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Quirk JT, Kupinski JM. Interspecific mitochondrial DNA restriction fragment length polymorphisms inAspergillussectionFlavi. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jeffrey T. Quirk
- Edinboro University of Pennsylvania, Department of Biology and Health Service, Edinboro, PA 16444
| | - John M. Kupinski
- Department of Biology, St. Bonaventure University, St. Bonaventure, New York 14778
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2
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Lee YC, Lee BJ, Kang HS. The RNA component of mitochondrial ribonuclease P from Aspergillus nidulans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 235:297-303. [PMID: 8631345 DOI: 10.1111/j.1432-1033.1996.00297.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Several RNA molecules that copurified with Aspergillus nidulans mitochondrial ribonuclease (RNase) P were identified [Lee, Y C., Lee, B. J., Hwang, D. S. & Kang, H. S. (1996) Eur J. Biochem. 235, 289-296], and their partial sequences were determined. Using an oligonucleotide probe, we cloned and mapped the gene encoding this putative RNA component of RNase P (RNase P-RNA), situated between URFA3 (unidentified reading frame A3) and cobA (apocytochrome b) genes in the mitochondrial genome of A. nidulans. The gene is extremely (A+T)-rich and contains two regions of sequence similarity conserved among the known mitochondrial RNase P-RNAs and the eubacterial RNase P-RNAs. The determination of 5' and 3' termini by primer extension and sequencing indicated that the length of the RNA transcript is 232 nucleotides. Northern-blot analysis revealed that its only subcellular location was the mitochondria. Two RNase P-RNA fragments of 110 nucleotides and 80 nucleotides, each containing one of the two conserved regions, could be recovered from the nuclease-treated enzyme without significant loss of activity. The sizes of these fragments appeared to be the minimum lengths required for the vitro activity of the enzyme.
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Affiliation(s)
- Y C Lee
- Department of Microbiology, College of Natural Sciences, Seoul National University, Korea
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3
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Duro G, Izzo V, Barbieri R. Methods for recovering nucleic acid fragments from agarose gels. JOURNAL OF CHROMATOGRAPHY 1993; 618:95-104. [PMID: 7693742 DOI: 10.1016/0378-4347(93)80029-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Agarose gel electrophoresis is a powerful technique for the separation of nucleic acids on the basis of their size and conformation. The development of methods to recover size-fractionated nucleic acids molecules from agarose gels has greatly facilitated recombinant DNA technologies. Although several methods for recovering DNA and RNA molecules have been developed during the past fifteen years, none of them has been universally accepted. In this review we describe, discuss and evaluate the most common procedures with which we have had experience. Our evaluation is based on the criteria of yield, purity, speed, simplicity and low cost. We have considered three different approaches to the problem of recovering nucleic acids: chemical gel dissolution, physical gel disruption and physical extrusion from intact gels.
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Affiliation(s)
- G Duro
- Istituto di Biologia dello Sviluppo, C.N.R., Palermo, Italy
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4
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Wolf K, Del Giudice L. The variable mitochondrial genome of ascomycetes: organization, mutational alterations, and expression. ADVANCES IN GENETICS 1988; 25:185-308. [PMID: 3057820 DOI: 10.1016/s0065-2660(08)60460-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- K Wolf
- Institut für Genetik und Mikrobiologie, Universität München, Munich, Federal Republic of Germany
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5
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McEnery MW, Angus CW, Moss J. Affinity chromatographic procedure for the quantitative recovery of DNA fragments from agarose gels. Anal Biochem 1986; 156:72-5. [PMID: 3017150 DOI: 10.1016/0003-2697(86)90156-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A simple and reliable method for the recovery of specific fragments of DNA from agarose gels is presented. The electroelution of the DNA onto the NENSORB cartridge matrix with the subsequent elution of the bound DNA by a methanol (50% v/v) wash has been shown to result in the quantitative recovery of the restriction fragment. Of importance is the fact that the DNA purified by this procedure is a viable substrate for further digestion by a second restriction endonuclease. The method does not require either phenol extraction or extensive desalting of the sample.
