376
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Robin J, Rodrigue A. Purification and biochemical properties of Egtved viral RNA. Can J Microbiol 1977; 23:1489-91. [PMID: 922601 DOI: 10.1139/m77-219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
32P-labeled Egtved virus RNA was released from highly purified virus by phenol-SDS extraction. The single-stranded nature of the RNA was demonstrated by (1) its buoyant density of 1.69 g/cm3 in Cs2-SO4, (2) its susceptibility to digestion by pancreatic ribonuclease in either 1 X SSC or 0.01 X SSC (standard saline citrate), (3) its base composition (29.3% C, 23.6% A, 14.5% U. 32.6% G). This Egtved virus is different from the other rhabdoviruses since the base composition of its genomic RNA is lower in its composition of A + U. Such a result could have possible taxonomic implications concerning the orignin and evolution of Egtved Virus relative to the other known rhabdoviruses.
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377
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Donis-Keller H, Maxam AM, Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res 1977; 4:2527-38. [PMID: 409999 PMCID: PMC342589 DOI: 10.1093/nar/4.8.2527] [Citation(s) in RCA: 1244] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The positions of adenines, guanines, and pyrimidines can be determined by partial nuclease digestion of a terminally labeles RNA molecule. In urea, at elevated temperatures, RNase T1 generates a pattern reflecting cleavage at guanines while RNase U2 cleaves only at adenine. A limited alkaline hydrolysis provides a continuum of fragments derived from breaks at every phosphodiester bond. The reaction products are electrophoretically fractionated by size in adjacent lanes of a polyacrylamide gel. An autoradiograph of the gel displays the sequence up to 100 nucleotides from the end of the molecule, although uracil cannot as yet be distinguished from cytosine. These techniques form the basis of an RNA sequencing method and are demonstrated on yeast 5.8S ribosomal RNA.
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378
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Hershey ND, Conrad SE, Sodja A, Yen PH, Cohen M, Davidson N, Iigen C, Carbon J. The sequence arrangement of Drosophila melanogaster 5s DNA cloned in recombinant plasmids. Cell 1977; 11:585-98. [PMID: 407004 DOI: 10.1016/0092-8674(77)90076-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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379
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380
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381
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Kjellstrand PT. Temperature and acid concentration in the search for optimum Feulgen hydrolysis conditions. J Histochem Cytochem 1977; 25:129-34. [PMID: 65418 DOI: 10.1177/25.2.65418] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Exposure and removal of aldehyde groups during Feulgen acid hydrolysis were studied at a wide range of temperature and acid concentrations. Temperatures between 9 and 75degreesC were found to influence only the rate of the hydrolysis reaction over the entire range from high (6 M) to low (0.05 M) HCl concentrations. The temperature dependence was high, and around +5degreesC was sufficient to double the reaction rate. The influence of acid concentrations between 0.02 and 6 M was studied, and the extraction rates that determine the peak values of the Feulgen hydrolysis curve were found to depend in the same way on the (H+) concentration. A diagram is given that makes it possible to determine the time to reach the point during hydrolysis where the maximum amount of aldehyde groups are developed for a wide range of temperatures and acid concentrations. Temperatures slightly above room temperature in combination with high acid concentration is recommended for Feulgen hydrolysis.
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382
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Issaq HJ, Barr EW. Detection reagent for adenine, guanine, uracil, cytosine and their alkylated bases, nucleotides and nucleosides on thin-layer plates. J Chromatogr A 1977; 132:121-7. [PMID: 833219 DOI: 10.1016/s0021-9673(00)93778-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The detection of alkylated bases at the nanogram level is reported. The reaction is based on two steps, first, chlorination of the bases and, secondly, spraying the chlorinated product with o-tolidine solution to give a dark blue color. The detection of nucleotides and nucleosides is also possible. The optimum conditions and the possible mechanism of the reaction are discussed.
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383
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Abstract
DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave DNA preferentially at guanines, at adenines, at cytosines and thymines equally, and at cytosines alone. When the products of these four reactions are resolved by size, by electrophoresis on a polyacrylamide gel, the DNA sequence can be read from the pattern of radioactive bands. The technique will permit sequencing of at least 100 bases from the point of labeling.
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384
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Stuart WD, Woodward DO. New class of ribonucleic acid in Neurospora associated with the outer cell envelope. J Bacteriol 1977; 129:395-9. [PMID: 137232 PMCID: PMC234938 DOI: 10.1128/jb.129.1.395-399.1977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Extrinsic ribonucleic acid (RNA) can be isolated from a KCl extract of Neurospora crassa conidial cell surface products. It is heterogeneous in size. The bulk of this RNA travels as a broad band, trailing the 5.8S ribosomal marker RNA on electrophoretic gels. The extrinsic RNA, when denatured, exhibites several discrete lengths between 50,000 and 130,000 daltons. Melting profiles confirm the heterogeneity of the RNA and indicate that 58% of the bases are involved in hydrogen bonding. Analyses of alkaline hydrolysis products reveal no extensive methylation and few or none of the unusual bases present in transfer RNA. The bases are present in approximately equivalent amounts. Extrinsic RNA represents 2 to 3% of the total cellular RNA. Since this membrane-associated class of RNA does not resemble ribosomal RNA, messenger RNA, or transfer RNA and since it is extracted from the cell exterior by methods used to remove extrinsic membrane molecules, we have designated it extrinsic RNA.
