Room-temperature chromatography of nucleic acids on hydroxylapatite columns in the presence of formamide

DNA chain elongation rates in marrow cells from vitamin B12-deficient patients and methotrexate-treated mice

The DNA synthesized by marrow cells from patients with vitamin B12 deficiency and mice previously given methotrexate (MTX), has been investigated. Suspensions of bone marrow cells were pulse-labelled with [methyl-3H]thymidine or deoxy [5-3H]cytidine for 30 s and the radioactivity in the DNA was chased thereafter in the presence of 10 microM non-radioactive nucleoside for periods up to 60 min. The rates of elongation of new daughter strands were then assessed by hydroxyapatite chromatography of alkali-denatured DNA samples. No significant differences were found between the average rates of elongation of daughter strands from control marrow cells on the one hand and the vitamin B12-deficient or the methotrexate-affected cells on the other. This is to be contrasted with the results of previous studies which have shown a retardation in the rates of movement of replication forks in stimulated, cultured lymphocytes obtained from vitamin B12- or folate-deficient patients.

Frequency distribution of messenger sequences within polysomal mRNA and nuclear RNA from rat liver

DNA complementary to polysomal poly(A)-containing mRNA (cDNA) of male rat liver was used to study the diversity of messenger sequences in the nucleus and in polysomes. 1. Hybridization of cDNA against an excess of its own polysomal mRNA template revealed that about 10,000 different mRNA species are expressed in the liver tissue. They are distributed in a wide frequency range derived from approximately 0.5% of the total genome. 2. Hybridization of the cDNA against total nuclear RNA shows that messenger sequences comprise less than 1% of the mass of total nuclear RNA. Messenger sequences have a different frequency distribution in nucleus and cytoplasm. 3. In hybridizations using cDNA, which had been fractionated into sequences representing abundant and scarce polysomal mRNA molecules, it was found that although abundant cytoplasmic messenger sequences are also abundant in the nucleus, they exist in a significantly lower frequency range in the nuclear compartment.

Size distribution of rat liver nuclear RNA containing mRNA sequences

Total rat liver poly(A)-containing polysomal mRNA was size-fractionated on polyacrylamide gels in 98% formamide. Complementary DNA (cDNA) was prepared from the 8--14-S mRNA fraction and separated into sequences representing abundant and non-abundant mRNAs. The cDNA complementary to the abundant small mRNA of the rat liver cell (approximately 20 species) was hybridized to nuclear RNA of different lengths to determine the size distribution of nuclear RNA molecules which contain these messenger sequences. It was found that: 1. All abundant 8--14-S poly(A)-containing mRNAs have larger nuclear precursor molecules; 20% of the different messenger sequences are found in nuclear RNA of several times their cytoplasmic length. 2. 70% of the mass of the examined nuclear messenger sequences is in RNA molecules of a size similar to their polysomal mRNA; 30% are in larger than 18-S RNA and 2% are between 37 S and 44 S. 3. The majority of small messenger-containing RNA molecules in the RNA prepared from isolated nuclei are of true nuclear origin, since their frequency distribution differs significantly from that of the polysomal 8--14-S mRNA.

Thermal elution chromatography of nucleic acids on hydroxyapatite

Hydroxyapatite thermal elution chromatography was studied from an empirical standpoint. The dependence of elution temperature on elution buffer concentration was determined for various types of buffer, hydroxyapatite and nucleic acid. The results are analyzed in terms of the proper design and interpretation of thermal elution experiments. The potential for serious artifacts is demonstrated and the means by which they may be avoided is described. Various commercially available hydroxyapatites were tested in conjunction with various aqueous and partially non-aqueous buffer systems. Among the materials tested, potassium phosphate and Bio-Rad HTP were found to constitute the best buffer-hydroxyapatite system for most types of thermal elution study.