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6
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Mitochondrial DNA of the filamentous ascomycete Cochliobolus heterostrophus. Curr Genet 1984; 8:621-8. [DOI: 10.1007/bf00395708] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/1984] [Indexed: 10/26/2022]
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7
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Chromatographic resolution of nucleic acids extracted from Penicillium chrysogenum. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00383539] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Stevens L, McLennan P. Intracellular location of proteinases and proteinase inhibitors inAspergillus nidulans. FEMS Microbiol Lett 1983. [DOI: 10.1111/j.1574-6968.1983.tb00093.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Henrich B, Lubitz W, Fuchs E. Use of benzoylated-naphthoylated DEAE-cellulose to purify and concentrate DNA eluted from agarose gels. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1982; 6:149-57. [PMID: 6213700 DOI: 10.1016/0165-022x(82)90061-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Köchel HG, Küntzel H. Nucleotide sequence of the Aspergillus nidulans mitochondrial gene coding for the small ribosomal subunit RNA: homology to E. coli 16S rRNA. Nucleic Acids Res 1981; 9:5689-96. [PMID: 6273804 PMCID: PMC327553 DOI: 10.1093/nar/9.21.5689] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The complete primary structure of the 1437 bp gene coding for mitochondrial 15S rRNA and its flanking regions was determined by Maxam-Gilbert sequencing of cloned HindIII fragment H3 of A. nidulans mtDNA. The gene product reveals significant homology (59%) to E. coli 16S rRNA, and the potential secondary structures of both rRNA molecules are very similar, except that the hairpin structures 7, 8 and 30 of the Brimacombe 16S rRNA model are deleted, and that two sequences of 8 and 31 nucleotides are inserted in the mitochondrial species.
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12
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Lazarus CM, K�ntzel H. Anatomy of amplified mitochondrial DNA in ?Ragged? mutants of Aspergillus amstelodami: Excision points within protein genes and a common 215 bp segment containing a possible origin of replication. Curr Genet 1981; 4:99-107. [DOI: 10.1007/bf00365688] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/1981] [Indexed: 11/27/2022]
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13
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Bartnik E, Biderman AW, Hahn U, Küntzel H, Stepień PP. The cloning of Aspergillus nidulans mitochondrial DNA in Escherichia coli on plasmid pBR322. MOLECULAR & GENERAL GENETICS : MGG 1981; 182:332-5. [PMID: 6270505 DOI: 10.1007/bf00269679] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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High frequency transfer of species specific mitochondrial DNA sequences between members of the aspergillaceae. Curr Genet 1981; 3:221-8. [DOI: 10.1007/bf00429824] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/1981] [Indexed: 11/25/2022]
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Piechulla B, Hahn U, McLaughlin LW, Küntzel H. Nucleotide sequence of 5S ribosomal RNA from Aspergillus nidulans and Neurospora crassa. Nucleic Acids Res 1981; 9:1445-50. [PMID: 6453331 PMCID: PMC326768 DOI: 10.1093/nar/9.6.1445] [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: 01/20/2023] Open
Abstract
The nucleotide sequences of 5S rRNA molecules isolated from the cytosol and the mitochondria of the ascomycetes A. nidulans and N. crassa were determined by partial chemical cleavage of 3'-terminally labelled RNA. The sequence identity of the cytosolic and mitochondrial RNA preparations confirms the absence of mitochondrion-specific 5S rRNA in these fungi. The sequences of the two organisms differ in 35 positions, and each sequence differs from yeast 5S rRNA in 44 positions. Both molecules contain the sequence GCUC in place of GAAC or GAUY found in all other 5S rRNAs, indicating that this region is not universally involved in base-pairing to the invariant GTpsiC sequence of tRNAs.
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Köchel HG, Lazarus CM, Basak N, Küntzel H. Mitochondrial tRNA gene clusters in Aspergillus nidulans: organization and nucleotide sequence. Cell 1981; 23:625-33. [PMID: 7008953 DOI: 10.1016/0092-8674(81)90158-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Lazarus CM, Earl AJ, Turner G, Küntzel H. Amplification of a mitochondrial DNA sequence in the cytoplasmically inherited 'ragged' mutant of Aspergillus amstelodami. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 106:633-41. [PMID: 6249580 DOI: 10.1111/j.1432-1033.1980.tb04611.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A comparison has been made between mtDNA of the cytoplasmically inherited 'ragged' mutant of Aspergillus amstelodami and that of the wild-type strain. Ragged mitochondria contain both the wild-type mitochondrial genome and several large DNA molecules which are not cleaved by the restriction endonucleases BamHI, HaeIII, HhaI, HindII, HindIII, PstI and MboI, but are converted by either EcoRI or HpaII into a single 820-840 base-pair fragment. Restriction analysis and molecular hybridization data indicate that this fragment contains sequences of wild-type mtDNA located within a 1200-base-pair segment of the 40,500-base-pair genome, for which a basic restriction map has been deduced. It is concluded that in the ragged mutant a small segment of wild-type mtDNA has been amplified as tandem repeats, which is reminiscent of the Rho- petite phenotype of yeast. The results are discussed in relation to the phenomenon of senescence in Podospora anserina.
