The Radioiodination of Ribopolymers for Use in Hybridizational and Molecular Analyses

Iodo-Gen-mediated radioiodination of nucleic acids

Iodo-Gen (1,3,4,6-tetrachloro-3a,6a-diphenylglycoluril), widely used as an oxidizing agent for iodination of proteins, can also be used for iodination of nucleic acids. Optimal conditions were determined for efficient labeling of RNA and DNA with 125I. The proposed procedure for radioiodination of nucleic acids is more beneficial than the methods utilizing TlCl3 because of the milder reaction conditions, the simplicity and completeness of separation of reaction products from the oxidizing agents, and the absence of a toxic catalyst. Using the standard procedure for Iodo-Gen-mediated iodination a specific radioactivity of up to 1.3 X 10(9) dpm/micrograms RNA can be achieved. The proposed procedure is also suitable for radioiodination of DNA.

Cloning and characterization of the ribosomal RNA genes of Rhynchosciara americana

The ribosomal RNA genes (rDNA) of Rhynchosciara americana were analysed using Southern transfers of DNA cleaved with EcoRI, HindIII, BamHI and PstI. The results show that the rDNA is heterogeneous in structure. Following digestion with EcoRI and hybridization to rRNA three bands corresponding to fragments of 9.5, 7.5 and 5.5 kilobases (kb) were detected. Recombinants containing EcoRI fragments of R. americana DNA were prepared using the vector lambda gt lambda B. Three different recombinants (lambda gt Ra1, lambda gt Ra23 and lambda gt Ra5) were isolated containing the rDNA fragments of 9.5, 7.5 and 5.5 kb, respectively. These fragments were transferred to pBR325 and analysed with restriction enzymes and Southern hybridization with 28 S and 18 S rRNA. The lambda gt recombinants were further analysed by R-loop mapping. The data show that the rDNA occurs in two different repeating gene units. A shorter repeat of 9.5 kb and a longer repeat of 13 kb, in which the 28 S rRNA coding sequence contains an insertion of 3.5 kb.

Study of salivary gland specific transcripts in Chironomus tentans by cDNA analysis

Preparative amounts of polyA-containing RNA were purified from isolated salivary glands from Chironomus tentans and used as a template for the synthesis of cDNA by AMV reverse transcriptase. The yield of cDNA corresponded to 8-14% of the input polyA RNA. Using the Alwine hybridization method (Alwine et al., 1977) it was shown that only a minor part of the cDNA hybridized to the 75S RNA band and that the major hybridization occurred to a hitherto unknown gland-specific polyA RNA transcript of 1.3 kb length. In addition, the cDNA hybridized to a gland-specific polyA-RNA transcript of 2 kb length. - The majority of the cDNA had a size of 0.4 or 0.7 kb in equal amounts. A Southern hybridization of the cDNA to an EcoRI digest of genomic DNA showed in addition to a very weak hybridization to the 40 kb band of the Balbiani ring genes, hybridization to several restriction fragments with sizes from 1.3 to 16 kb.

A structural analysis of Balbiani ring dna sequences in Chironomus tentans

The Balbiani rings in the salivary gland polytene chromosomes of Chironomus tentans include the most active structural genes in this organ. Two of them (BR1 and BR2) contain repetitive sequences and are transcribed into giant RNA molecules. On Southern blots of restriction digests, we have identified fragments of genomic DNA which contain BR sequences. One of these fragments with a length of about 150 bp has been cloned and shown to hybridize preferentially to the BR1 transcription unit. Determination of its nucleotide sequence revealed several recognition sites for restriction enzymes which cleave the giant BR gene(s) into small pieces of approximately 240 bp. It is concluded that the cloned fragment represents part of the basic 240 bp repeat unit of a BR1 gene. Data obtained from partial restriction digests using the cloned DNA segment as a probe indicate that probably the entire BR1 gene comprises tandem repeats of 240 bp. Evidence is presented that the cloned BR1 sequence significantly cross-hybridizes to BR2 and to a lesser extent to BR6. BR2 sequences are present on a MboI fragment of 40 kb and seem to be organized in a very similar way as found for the BR1 gene.