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385
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Tomasz J. Two-dimensional combination of the hydrogen and the ammonium forms of a cation-exchange layer for the separation of minor nucleic acid bases. J Chromatogr A 1976; 128:304-8. [PMID: 1002785 DOI: 10.1016/s0021-9673(00)99263-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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386
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Kinniburgh AJ, Martin TE. Oligo (A) oligo (A)-adjacent sequences present in nuclear ribonucleoprotein complexes and mRNA. Biochem Biophys Res Commun 1976; 73:718-26. [PMID: 827295 DOI: 10.1016/0006-291x(76)90869-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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387
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Wolstenholme DR, Fauron CM. A partial map of the circular mitochondrial genome of Drosophila melanogaster. Location of EcoRI-sensitive sites and the adenine-thymine-rich region. J Cell Biol 1976; 71:434-48. [PMID: 825520 PMCID: PMC2109754 DOI: 10.1083/jcb.71.2.434] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The mitochondrial genome of Drosophila melanogaster is a circular DNA molecule of mol wt 12.35 X 10(6) daltons. A single region accounting for approx. 25% of this molecule can be reproducibly differentially denatured presumably because it is rich in adenine and thymine. We have mapped on the circular mitochondrial genome of D. melanogaster the relative positions of this adenine-thymine (A-T) rich region and the sites sensitive to cleavage by the restriction endonuclease EcoRI, using agarose gel electrophoresis and electron microscopy. Digestion of mitochondrial DNA (mtDNA) molecules to completion with EcoRI resulted in the production of four fragments, A, B, C, and D which represent (+/- SD) 58.9 +/- 1.1%, 27.5 +/- 0.8%, 8.9 +/- 0.5%, and 4.5 +/- 0.3%, of the circular genome length, respectively. Fragments produced by EcoRI digestion and circularized by incubation at 2 degrees C also fell into four distinct length groups with means (+/- SD) of 59.1 +/- 0.5%, 27.5 +/- 0.5%, 9.2 +/- 0.3%, and 4.6 +/- 0.2% of the circular genome length. From a consideration of the lengths of fragments resulting from incomplete EcoRI digestion, it was determined that the arrangement of the fragments in the circular genome was A-C-B-D. By electron microscope examination of partially denatured EcoRI fragments, the A-T-rich region was shown to be located in the A fragment closer to one end than to the other. By similar partial-denaturation studies of fragments resulting from incomplete EcoRI digestion, it was determined that, in the circular genome, of the two EcoRI sites which define the limits of the A fragment, the site between the A and D fragment lies nearest to the A-T-rich region.
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388
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Solodova AF, Kotko NV, Shcherbakova LN. [Spectrophotometric determination of adenine]. FARMATSIIA 1976; 25:55-6. [PMID: 1001512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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389
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Varricchio F, Raska K. Synthesis of VA RNA in productive and abortive infections with adenovirus type 12. Virology 1976; 74:450-8. [PMID: 982836 DOI: 10.1016/0042-6822(76)90351-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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390
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Abstract
DNAs from the genomes of Clostridium perfringens and Cytophaga johnsonii display orthodox A-DNA and B-DNA structures despite their high (A+L) nucleotide content. Unique structures, such as those found for synthetic DNAs having specific special sequences, do therefore not necessarily occur for DNAs having more random base sequence even if these have unusual base compositions. Clostridium perfringens DNA exhibits unusual structural properties only prior to purification by gel filtration.
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391
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Fauron CM, Wolstenholme DR. Structural heterogeneity of mitochondrial DNA molecules within the genus Drosophila. Proc Natl Acad Sci U S A 1976; 73:3623-7. [PMID: 1068475 PMCID: PMC431170 DOI: 10.1073/pnas.73.10.3623] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have determined by electron microscopy the molecular weight of circular mitochondrial DNA (mtDNA) molecules from 39 species representing 13 groups of five subgenera of the genus Drosophila. mtDNA molecules of all species examined, other than members of the melanogaster group, had, with one exception, molecular weights in the rather narrow range 9.90 X 10(6). The one exception was D. robusta, which had a molecular weight of 10.61 X 10(6). In contrast, mtDNA molecules from species within the melanogaster group had molecular weights covering the considerably greater range 9.92 X 10(6) to 12.35 X 10(6). Applying the electron microscope denaturation mapping technique of Inman to mtDNA molecules of eight species of the melanogaster group, we found each of them to contain a region [presumably rich in adenine and thymine (A+T)] which denatured at a specific temperature (40 degrees) at which most of the remainder of the molecule remained undenatured. The size of the A+T-rich region was constant for mtDNA molecules of a species, but varied from 0.62 X 10(6) to 3.41 X 10(6) for mtDNA molecules of different species. It was demonstrated that the differences in molecular weights of the A+T-rich regions can almost completely account for the differences in total molecular weights of the mtDNA molecules from species of the melanogaster group.