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Lazarus CM, Lünsdorf H, Hahn U, Stepień PP, Küntzel H. Physical map of Aspergillus nidulans mitochondrial genes coding for ribosomal RNA: an intervening sequence in the large rRNA cistron. MOLECULAR & GENERAL GENETICS : MGG 1980; 177:389-97. [PMID: 6246396 DOI: 10.1007/bf00271477] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A detailed map of the 32 kb mitochondrial genome of Aspergillus nidulans has been obtained by locating the cleavage sites for restriction endonucleases Pst I, Bam H I, Hha I, Pvu II, Hpa II and Hae III relative to the previously determined sites for Eco R I, Hind II and Hind III. The genes for the small and large ribosomal subunit RNAs were mapped by gel transfer hybridization of in vitro labelled rRNA to restriction fragments of mitochondrial DNA and its cloned Eco R I fragment E3, and by electron microscopy of RNA/DNA hybrids. The gene for the large rRNA (2.9 kb) is interrupted by a 1.8 kb insert, and the main segment of this gene (2.4 kb) is separated from the small rRNA gene (1.4 kb) by a spacer sequence of 2.8 kb length. This rRNA gene organization is very similar to that of the two-times larger mitochondrial genome of Neurospora crassa, except that in A. nidulans the spacer and intervening sequences are considerably shorter.
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Mannella CA, Goewert RR, Lambowitz AM. Characterization of variant Neurospora crassa mitochondrial DNAs which contain tandem reiterations. Cell 1979; 18:1197-207. [PMID: 160287 DOI: 10.1016/0092-8674(79)90232-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two variant mtDNA types ((types IIa and HI-10) have been identified in individual subcultures of the extra-nuclear [poky] mutant of Neurospora crassa. Eco RI digests of type IIa mtDNA are characterized by an extra band, alpha, Mr = 1.4 Mdal, which arises from tandemly inserted reiterations of a 1.4 Mdal sequence. Restriction enzyme analysis and Southern hybridization experiments show: that the 1.4 Mdal repeats are located at the junction of Eco RI-4 and -6, that the repeats contain sequences ordinarily present in Eco RI-4 and -6, that the repeats are oriented head-to-tail and that the number of repeats per molecule (n) varies from n = 0 to n = 8, with about half of the molecules containing no repeats. The 1.4 Mdal repeats appear to be actively mained in type IIa mtDNA populations as a result of a specific alteration in mtDNA. Data are presented which suggest that this alteration may be located near small deletions and/or sequence changes in Eco RI-3 and -10, fragments almost exactly opposite the site of the repeats on the genome. The second variant, HI-10 mtDNA, arose in a heteroplasmic strain in which type IIa mtDNA was one component. The most striking feature of HI-10 mtDNA is the up to 5-fold amplification of an 18 Mdal segment extending from Eco RI-4 (the site of the 1.4 Mdal repeats) through the rRNA genes. Eco RI digests show that HI-10 possesses characteristic features of type IIa mtDNA, including the 1.4 Mdal repeats and the alteration in Eco RI-10. HI-10 mtDNA also shows a novel Eco RI fragment, beta, Mr = 2.9 Mdal. The variant Neurospora mtDNAs may be generated by mechanisms analogous to those which give rise to defective mtDNAs of yeast petite mutants. The possible consequences of defective mtDNAs in obligately aerobic organisms are discussed.