Variation in the molecular size of the DNA from closely related strains of type I herpes simplex virus

We have investigated the comparative genome size of five strains of HSV type 1 (HSV-1). Two of these strains have a common origin and differ in their plaque morphology on HeLa cells, one strain is a wild type isolate, and two others are established laboratory strains. All strains show high sequence homology based on the melting behavior of heteroduplexes. The greatest sequence divergence between any two strains was found to be no more than 10%. There are real differences in the size of the genomes of these strains of HSV-1 as measured by electron microscopy. The shortest and largest genomes measured differ in size by 10%, however, the size of the genomes of all strains are within 5% of a median valve of 87-88X106.

5-Methylcytosine in Chlorelle pyrenoidosa DNAs

The presence of 5-methylcytosine in Chlorella pyrenoidosa (strain 211/8b) DNA's has been investigated by means of paper chromatography and thermal chromatography on hydroxyapatite. It has been shown that nuclear DNA contains 3.5 mol% 5-methylcytosine whereas no significant amount of this base can be detected in chloroplast DNA. The thermal chromatography of nuclear DNA labelled from [6-3H]- or [Me-14C] methionine lead us to conclude that the 5-methylcytosine content is directly proportional to the G + C content of the various DNA fractions. The existence of methylated sequences in DNA is postulated and the biological function of the 5-methylcytosine is discussed.

Interspersion and transcription of repeated sequences of rat DNA

Repetitive rat DNA reassociated to Cot=0.1 and deprived of "foldback" sequences showed close interspersion with unique sequences. As measured by electron microscopy, the average length of repetitive segments was about 600 +/- 400, and of unique segments 1800-3600 base pairs. Pyrimidine tracts over 80 nucleotides in length were found mainly in foldback and repetitive fractions. Oligo(dT) tracts, 20-30 bases in length prevailed in the DNA fraction reassociated to Cot=0.1. Repetitive and unique DNA fractions were annealed to Millipore filters and hybridized with hnRNA. Up to 1.6% of repetitive DNA reassociated to Cot=0.05 showed base complementarity with hnRNA, whereas the comparative figures for DNA reassociated to Cot=10 and for the unique fraction were 0.8% and 0.3% respectively. When hybridization of hnRNA was carried out in solution in vast DNA excess, no hybrid formation with repetitive sequences reassociated to Cot=0.1 was observed, although hybridization with DNA reassociated to Cot=10 was noticeable.

Restriction enzyme digests of rapidly renaturing fragments of vaccinia virus DNA

Vaccinia virus DNA fragments that have been denatured by alkali and then neutralized contain a fraction that rapidly reforms duplex structures. The fraction is enriched by fractionating on hydroxyapatite columns and serves as as substrate for digestion by two restriction endonucleases isolated from Hemophilus parainfluenzae, Hpa I and HPa II. The patterns obtained by gel electrophoresis of the digested fragments show the presence of three major bands after Hpa I digestion and four major bands after Hpa II digestion. The DNA that is isolated from some of these bands quickly reforms duplex regions after alkaline denaturation. The size of the DNA segments in the major bands has been estimated to be in the range of 0.44 X 10(6) to 3.2 X 10(6) daltons. The fragments which rapidly reform duplex chains after denaturation are sensitive to single-strand-specific nucleases. These results are consistent with a model of vaccinia virus DNA which has a covalent link connecting complementary chains.

Ribosomal RNA genes in the amoebal and plasmodial forms of the slime mould Physarum polycephalum

1. The degree of homology between ribosomal RNA isolated from microplasmodia and amoebae of the slime mould Physarum polycephalum has been determined by competive hybridisation of the RNA from the two sources to homologous DNA in solution. The extent of competition was measured both by hybridisation to saturation and by following the kinetics of hybrid formation. In each case competition was found to be 100%, indicating that the ribosomal RNAs from the two, quite different vegetative forms of the organism exhibit a high degree of homology and are probably transcribed from the same genes. 2. The relationship between the amount of nuclear DNA that codes for ribosomal RNA (rDNA) and ploidy has been investigated in three strains of P. polycephalum which exhibit a 1:2:5 variation in the amount of DNA per nucleus. Ribosomal RNA saturation values were determined by hybridisation to DNA isolated from prophase nuclei of plasmodia. The proportion of rDNA was found to be constant at 0.16--0.18% of the total genome in the three strains.