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Journal articles on the topic 'EcoRI'

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Author: Grafiati
Published: 10 March 2023

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1

LUKE, PETER A., and STEPHEN E. HALFORD. "Fluorescent labelling of EcoRI and EcoRV." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 259–60. http://dx.doi.org/10.1042/bst0140259a.

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2

Nascimento, Elmiro R., Al J. DaMassa, Richard Yamamoto, and M. Graça F. Nascimento. "Plasmids in Mycoplasma species isolated from goats and sheep and their preliminary typing." Revista de Microbiologia 30, no. 1 (1999): 32–36. http://dx.doi.org/10.1590/s0001-37141999000100006.

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One-hundred-five (105) clinical isolates of mycoplasma from caprine origin and one isolate from ovine were surveyed for plasmids, which were present in thirty-three (31%) of them. These mycoplasmas originated from 13 herds. Ten of them were symptomatic for mycoplasmal disease (mastitis, polyarthritis, septicemia) and three herds were asymptomatic, i.e., clinically normal. Twenty-eight isolates were Mycoplasma mycoides subspecies mycoides LC (large colony or caprine biotype), four were Mycoplasma capricolum subsp. capricolum and one was Mycoplasma cottewii. The isolated plasmids were linearized by EcoRI, EcoRV, EcoRI and EcoRV or BamHI and EcoRV, and were of five sizes (1.1, 1.6, 1.7, 1.8, and 1.9 Kbp). Based on restriction enzyme digestion and size of the linearized supercoiled extrachromosomal DNA, five plasmid types were recovered (p1II, p2III, p2V, p3I, and p4IV). The small size of these DNA elements probably exclude replicative forms of DNA virus, which are equal or larger than 8.0 Kbp.
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3

KENNETT, CHARLES A., and BENJAMIN STARK. "Automated Ribotyping for the Identification and Characterization of Foodborne Clostridia." Journal of Food Protection 69, no. 12 (December 1, 2006): 2970–75. http://dx.doi.org/10.4315/0362-028x-69.12.2970.

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The DuPont Qualicon RiboPrinter was employed to determine if automated ribotyping could be used to differentiate between and characterize various species of foodborne clostridia. EcoRI digests were used to ribotype 49 isolates that represented seven Clostridium species: C. aerotolerans, C. beirjerinckii, C. botulinum, C. butyricum, C. perfringens, C. putrificum, and C. sporogenes. EcoRV digests were also used to ribotype 17 C. botulinum isolates to determine if an alternate restriction enzyme was more suitable than was EcoRI for toxin typing. It was concluded that the RiboPrinter could be potentially used to identify most of the clostridia represented in the study, but that the system has difficulty distinguishing between C. botulinum and C. sporogenes. The system may also be potentially used to characterize clostridia based on phenotypic characteristics. Toxin typing of clostridia remains problematic, but may be improved by the use of restriction enzyme combinations.
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4

del Arco, A., and M. Izquierdo. "De novo methylation causes a tissue-specific polymorphic EcoRI pattern at the human epidermal growth factor receptor gene." Biochemical Journal 292, no. 2 (June 1, 1993): 591–95. http://dx.doi.org/10.1042/bj2920591.

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A novel restriction polymorphism, probably due to tissue-specific methylation, has been identified at the human epidermal-growth-factor-receptor (EGF-R) gene. DNA isolated from smooth muscle showed altered EcoRI restriction bands when hybridized with different fragments of the EGF-R cDNA. These bands were absent in brain or leucocyte DNA samples from the same individuals. Three restriction sites, partly resistant to cleavage by EcoRI, were characterized in muscle DNA which were not clustered but instead were scattered along the gene. The flanking sequences of one of these resistant EcoRI sites were determined. This specific EcoRI site was followed by a 3′-guanosine generating a methylatable EcoRI sequence. This suggests that the failure to digest to completion these EcoRI sites was due to modification by methylation. In addition, we noted that EcoRI sites were affected at both alleles, indicating that de novo methylation changes, and not methylation events related to genomic imprinting, would cause the muscle-specific EcoRI pattern. Also abnormal restriction fragments with XbaI were observed in muscle DNA. A large number of unrelated muscle DNA samples have been analysed, and all of them displayed an identical EcoRI polymorphic pattern, suggesting that DNA modification by de novo methylation events could be functionally relevant.
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5

Kodogo, Vitaris, Danai Tavonga Zhou, Olav Oektedalen, Kerina Duri, Babill Stray-Pedersen, and Exnevia Gomo. "Apolipoprotein B Gene Polymorphisms and Dyslipidemia in HIV Infected Adult Zimbabweans." Open AIDS Journal 10, no. 1 (September 30, 2016): 190–98. http://dx.doi.org/10.2174/1874613601610010190.