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Mannella CA, Lambowitz AM. Unidirectional gene conversion associated with two insertions in neurospora crassa mitochondrial DNA. Genetics 1979; 93:645-54. [PMID: 232451 PMCID: PMC1214103 DOI: 10.1093/genetics/93.3.645] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial phenotype of [poky] and other extranuclear Neurospora mutants is known to predominate over that of wild type in heteroplasmons. In the present work, we have investigated the interaction between wild-type and [poky] mtDNAs using as many as four physical markers to distinguish the two types of mtDNAs. Two insertions, one of 1200 bp in Eco RI-5 and the other 50 bp in Eco RI-9, are identified as sites of high frequency, unidirectional gene conversion leading to their spread through mtDNA populations in heteroplasmons. However, the transmission of the [poky] mutation does not appear to be correlated with the transmission of either of these insertions or of other physical markers. The possibility that other loci of nonreciprocal recombination might be responsible for the "dominance" of Neurospora extranuclear mutants is discussed.
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Turner G, Imam G, Küntzel H. Mitochondrial ATPase complex of Aspergillus nidulans and the dicyclohexylcarbodiimide-binding protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 97:565-71. [PMID: 157278 DOI: 10.1111/j.1432-1033.1979.tb13145.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dicyclohexylcarbodiimide-binding protein of Aspergillus nidulans has been identified as the smallest subunit of the mitochondrial ATPase complex, and has a molecular weight of approximately 8000. It is extractable from whole mitochondria and from the purified enzyme in neutral chloroform/methanol, contains 30% polar amino acids, and the N-terminal amino acid has been identified as tyrosine. Using a double-labelling technique in the absence and presence of cycloheximide, followed by immunoprecipitation of the enzyme complex with antiserum against Neuospora crassa F1 ATPase, it has been shown that this subunit is synthesized on cytoplasmic ribosomes.
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Hahn U, Lazarus CM, Lünsdorf H, Küntzel H. Split gene for mitochondrial 24S ribosomal RNA of Neurospora crassa. Cell 1979; 17:191-200. [PMID: 156584 DOI: 10.1016/0092-8674(79)90307-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 60 kb circular mitochondrial genome of N. crassa has previously been shown to contain a single transcription unit for 17S and 24S rRNA mapping within the largest Eco RI fragment E1 (19.6 kb). This fragment was isolated from uncloned mitochondrial DNA and further analyzed by cleavage with restriction endonucleases Hind II, Hind III, Bam HI, Pvu II and BgI I, and by electron microscopy of rRNA/DNA hybrids. The resulting map shows a 2.3 kb intervening sequence interrupting the gene for 24S rRNA. The main part (2.7 kb) of this gene is separated from the 17S rRNA gene by a 5 kb segment which contains several transfer RNA genes. This segment is much longer than the putative 1 kb spacer sequence within the 32S precursor molecule for both rRNAs, suggesting a second splicing event in that region.
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Cummings DJ, Belcour L, Grandchamp C. Mitochondrial DNA from Podospora anserina. I. Isolation and characterization. MOLECULAR & GENERAL GENETICS : MGG 1979; 171:229-38. [PMID: 286867 DOI: 10.1007/bf00267577] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mitochondrial (Mt) DNA from Podospora anserina was isolated and characterized with respect to density in CsCl, contour length and endonuclease restriction enzymes. The density of Mt DNA for four races examined was 1.694 g/cm3, compared with 1.712 g/cm3 for nuclear DNA. Extraction in the presence of a nuclease inhibitor, aurintricarboxylic acid and isolation in DAPI CsCl gradients allowed us to isolate high molecular weight DNA. Mt DNA isolated by total DNA extraction contained ca. 1% of circular molecules, 31 micron in contour length; Mt DNA isolated from purified mitochondria contained 2--4% of these 31 micron circles. Analysis with Eco RI restriction endonuclease revealed that each of the four races examined, s, A, T and E had a characteristic fragment pattern. Races s and A Mt DNA differed by only one fragment after Eco RI enzymatic digestion; similarly, these two DNA differed by only one or two fragments after Hae III digestion.
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25
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Bartnik E, Pieniazek NJ, Stepień PP. Molecular cloning of the 4.2 Md EcoRI fragment of Aspergillus nidulans mitochondrial DNA. MOLECULAR & GENERAL GENETICS : MGG 1979; 171:75-8. [PMID: 375024 DOI: 10.1007/bf00274017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 4.2 Md EcoRI fragment of Aspergillus nidulans mitochondrial DNA was cloned using the plasmid pBR 332 as vector and E. coli as host. Hitherto unknown sequence of HindIII sites within this region of mitochondrial genome was established.
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