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392
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Thomason AR, Brian DA, Velicer LF, Rottman FM. Methylation of high-molecular-weight subunit RNA of feline leukemia virus. J Virol 1976; 20:123-32. [PMID: 185408 PMCID: PMC354973 DOI: 10.1128/jvi.20.1.123-132.1976] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The high-molecular-weight subunit RNA of feline leukemia virus (Rickard strain) (FeLV-R) was analyzed for the presence of methyl groups. After purification of native 50-60S FeLV-R RNA on nondenaturing aqueous sucrose density gradients. FeLV-R 28S subunit RNA, doubly labeled with [14C]uridine and [methyl-3H]methionine, was isolated by centrifugation through denaturing sucrose density gradients in dimethyl sulfoxide. As calculated from their respective 3H/14C ratios. FeLV-R 28S RNA was methylated to the same degree as host cell poly(A)+ mRNA. When the 28S FeLV-R RNA was hydrolyzed to completion with RNase T2 or alkali, all of the methyl-3H chromatographed with mononucleotides on Pellionex-WAX, a weak anion exchanger. The methyl-labeled material co-chromatographed with 6-methyladenosine if the mononucleotide fraction obtained by Pellionex-WAX chromatography was hydrolyzed to nucleosides by bacterial alkaline phosphatase or with 6-methyladenine if purine bases were released from the mononucleotides by acid hydrolysis. In another experiment in which FeLV-R 28S RNA uniformly labeled with 32P was hydrolyzed and then analyzed by Pellionex-WAX chromatography, all of the 32P label again co-chromatographed with mononucleotides. Thus FeLV-R 28S RNA does not appear to contain a 5' structure, either methylated or nonmethylated similar to those recently reported for cellular and some animal virus mRNA's.
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393
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Capesius I. Isolation and characterization of native AT-rich satellite DNA from nuclei of the orchid Cymbidium. FEBS Lett 1976; 68:255-8. [PMID: 976478 DOI: 10.1016/0014-5793(76)80448-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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394
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Margison GP, Margison JM, Montesano R. Methylated purines in the deoxyribonucleic acid of various Syrian-golden-hamster tissues after administration of a hepatocarcinogenic dose of dimethylnitrosamine. Biochem J 1976; 157:627-34. [PMID: 985411 PMCID: PMC1163904 DOI: 10.1042/bj1570627] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
1. DNA was extracted from livers, kidneys and lungs of Syrian golden hamsters at various times (up to 96h) after injection of a hepatocarcinogenic dose of [14C]dimethylnitrosamine. Purine bases were released from the DNA by mild acid hydrolysis and separated by Sephadex G-10 chromatography. 2. At 7h after dimethylnitrosamine administration liver DNA was alkylated to the greatest extent, followed by that of lung and kidney, the values for which were 8 and 3% respectively of those for liver. 3. The O6-methylguanine/7-methylguanine ratios were initially the same in all three organs and in the liver DNA of rats under similar conditions of dose. 4. O6-Methylguanine was the most persistent alkylated purine in all three hamster tissues. There was evidence for excision of 7-methyl-guanine, the highest activity for this being present in the liver. 5. Detectable amounts of the minor products 3-methyladenine, 1-methyladenine, 3-methylguanine and 7-methyladenine were present in most hamster tissues, and their individual rates of loss from liver DNA were determined. 6. Ring-labelling of the normal purines in DNA was highest in the liver, followed closely by the lung (80% of that in liver) whereas the kidney had very low incorporation (3% of that in liver). 7. The results are discussed with respect to the hepatotoxicity of dimethylnitrosamine, the miscoding potential of the various alkylation products and the induction of liver tumours in hamsters.