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Background:Dyslipidemia does not occur in all HIV-infected or antiretroviral therapy-experienced patients suggesting role of host genetic factors but there is paucity of data on association between dyslipidemia and gene polymorphisms in Zimbabwe.Objective:To determine association of lipoprotein levels andapolipoprotein Bpolymorphisms in HIV-infected adults.Method:Demographic data were collected from 103 consenting patients; lipoprotein levels were determined and blood samples were successfully genotyped for bothapolipoprotein B2488C>T Xba1 andapolipoprotein B4154G>A p.Gln4154Lys EcoR1 polymorphisms by real time polymerase chain reaction.Results:Mean age of genotyped patients was 40.3 ± 10.1 years, 68% were female; prevalence of dyslipidemia was 67.4%. Of 103 samples genotyped forapolipoprotein BXba1 polymorphism, 76 (74%) were homozygous C/C, 24 (23%) were heterozygous C/T and only three (3%) were homozygous T/T.Apolipoprotein BEcoR1 polymorphism showed little variability, one participant had rare genotype A/A, 68.3% had wild type genotype G/G.Conclusion:Observed frequencies ofapolipoprotein BXbaI and EcoRI polymorphisms matched other African studies. In spite of low numbers of rare variants, there was positive association between both total cholestrol and high density lipoprotein with ECoR1 wild type G/G genotype, suggesting that ECoRI 4154 G allele could be more protective against coronary heart disease than EcoR1 4154 A allele. There is need for further research at population level to confirm whetherapolipoprotein BECoR1 genotyping is useful for predicting risk of dyslipidemia in HIV patients in our setting.
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6

Chen, Jianzhu, Leonard A. Herzenberg, and Leonore A. Herzenberg. "Heparin inhibits EcoRI endonuclease cleavage of DNA at certain EcoRI sites." Nucleic Acids Research 18, no. 11 (1990): 3255. http://dx.doi.org/10.1093/nar/18.11.3255.

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7

Song, Yonghai, Dan Luo, Shuhong Ye, Mei Huang, Dandan Zhong, Zhenzhong Huang, Haoqing Hou, and Li Wang. "Spectroscopic studies on the interaction between EcoRI and CdS QDs and conformation of EcoRI in EcoRI-CdS QDs bioconjugates." Physical Chemistry Chemical Physics 14, no. 47 (2012): 16258. http://dx.doi.org/10.1039/c2cp42562a.

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8

Liu, Yaoping, Asao Ichige, and Ichizo Kobayashi. "Regulation of the EcoRI restriction–modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene." Gene 400, no. 1-2 (October 2007): 140–49. http://dx.doi.org/10.1016/j.gene.2007.06.006.

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9

Terry, B. J., W. E. Jack, and P. Modrich. "Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis." Journal of Biological Chemistry 260, no. 24 (October 1985): 13130–37. http://dx.doi.org/10.1016/s0021-9258(17)38848-8.

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10

OLD, D. C., S. A. CHISHOLM, P. B. CRICHTON, and A. TAYLOR. "Grouping of Salmonella enterica serotype Montevideo strains by ribotyping and IS200 profiling." Epidemiology and Infection 124, no. 3 (June 2000): 375–82. http://dx.doi.org/10.1017/s0950268899004033.

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One-hundred and twenty-one isolates of Salmonella enterica serotype Montevideo, representing different biotypes and incidents of infection detected in the UK between 1977 and 1995, were analysed by EcoRI ribotyping, PvuII ribotyping and IS200 fingerprinting. Among the isolates examined, 7 EcoRI ribotypes, 5 PvuII ribotypes and 55 IS200 profile types were recognized and 4 arbitrary groups defined. All 33 isolates of biotype 2d belonged to EcoRI/PvuII ribotype 1/1 and IS200 lineage A and comprised Group I. The other 88 isolates of biotype 10di and its variants were assigned to Groups II–IV. All 27 isolates in Group II were of EcoRI/PvuII ribotype 2/2 and IS200 lineage B. Among the 43 isolates in Group III, 42 of which were of EcoRI/PvuII ribotype 3/3, IS200 analysis identified 38 profiles in lineages C–I. Six EcoRI/PvuII ribotypes and 8 IS200 profiles, mostly in lineages C–E, were recognized among the 18 isolates in Group IV. The combined use of biotyping and ribotyping, and to some extent IS200 profiling, has enhanced our understanding of the clonal structure of serotype Montevideo and provides a basis for further study.
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11