The organization of the ribosomal RNA genes of Chironomus tentans and some closely related species

Southern gel analysis of total DNA from Chironomus tentans showed that the rRNA genes (rDNA) are homogeneous in structure. After cloning in Escherichia coli plasmid pBR313, the rDNA organisation was further studied by restriction fragment analysis and R-loop mapping. No heterogeneity could be detected by heteroduplex analysis of six different cloned rRNA cistrons. R-loop sizes of 1.69 and 3.63 kilobases (kb) were measured for the 18S and 28S rRNA coding sequences. The two spacers are 0.75 and 1.77 kb long. Southern gel analysis showed also a homogeneous rDNA structure for a Canadian population of C. tentans and C. pallidivittatus. The same technique indicated, however, that the rDNA of two other closely related species of C. thummi and C. melanotus is heterogeneous in structure. A possible correlation between this heterogeneity and the presence of heterochromatin in these species is discussed.

Cloning of an E. coli ribosomal RNA gene and its promoter region from lambdarifd18

The DNA of the specialized transducing phage lambdarifd18, which carries a bacterial rRNA transcription unit, was digested with restriction enzymes EcoRI and/or BamHI. Attempts were made to clone fragments containing the presumed rRNA promoter region or the entire rRNA gene in RSF2124 or pBR313 plasmid vectors with the following results: (1) We failed to clone an EcoRI fragment with the rRNA promoter region in plasmid RSF2124. (2) A smaller EcoRI-BamHI fragment with the rRNA promoter was also unclonable by itself, but one recombinant was found containing this fragment together with another large (7 Mdaltons) fragment, derived from phage lambda. The presence of this large fragment proved to be essential. The identity of these DNA fragments in the recombinant clone was confirmed by redigestion with several restriction enzymes, hybridization with rRNA, and in vitro transcription experiments, which showed preferential rRNA transcription. (3) A BamHI fragment encompassing the entire rRNA gene was easily cloned. Such stable clones carried a doubled number of rRNA genes. In vitro transcription using the recombinant plasmid resulted in 70% rRNA transcription. These recombinant clones allow the easy purification of the relevant DNA fragments for further investigation including sequencing.

Physical mapping of genes on yeast mitochondrial DNA: localization of antibiotic resistance loci, and rRNA and tRNA genes

We have physically mapped the loci conferring resistance to antibiotics that inhibit mitochondrial protein synthesis (erythromycin, chloramphenicol and paromomycin) or respiration (oligomycin I and II), as well as the 21s and 14s rRNA and tRNA genes on the restriction map of the mitochondrial genome of the yeast Saccharomyces cerevisiae. The mitochondrial genes were localized by hybridization of labeled RNA probes to restriction fragments of grande (strain MH41-7B) mitochondrial DNA (mtDNA) generated by endonucleases EcoRI, HpaI, BamHI, HindIII, SalI, PstI and HhaI. We have derived the HhaI restriction fragment map of MH41-7B mit DNA, to be added to our previously reported maps for the six other endonucleases. The antibiotic resistance loci (antR) were mapped by hybridization of 3H-cRNA transcribed from single marker petite mtDNA's of low kinetic complexity to grande restriction fragments. We have chosen the single Sal I site as the origin of the circular physical map and have positioned the antibiotic loci as follows: C (99.5-1.Ou)--P (27-36.Ou)--OII (58.3-62u--OI (80-84u)--E (94.4-98.4u). The 21s rRNA is localized at 94.4-99.2u, and the 14s rRNA is positioned between 36.2-39.8u. The two rRNA species are separated by 36% of the genome. Total mitochondrial tRNA labeled with 125I hybridized primarily to two regions of the genome, at 99.5-11.5u and 34-44u. A third region of hybridization was occasionally detected at 70--76u, which probably corresponds to seryl and glutamyl tRNA genes, previously located to this region by petite deletion mapping.

Iodination-deiodination. A radiochemical method for detection of structure and changes in structure in RNA

Bound iodine is released from radioiodinated nucleotides in polymers exposed to sodium bisulfite. The rate of bisulfite-catalyzed deiodination of pyrimidines can be controlled both by change of temperature of pH and is also dependent on the molecular association of the nucleotide. The rate of release of iodine from iodocytidine in polycytidylate is greater than the rate of elimination from RNA. Experiments testing the influence of base-pairing of the iodopyrimidines in synthetic polynucleotides showed that pairing of the substituted nucleotide protected the iodine bond. The rates of bisulfite-catalyzed deiodination of several radioiodinated RNAs were measured. The action of bisulfite on all single stranded RNAs tested was multiphasic consisting of a rapid early deiodination reaction supplanted by a slower phase which was followed by reacceleration of release. The release of iodine from double stranded RNA and DNA-RNA duplexes was retarded in comparison with the release from ribosomal and messenger RNA fractions. The deiodination profiles of single and double stranded RNA suggested that the intermediate stage iodine release is governed by melting of paired zones of low stability. Late release may result from destablization of the molecule through the addition of bisulfite to the pyrimidine ring or deamination. The effect of several substances expected to complex with polynucleotides was tested. Acridine orange and ethidium bromide increased loss of iodine from ribosomal RNA but slightly decreased elimination from double stranded viral RNA. A basic protein fraction isolated from ribosomal particles accelerated the deiodination of ribosomal RNA. While the destabilization caused by this protein fraction was greater than that caused by an equal amount of albumin, as tested the effect was non-specific. The results show that a change in sensitivity to chemical deiodination may folow the interaction of small amounts of protein with polynucleotides.