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395
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Schibler U, Perry RP. Characterization of the 5' termini of hn RNA in mouse L cells: implications for processing and cap formation. Cell 1976; 9:121-30. [PMID: 975236 DOI: 10.1016/0092-8674(76)90058-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An analysis of the phosphorylated and capped 5' termini of the heterogenous nuclear RNA of mouse L cells has revealed four types of structure: pppXp..., ppXp..., pXp..., and m7/GpppXmp.... The 5'triphosphate termini consists exclusively of pppGp... and pppAp..., whereas a large proportion of the 5' monophosphate termini are pUp.... The 5'diphosphate termini contain all four species of nucleotide in relative proportions that are roughly similar to those found at the Xm position of cap structures. These results indicate that initiation of hnRNA transcription occurre exclusively with purine nucleotides, and consequently that the hnRNA molecules containing pyrimidines at the 5' termini very probably arise by cleavages at internal sites of larger primary transcripts. Taken together with previous results relating cap structures of hnRNA and mRNA, the data favor a model in which some mRNA sequences are located at transcriptionally initiated proportions and others in internal regions of their precursors. According to this model, both the mRNA segments derived from initial 5' end, and those derived by cleavage at internal sites could be converted to diphosphate-terminated derivatives, which then condense with GTP to form cap structures according to the mechanism previously described for vaccinia and reovirus mRNA.
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396
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Johnson RB, Soeiro R, Fields BN. The synthesis of A-rich RNA by temperature-sensitive mutants of reovirus. Virology 1976; 73:173-80. [PMID: 960558 DOI: 10.1016/0042-6822(76)90071-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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397
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Simmonds HA, Van Acker KJ, Cameron JS, Snedden W. The identification of 2,8-dihydroxyadenine, a new component of urinary stones. Biochem J 1976; 157:485-7. [PMID: 962876 PMCID: PMC1163876 DOI: 10.1042/bj1570485] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Stones passed by a child homozygous for a deficiency of the enzyme adenine phosphoribosyltransferase have been identified by u.v., i.r. and mass spectrometry as 2,8-dihydroxyadenine.
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398
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Schaffner W, Gross K, Telford J, Birnstiel M. Molecular analysis of the histone gene cluster of psammechinus miliaris: II. The arrangement of the five histone-coding and spacer sequences. Cell 1976; 8:471-8. [PMID: 954100 DOI: 10.1016/0092-8674(76)90214-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Histone DNA of Psammechinus miliaris was obtained in an enriched form by buoyant density gradient centrifugation and was cleaved into 6 kb repeat units (Birnstiel et al., 1975a) by the action of the specific endonucleases EcoRI and HindIII. Since it was suspected that the 6 kb unit harbored all five histone-coding sequences, the histone DNA unit was subdivided into five segments with the aim of providing five fragments carrying just one coding sequence each. This was achieved by the combined use of EcoRI Hindll, Hindlll, and Hpa I. A physical map was constructed from the overlaps arising in these restriction experiments. Each of the five segments was shown to hybridize uniquely with just one of the five highly purified histone mRNAs (Gross et al., 1976a). By this procedure, the order of the mRNA sequences on the histone DNA was found to be a, c, d, b, e (Gross et al., 1976a), and hence of the protein coding sequences H4, H2B, H3, H2A, and H1. Further evidence is presented that the 6 kb repeat unit, amplified by means of a Murray lambda vector phage, contains AT-rich DNA sequences which would be expected not to code for histone proteins.
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399
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Yoshioka M, Tamura Z. Fluorimetric determination of adenine and adenosine and its nucleotides by high-performance liquid chromatography. J Chromatogr A 1976; 123:220-4. [PMID: 181387 DOI: 10.1016/s0021-9673(00)81119-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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400
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Hattman S, Schlagman S, Goldstein L, Frohlich M. Salmonella typhimurium SA host specificity system is based on deoxyribonucleic acid-adenine methylation. J Bacteriol 1976; 127:211-7. [PMID: 776925 PMCID: PMC233053 DOI: 10.1128/jb.127.1.211-217.1976] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We have determined the nature of the deoxyribonucleic acid (DNA) modification governed by the SA host specificity system of Salmonella typhimurium. Two lines of evidence indicate that SA modification is based on methylation of DNA-adenine residues. (i) The SA+ locus of Salmonella was transferred into Escherichia coli B, a strain that does not contain 5-methylcytosine in its DNA; although the hybrid strain was able to confer SA modification, its DNA still did not contain 5-methylcytosine. (ii) the N6-methyladenine content of phage L DNA was measured after growth in various host strains; phage lacking SA modification contained fewer N6-methyladenine residues per DNA. We also investigated the possibility, suggested by others (32), that SA modification protects phage DNA against restriction by the RII host specificity system. Phages lambda, P3, and L were grown in various SA+ and SA- hosts and tested for their relative plating ability on strains containing or lacking RII restriction; the presence or absence of SA modification had no effect on RII restriation. In vitro studies revealed, however, that Salmonella DNA is protected against cleavage by purified RII restriction endonuclease (R-EcoRII). This protection is not dependent on SA modification; rather, it appears to be due to methylation by a DNA-cytosine methylase which has overlapping specificity with the RII modification enzyme, but which is not involved in any other known host specificity system.
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