Zhang, Jing, Zhilu Shi, and Yan Jin. "Enzyme-free and label-free signal amplification for monitoring endonuclease activity and inhibition via hybridization chain reaction." Analyst 140, no. 10 (2015): 3500–3506. http://dx.doi.org/10.1039/c5an00304k.

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12

WOLFES, Heiner, Anja FLIESS, Fritz WINKLER, and Alfred PINGOUD. "Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases." European Journal of Biochemistry 159, no. 2 (September 1986): 267–73. http://dx.doi.org/10.1111/j.1432-1033.1986.tb09863.x.

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13

Puspaningsih, Ni Nyoman Tri, Akhmaloka, and Afaf Baktir. "Analisis 6 DNA Rekombinan dengan enzim EcoRI." Journal of Biological Researches 3, no. 1 (June 1, 1997): 1–8. http://dx.doi.org/10.23869/bphjbr.3.1.19971.

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14

López-López, Karina, Frenyiline Jara-Tejada, and Juan Carlos Vaca-Vaca. "Caracterización molecular de un nuevo begomovirus aislado de cinco especies de arvenses colectadas en cultivos de tomate en Valle del Cauca." Acta Biológica Colombiana 24, no. 3 (September 1, 2019): 528–37. http://dx.doi.org/10.15446/abc.v24n3.79366.

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Las arvenses son hospederos alternos de begomovirus (Geminiviridae), los cuales facilitan su persistencia y propagación a cultivos de interés agronómico, como el tomate. El objetivo de esta investigación fue obtener el genoma completo de un begomovirus bipartita encontrado en Amaranthus dubius, Rivina humilis, Rhynchosia minima, Desmodium sp. y Caesalpinia sp., las cuales fueron colectadas en cultivos de tomate en Ginebra y Cerrito, Valle del Cauca. El genoma del begomovirus fue obtenido utilizando amplificación por círculo rodante y digestión con las enzimas EcoRI y EcoRV, las cuáles cortan el componente genómico A y B, respectivamente. Estos fragmentos fueron clonados, secuenciados y analizados. Finalmente, se verificó la presencia de este begomovirus en todas las arvenses mediante PCR específico. Se obtuvieron tres clonas EcoRI y cinco clonas EcoRV. Los fragmentos que portan los componentes A y B presentan un tamaño de 2 584 y 2 543 nt, respectivamente. El análisis de secuencia de nucleótidos del genoma begomoviral A con otros begomovirus previamente reportados, mostró la mayor identidad (90,9 %) con el virus del mosaico dorado de Rhynchosia de Yucatán. Tomando como base el criterio de demarcación actual para las especies de Begomovirus establecido por el Comité Internacional de Taxonomía de Virus, el geminivirus aislado de las arvenses A. dubius, R. humilis, R. minima, Desmodium sp. y Caesalpinia sp., constituye una nueva especie begomoviral. Con base en la sintomatología observada en campo, se propone el nombre de Virus del mosaico dorado de Rhynchosia de Colombia para designar a esta nueva especie.
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15

Gao, Congcong, Baoquan Che, and Hong Dai. "A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition." RSC Advances 11, no. 45 (2021): 28008–13. http://dx.doi.org/10.1039/d1ra04203c.

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A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.
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16

Reich, Norbert O., and Michael J. Danzitz. "EcoRI DNA methyltransferase-DNA interactions." Biochemistry 31, no. 7 (February 1992): 1937–45. http://dx.doi.org/10.1021/bi00122a006.

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17

Fliess, Anja, Heiner Wolfes, Andre Rosenthal, Konrad Schwellnus, Helmut Blöcker, Ronald Frank, and Alfred Pingoud. "Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonucleases." Nucleic Acids Research 14, no. 8 (1986): 3463–74. http://dx.doi.org/10.1093/nar/14.8.3463.