The existence of triphosphorylated 5'-ends in virus-specific RNA isolated from SV-40 transformed cells

The question about the nature of promoters in the transcriptional units containing SV-40 sequences in transformed cells was analyzed. It was found that the pulse-labeled RNA hybridizing to SV-40 DNA contains small but significant amounts of triphosphorylated 5'-ends detected as pppGp in alkaline hydrolyzates of this RNA. In another series of experiments the fragments of RNA containing triphosphorylated 5'-ends about 100 nucleotides in length have been isolated by hydroxyapatite chromatography. Some of them form hybrids with SV-40 DNA. The conclusion is drawn that at least some of SV-40 promoters are used for transcription initiation in SV-40 transformed cells.

Relative ribosomal RNA cistron multiplicity in oocytes and postembryonic stages of the eutelic nematode Panagrellus silusiae

The number of ribosomal RNA cistrons has been measured in the total DNA extracted from L2 juvenile and adult stages of the free-living nematode Panagrellus silusiae. Saturation hybridization studies with homologous rRNA indicate that both stages have about 275 ribosomal genes per haploid equivalent. Using homologous 125I-labelled rRNA for in situ hybridization, the mean number of silver grains per DNA content for oocyte, hypodermis and gut nuclei was similar. The mean DNA contents of maturing oocyte, hypodermis and gut nuclei are about 20C, 2C, and 10C respectively. We conclude that rDNA amplication alone is insufficient to account for the variation in DNA content of oocytes and that postembryonic development in this eutelic organism occurs without a significant differential increase in the number of ribosomal cistrons per worm.

Poly(adenylic acid)-containing RNA from plastids of maize

Hybridization experiments with chloroplast DNA and 125I-labeled RNA from maize seedlings suggest that chloroplasts and etioplasts contain detectable amounts of RNA that contains poly(adenylic aicd) (poly (A)) and was transcribed from chloroplast DNA. About 6% of the total poly(A)-containing RNA isolated from maize seedlings hybridized to chloroplast DNA. Poly(A)-containing RNA could also be isolated directly from purified chloroplasts that were treated with ribonucleases to reduce cytoplasmic contamination. At least 65% of this poly(A)-containing RNA hybridized to chloroplast DNA. Chloroplast poly(A) tracts average about 45 nucleotides in length, one-half the average size of poly(A) tracts from whole cells. The poly (A) tracts themselves are probably added to plastid RNAs following their transcription, because maize chloroplast DNA was found not to contain poly(dT).

Hybridization of maize chloroplast DNA with transfer ribonucleic acids

Hybridization of [125I] tRNA to chloroplast DNA indicates that 0.60-0.75% of maize chloroplast DNA contains sequences complementary to maize tRNA, corresponding to 20-26 tRNA cistrons. Green maize seedlings contain about twice the amount of chloroplast DNA-hybridizable tRNA as etiolated maize seedings. tRNA from green or etiolated maize seedlings was also aminoacylated in vitro with 21 labeled amino acids and then incubated with filters containing chloroplast DNA, tRNAs charging a total of at least 16 different amino acids hybridized with chloroplast DNA. Most of these plastid aminoacyl-tRNAs were present in higher concentrations in tRNA isolated from green maize seedlings, although there were several exceptions. The results are consistent with the hypothesis that a complete or nearly complete set or tRNAs can be transcribed from chloroplast DNA.

