukaryotic sources, whereas that of form IA was severalfold greater than the specific activities reported for other purified class I RNA polymerases. The complex subunit compositions of chromatographically purified RNA polymerases IA, IIA, and III were distinct when analyzed by polyacrylamide gradient gel electrophoresis under denaturing conditions, although all three classes contained polypeptides with Mr = 29,000, 23,000, and 19,000. Antibodies prepared against RNA polymerase III showed common antigenic determinants within the class I, II, and III enzymes. The sites responsible for the cross-reaction are located, at least in part, on the common 29,000-dalton polypeptide.