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18

Vipond, I. Barry, Geoffrey S. Baldwin, and Stephen E. Halford. "Divalent Metal Ions at the Active Sites of the EcoRV and EcoRI Restriction Endonucleases." Biochemistry 34, no. 2 (January 1995): 697–704. http://dx.doi.org/10.1021/bi00002a037.

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19

Faivre-Rampant, P., S. Jeandroz, F. Lefevre, M. Lemoine, M. Villar, and A. Berville. "Ribosomal DNA studies in poplars: Populus deltoides, P. nigra, P. trichocarpa, P. maximowiczii, and P. alba." Genome 35, no. 5 (October 1, 1992): 733–40. http://dx.doi.org/10.1139/g92-113.

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The nuclear rDNA physical maps of Populus nigra, P. deltoides, P. trichocarpa, P. maximowiczii, and P. alba have been built up for the restriction enzymes EcoRI, EcoRV, BamHI, PstI, and SacI. There is no HindIII site. A large variability appeared between the species in the intergenic spacer mainly for EcoRI and PstI. For several clones of each species two to three major unit types coexist in the genome, while several minor units as well as length variant units or new unit types have been found. The variability between the species is due to different major unit types, while the variability between clones in one species is due to the minor unit types. Every species carries several rDNA unit types either different in size (variable length unit) or variable in restriction sites (variable unit types). Four thousands copies of rDNA units were found in P. nigra, P. deltoides, and P. maximowiczii. The clones belonging to the same species carry the same major unit types but are different in their minor variable length units or minor unit types. The hybrid clones carry the sum of the major unit types of the two parental species. These facts suggested the existence of three rDNA loci. The combination of one enzyme EcoRI and one probe (flax entire rDNA unit) allowed to easily recognize each of the five species. Conversely, we detected the presence of rDNA fragments characteristic to P. deltoides in some clones belonging to P. nigra. We conclude that these clones are likely to have a hybridization in their stands but without observable phenotypic consequences. This technique will be used to verify the purity of each P. nigra candidate clone before exploiting it in a breeding or propagation program.Key words: Populus, nuclear rDNA, intergenic spacer variation, introgression.
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20

Dion, Michel, and Claude Hamelin. "Cartographie physique de l'ADN du cytomégalovirus humain souche AD169." Canadian Journal of Microbiology 36, no. 5 (May 1, 1990): 341–47. http://dx.doi.org/10.1139/m90-059.

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The whole human cytomegalovirus strain AD169 genome was cloned into plasmid pAT153 in the form of 25 HindIII fragments. Double and triple digestions of the recombinant plasmids with restriction endonucleases BamHI, BglII, ClaI, DraI, EcoRI, EcoRV, HindIII, HpaI, KpnI, PaeR7, PstI, SphI and XbaI yielded a detailed restriction map of human cytomegalovirus DNA. Knowing the exact position of numerous restriction sites in the viral DNA molecule, we have been able to examine very closely the heterologous region between the long and the short segments of the human cytomegalovirus genome. Key words: DNA, physical map, cytomegalovirus, restriction endonucleases, HCMV.
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21

EKATERINIADOU (Λ.Β. ΑΙΚΑΤΕΡΙΝΙΑΔΟΥ), L. V., E. BOUKOUVALA (Ε. ΜΠΟΥΚΟΥΒΑΛΑ), R. M. PAPI (Ρ.Μ. ΠΑΠΗ), A. ZDRAGAS (Α. ΖΔΡΑΓΚΑΣ), V. GIANTZI (Β. ΓΙΑΝΤΖΗ), and D. A. KYRIAKIDIS (Δ.Α. ΚΥΡΙΑΚΙΔΗΣ). "Antibiotic resistance and distribution of SodCI, sopE, sefA genes among Salmonella enteric serotype Enteritidis isolates from poultry." Journal of the Hellenic Veterinary Medical Society 66, no. 2 (January 31, 2018): 70. http://dx.doi.org/10.12681/jhvms.15589.