Proportionate representation of rDNA and Balbiani ring DNA in polytene chromosomes of Chironomus tentans

Attention was focussed on the question whether the most active genes of the polytene genome of Chironomus tentans, i.e. rDNA and Balbiani rings, have undergone the same number of duplications as the bulk of the genome. RNA was extracted from isolated salivary glands, enriched for messenger RNA by poly U sepharose chromatography, and labelled with 125Iodine. In situ hybridization showed that, apart from rRNA, Balbiani ring 1 and 2 transcripts are the major hybridizing RNA species present in this enriched preparation. BR1 hybridized only at the b-region. Transcripts of BR6 and puff I 17B are shown to be salivary gland specific and hybridize in situ to an extent of less than 5% of the RNA hybridized to BR1 plus BR2. Saturation hybridization levels of rRNA and Balbiani ring (BR1 plus BR2) RNA with polytene DNA from salivary glands were determined and compared with the saturation levels measured for DNA from adult flies and larvae. rRNA hybridized to the same level (0.09%) with polytene DNA as with DNA from primarily diploid cells (adult fly DNA) or from larvae. An equal hybridization level (0.04%) with each of these three types of DNA was also obtained for BR RNA. The results demonstrate that, during polytenization in C. tentans, the genes for rRNA and BR1 and 2 are duplicated to the same extent as the bulk of the genome.

Dual labeling in standard DNA-RNA hybridization studies using 125 I-labeled nuclear RNA and 3H-labeled DNA

Standard DNA-RNA hybridization studies, using nucleic acids isolated from mammalian tissues, are frequently hindered by relatively low levels of radioactivity in pulse-labeled RNA and in an inability to reliably estimate the amount of DNA present in the hybrid. In the method described here nuclear RNA is labeled in vitro with 125I to 400 000- 800 000 cpm/mug and DNA is obtained from a rat glial tumor line grown in culture and labeled to specific activities of 42 000-79 000 cpm/mug. DNA-RNA hybridization is conducted in an all solution system at RNA:DNA ratios of 3.5:1 to 18:1. Assay background is controlled by pretreatment of the hybrid and free RNA at the conclusion of the annealing study with RNase, then isolation of the hybrid together with a small fraction of free RNA oligonucleotides on hydroxyapatite. The partially purified hybrids are then trapped on Millipore filters. Assay background id 0.004% of total counts present in the annealing reaction. Comparison of the annealing reactions of pulse-labeled liver nuclear RNA and in vitro 125I-labeled nuclear RNA in saturation, kinetic, and competitive hybridization studies shows them to be essentially the same. Nuclear RNA labeled by either tritium or iodine shows a 10-20-fold greater concentration of the annealing sequences over that found in the microsomal RNA. Minor differences are noted between the nuclear RNAs in the initial rates of reaction and in the magnitude of the decrease in percent hybridization at low levels of unlabeled competitor RNA. This may be due to preferential labeling in pulse-labeled RNA of molecules which are present in lower concentrations or are transcribed from more frequently repeated DNA sequences than the average population of annealing RNA molecules. The technique has application in systems where the amount of tissue for RNA extraction is small or where the system does not permit the obtaining of pulse-labeled RNA, as in experimental rodent skin carcinogenesis or in dealing with RNA from the tissues of large mammals or humans.

Preparation of radioiodinated simian virus 40 DNA for use in DNA - DNA reassociation kinetics experiments

A method is described for the preparation of 125I-labelled SV40 DNA. Using this method, SV40 DNA can be routinely labelled to 15 - 10(6) dpm per mug; much higher specific activities are easily obtained by minor modifications of the method. Once incorporated, the radioactive label dissociates from DNA exceedingly slowly at 4 degrees C or at 68 degrees C. Iodinated SV40 DNA is shown to be useful in the quantitation of viral nucleic acid sequences in SV40-transformed 3T3 cells by DNA - DNA reassociation kinetics.

Direct covalent mercuration of nucleotides and polynucleotides

Nucleotides of cytosine and uracil are readily mercurated by heating at 37-50 degrees in buffered aqueous solutions (pH 5.0-8.0) containing mercuric acetate. Proton magnetic resonance, elemental, electrophoretic, and chromatographic analyses have shown the products to be 5-mercuricytosine and 5-mercuriuracil derivatives, where the mercury atom is covalently bonded. Polynucleotides can be mercurated under similar conditions. Cytosine and uracil bases are modified in RNA while only cytosine residues in DNA are substituted. There is little, if any, reaction with adenine, thymine, or guanine bases. The rate of polymer mercuration is, unlike that of mononucleotides, markedly influenced by the ionic strength of the reaction mixture: the lower the ionic strength the faster the reaction rate. Pyrimidine residues in single- and double-stranded polymers react at essentially the same rate. Although most polynucleotides can be extensively mercurated at pH 7.0 in sodium or Trisacetate buffers, tRNA undergoes only limited substitution in Tris buffers. The mild reaction conditions give minimal single-strand breakage and, unlike direct iodination procedures, do not produce pyrimidine hydrates. Mercurated polynucleotides can be exploited in a variety of ways, particularly by crystallographic and electron microscopic techniques, as tools for studying polynucleotide structure.