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Present work aimed to examine the antibiotic resistance of the Salmonella enterica serotype Enteritidis (SE) isolates from poultry, to study the plasmid-mediated ampicillin resistance and to detect and determine the distribution of sodCI, sopE and sefA genes. Thirty-five SE isolates from one-day chicks, layers and broilers were studied for susceptibility/resistance to sixteen antimicrobial agents; 23 (65.7%) of them showed resistance to ampicillin, 5 (14.3%) to ampicillin and tetracycline, 4 (11.45%) to tetracycline and 1 (2.9%) isolate showed multi-drug resistance. Ampicillin (AmpR) and ampicillin/tetracycline (AmpRTeR) resistance was easily transferred by conjugation, and all isolates except two possessed a common band. The molecular mass of the plasmid carrying ampicillin resistance was approximately determined at 41kb after DNA digestion with BamHI, HindIII, EcoRI, EcoRV and PstI restriction enzymes and ligation of EcoRI fragments to pET29c. For the detection of TEM-1 or/and TEM-2 ß-lactamases, two pairs of primers were used in a polymerase chain reaction (PCR). The PCR products showed the presence of blaTEM-1 gene in all isolates. The presence of SodCI, sopE, sefA genes was also examined by PCR. Twenty-two (62,8%) isolates carried the sodCI gene, thirty-four (97,2%) isolates carried the sopE gene and all isolates carried the sefA fimbrial locus.
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22

Pillay, Michael. "Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter." Genome 40, no. 6 (December 1, 1997): 815–21. http://dx.doi.org/10.1139/g97-805.

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Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11–42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.Key words: Eragrostis tef, ribosomal DNA, restriction map, genetic variation.
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23

Nikolajevic Starcevic, Jovana, Marija Santl Letonja, Zala J. Praznikar, Jana Makuc, Andreja C. Vujkovac, and Daniel Petrovic. "Polymorphisms XbaI (rs693) and EcoRI (rs1042031) of the ApoB gene are associated with carotid plaques but not with carotid intima-media thickness in patients with diabetes mellitus type 2." Vasa 43, no. 3 (May 1, 2014): 171–80. http://dx.doi.org/10.1024/0301-1526/a000346.

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Background: Apolipoprotein B is a key structural component of all the atherogenic lipoproteins (LDL, VLDL and IDL). Genetic variations of the ApoB gene may affect plasma ApoB and lipid levels, thus influencing atherogenesis. The present study was designed to investigate the association of polymorphisms XbaI (rs693) and EcoRI (rs1042031) of the ApoB gene with plasma ApoB level, lipid levels and the different ultrasound phenotypes of carotid atherosclerosis in patients with diabetes mellitus type 2. Patients and methods: 595 patients with diabetes (399 on statin therapy and 196 without) and 200 healthy controls were enrolled in the study. The carotid intima-media thickness (CIMT) and plaque characteristics (presence and structure) were assessed ultrasonographically. Biochemical analyses were performed using standard biochemical methods. Both XbaI (rs693) and EcoRI (rs1042031) genotypes were determined by real-time PCR. Results: Genotype distributions and allele frequencies of the XbaI and EcoRI polymorphisms were not statistically significantly different between diabetic patients and controls. No statistically significant difference in lipid parameters, ApoA1, ApoB, hs-CRP and fibrinogen as well as CIMT was observed in diabetic patients regarding XbaI and EcoRI polymorphisms, even after adjustment for statin treatment. The risk of having plaques on carotid arteries was higher in homozygous carriers of the mutant X + allele (OR = 1.74, p = 0.03) and lower in diabetics carrying mutant E- alleles (OR = 0.48, p = 0.02). Neither XbaI nor EcoRI polymorphism was associated with CIMT or presence of unstable plaques in diabetic patients. Plasma ApoB level was not independently associated with any of the ultrasonographic parameters of carotid atherosclerosis. Conclusions: Both XbaI and EcoRI polymorphisms were associated with presence of plaques on carotid arteries but not with CIMT or presence of unstable plaques. Plasma ApoB level was not independently associated with ultrasonographic phenotypes of carotid atherosclerosis in patients with diabetes mellitus.
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24

Germann, Markus W., Bernd W. Kalisch, James M. Varnum, Hans J. Vogel, and Johan H. van de Sande. "NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 391–402. http://dx.doi.org/10.1139/o98-031.

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We have correlated the structural perturbations caused by DNA mismatches with the enzymatic data of the interaction of the restriction endonuclease EcoRI with DNA. Oligonucleotides d(CGAGAATTCTCA5GAXAATTCT) (X = G, A, T) and d(CGCGAATTYGCGT4CGCXAATTCGCG) (Y = C, X = G, T and Y = A, X = T) containing single mismatches within the EcoRI recognition site were characterized by NMR spectroscopy and by their EcoRI substrate properties. UV melting and gel electrophoresis studies confirm that the oligonucleotides form hairpin structures. The presence of either a CT or a CA mismatch results in markedly lower Tm and van't Hoff enthalpies compared with the fully base paired control. NMR imino proton spectra of these hairpins demonstrate that the perturbation caused by the two mispairs or a noncanonical AT pair is localized and limited to one or two base pairs on either side of the perturbation. The DNA hairpin structures containing single mismatches, and to a lesser extent also sequences with a single noncanonical base pair, are substrates for the restriction endonuclease. In addition to the strand scission at the nonperturbed GpA phosphodiester bond some cleavage is observed at the mismatched position. The interactions of the CA and CT mismatched hairpin with the enzyme are characterized by binding constants that are only 33 and 57 times lower, respectively, than that for the canonical sequence, corresponding to 8-10 kJ·mol-1 less favorable free binding energy. This, taken together with the NMR data, indicates that the CA and CT mismatches have only small effects on the EcoRI recognition of the DNA substrate. We conclude that two out of the three hydrogen bonds that characterize the interaction of EcoRI with the CG base pair in the canonical sequence can still be formed for either the CT or CA mismatched recognition site.Key words: DNA hairpins, EcoRI recognition, mismatches, imino protons.
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25

Coucheron, Dag H. "Acetobacterstrains contain DNA modified at GAATTC and GANTC." Canadian Journal of Microbiology 43, no. 5 (May 1, 1997): 456–60. http://dx.doi.org/10.1139/m97-064.

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Total DNAs from nine strains of Acetobacter xylinum, two strains of Acetobacter aceti, and one Acetobacter pasteurianus strain were examined for the extent of digestion by various restriction endonucleases. The majority of the endonucleases cleaved the total DNAs with a frequency expected from the number of sites present in DNA sequences deposited in the GenBank data base. However, the restriction enzyme digestions identified two different genomic DNA modifications in Acetobacter. One sequence-specific modification protected total DNAs from seven of the A. xylinum strains against cleavage by EcoRI (GAATTC). Digestion of total DNAs from A. xylinum ATCC 10245 (DNA not cut by EcoRI) and the closely related A. xylinum NRCC 17005 (DNA cut by EcoRI) with Tsp509I (AATT) revealed differences in restriction frequencies that indicated methylation of the first or second adenine within GAATTC. Another sequence-specific modification rendered total DNAs from all the 12 strains recalcitrant to digestion by HinfI. The latter modification indicated that species of the genus Acetobacter contain a solitary DNA methyltransferase that probably methylates adenine in GANTC.Key words: Acetobacter, genomic DNA, modifications, EcoRI, HinfI.
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26

Nakajima, H., T. Noguchi, T. Hamaguchi, K. Tomita, T. Hanafusa, N. Kono, T. Tanaka, M. Kuwajima, and Y. Matsuzawa. "Expression of mouse phosphofructokinase-M gene alternative transcripts: evidence for the conserved two-promoter system." Biochemical Journal 303, no. 2 (October 15, 1994): 449–53. http://dx.doi.org/10.1042/bj3030449.

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Molecular cloning of the 5′ part of mouse phosphofructokinase-M cDNA was performed. In the 46 cDNA clones isolated, there were two classes of 5′ untranslated sequences. One had an EcoRI site within its 5′ untranslated sequence. This showed 83.0% similarity with human type B mRNA for phosphofructokinase-M. The other lacked an EcoRI site, showing 92.9% similarity with human type C mRNA. Using the reverse-transcription PCR technique, we found that the transcript with an EcoRI site was exclusively expressed in cardiac and skeletal muscles, while that without an EcoRI site was expressed in all the mouse tissues examined. The results suggested that the mouse phosphofructokinase-M gene was transcribed through alternative splicing by the multiple promoters. This transcription mechanism was considered to be evolutionarily conserved. The level of phosphofructokinase-M gene expression in mouse cardiac and skeletal muscles decreased in the ketotic diabetic state. Although the regulatory mechanism and the physiological significance are not fully known, this would indicate that phosphofructokinase-M gene transcripts are affected during the diabetic state.
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27

Jeltsch, A., J. Alves, H. Wolfes, G. Maass, and A. Pingoud. "Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes." Proceedings of the National Academy of Sciences 90, no. 18 (September 15, 1993): 8499–503. http://dx.doi.org/10.1073/pnas.90.18.8499.

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28

Morgan, W. F., M. L. Fero, M. C. Land, and R. A. Winegar. "Inducible expression and cytogenetic effects of the EcoRI restriction endonuclease in Chinese hamster ovary cells." Molecular and Cellular Biology 8, no. 10 (October 1988): 4204–11. http://dx.doi.org/10.1128/mcb.8.10.4204-4211.1988.

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The cytogenetic endpoints sister chromatid exchange (SCE) and chromosome aberrations are widely used as indicators of DNA damage induced by mutagenic carcinogens. Chromosome aberrations appear to result directly from DNA double-strand breaks, but the lesion(s) giving rise to SCE formation remains unknown. Most compounds that induce SCEs induce a spectrum of lesions in DNA. To investigate the role of double-strand breakage in SCE formation, we constructed a plasmid that gives rise to one specific lesion, a staggered-end ("cohesive") DNA double-strand break. This plasmid, designated pMENs, contains a selectable marker, neo, which is a bacterial gene for neomycin resistance, and the coding sequence for the bacterial restriction endonuclease EcoRI attached to the mouse metallothionein gene promoter. EcoRI recognizes G decreases AATTC sequences in DNA and makes DNA double-strand breaks with four nucleotides overhanging as staggered ends. Cells transfected with pMENS were resistant to the antibiotic G418 and contained an integrated copy of the EcoRI gene, detectable by DNA filter hybridization. The addition of the heavy metal CdSO4 resulted in the intracellular production of EcoRI, as measured by an anti-EcoRI antibody. Cytogenetic analysis after the addition of CdSO4 indicated a dramatic increase in the frequency of chromosome aberrations but very little effect on SCE frequency. Although there was some intercellular heterogeneity, these results confirm that DNA double-strand breaks do result in chromosome aberrations but that these breaks are not sufficient to give rise to SCE formation.
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29

DE CESARE, A., G. MANFREDA, M. MACRÌ, and C. CANTONI. "Application of Automated Ribotyping To Support the Evaluation of Listeria monocytogenes Sources in a Taleggio Cheese Producing Plant." Journal of Food Protection 70, no. 5 (May 1, 2007): 1116–21. http://dx.doi.org/10.4315/0362-028x-70.5.1116.

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In March 2005, Listeria monocytogenes was detected on the rinds of Taleggio cheeses produced in an Italian plant. To identify the pathogen source, 154 rinds of cheeses that had been manually and automatically salinated and 52 environmental swabs collected from salting equipment, ripening cloths, and ripening boxes were tested for L. monocytogenes. Twenty-seven strains isolated from cheese samples and 16 strains isolated from environmental samples were genotyped by EcoRI and PvuII automated ribotyping. The microbiological results revealed a significant incidence of contamination of cheeses that were automatically salinated and contamination on the salting equipment, ripening cloths, and boxes. All cheese and environmental strains had the same EcoRI and PvuII ribotyping profiles, designated 153-204-S5 and 153-210-S-2, respectively. The only exception were three Taleggio strains, isolated from the same lot of product, that had EcoRI and PvuII ribotyping profiles designated 153-289-S6 and 153-214-S-5, respectively. Strains with EcoRI profile 153-204-S5 were classified as DUP-ID 1045 and serotype 1/2a, whereas strains with EcoRI profile 153-289-S6 were classified as DUP-ID 1034 and serotype 1/2b. The microbiological and molecular typing data collected in this study suggest that the source of the L. monocytogenes contamination in the Taleggio plant under study was the automated salting equipment. The isolate DUP-IDs were used to trace the introduction of potentially dangerous strains, such as those characterized as DUP-ID 1034, in the processing plant.
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30

Ichige, Asao, and Ichizo Kobayashi. "Stability of EcoRI Restriction-Modification Enzymes In Vivo Differentiates the EcoRI Restriction-Modification System from Other Postsegregational Cell Killing Systems." Journal of Bacteriology 187, no. 19 (October 1, 2005): 6612–21. http://dx.doi.org/10.1128/jb.187.19.6612-6621.2005.

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ABSTRACT Certain type II restriction modification gene systems can kill host cells when these gene systems are eliminated from the host cells. Such ability to cause postsegregational killing of host cells is the feature of bacterial addiction modules, each of which consists of toxin and antitoxin genes. With these addiction modules, the differential stability of toxin and antitoxin molecules in cells plays an essential role in the execution of postsegregational killing. We here examined in vivo stability of the EcoRI restriction enzyme (toxin) and modification enzyme (antitoxin), the gene system of which has previously been shown to cause postsegregational host killing in Escherichia coli. Using two different methods, namely, quantitative Western blot analysis and pulse-chase immunoprecipitation analysis, we demonstrated that both the EcoRI restriction enzyme and modification enzyme are as stable as bulk cellular proteins and that there is no marked difference in their stability. The numbers of EcoRI restriction and modification enzyme molecules present in a host cell during the steady-state growth were estimated. We monitored changes in cellular levels of the EcoRI restriction and modification enzymes during the postsegregational killing. Results from these analyses together suggest that the EcoRI gene system does not rely on differential stability between the toxin and the antitoxin molecules for execution of postsegregational cell killing. Our results provide insights into the mechanism of postsegregational killing by restriction-modification systems, which seems to be distinct from mechanisms of postsegregational killing by other bacterial addiction modules.
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31

Morgan, W. F., M. L. Fero, M. C. Land, and R. A. Winegar. "Inducible expression and cytogenetic effects of the EcoRI restriction endonuclease in Chinese hamster ovary cells." Molecular and Cellular Biology 8, no. 10 (October 1988): 4204–11. http://dx.doi.org/10.1128/mcb.8.10.4204.

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The cytogenetic endpoints sister chromatid exchange (SCE) and chromosome aberrations are widely used as indicators of DNA damage induced by mutagenic carcinogens. Chromosome aberrations appear to result directly from DNA double-strand breaks, but the lesion(s) giving rise to SCE formation remains unknown. Most compounds that induce SCEs induce a spectrum of lesions in DNA. To investigate the role of double-strand breakage in SCE formation, we constructed a plasmid that gives rise to one specific lesion, a staggered-end ("cohesive") DNA double-strand break. This plasmid, designated pMENs, contains a selectable marker, neo, which is a bacterial gene for neomycin resistance, and the coding sequence for the bacterial restriction endonuclease EcoRI attached to the mouse metallothionein gene promoter. EcoRI recognizes G decreases AATTC sequences in DNA and makes DNA double-strand breaks with four nucleotides overhanging as staggered ends. Cells transfected with pMENS were resistant to the antibiotic G418 and contained an integrated copy of the EcoRI gene, detectable by DNA filter hybridization. The addition of the heavy metal CdSO4 resulted in the intracellular production of EcoRI, as measured by an anti-EcoRI antibody. Cytogenetic analysis after the addition of CdSO4 indicated a dramatic increase in the frequency of chromosome aberrations but very little effect on SCE frequency. Although there was some intercellular heterogeneity, these results confirm that DNA double-strand breaks do result in chromosome aberrations but that these breaks are not sufficient to give rise to SCE formation.
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32

Rudd, Kenneth E. "Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map." Microbiology and Molecular Biology Reviews 62, no. 3 (September 1, 1998): 985–1019. http://dx.doi.org/10.1128/mmbr.62.3.985-1019.1998.

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SUMMARY A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.
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33

URWIN, NIGEL, ANDRÉ ROSENTHAL, and ALAN D. B. MALCOLM. "Cleavage of synthetic oligonucleotides by EcoRI." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 264. http://dx.doi.org/10.1042/bst0140264.

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34

Dozier, C., S. Walbaum, D. Leprince, and D. Stehelin. "EcoRI RFLP linked to the humanmybgene." Nucleic Acids Research 14, no. 4 (1986): 1928. http://dx.doi.org/10.1093/nar/14.4.1928.

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35

Needels, M. C., S. R. Fried, R. Love, J. M. Rosenberg, H. W. Boyer, and P. J. Greene. "Determinants of EcoRI endonuclease sequence discrimination." Proceedings of the National Academy of Sciences 86, no. 10 (May 1, 1989): 3579–83. http://dx.doi.org/10.1073/pnas.86.10.3579.

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36

Bircakova, Miroslava, Martin Truksa, and William H. Scouten. "Oriented immobilization of restriction endonuclease ecori." Journal of Molecular Recognition 9, no. 5-6 (October 1996): 683–90. http://dx.doi.org/10.1002/(sici)1099-1352(199634/12)9:5/6<683::aid-jmr321>3.0.co;2-e.

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37

GENDEL, STEVEN M., and JODIE ULASZEK. "Ribotype Analysis of Strain Distribution in Listeria monocytogenes." Journal of Food Protection 63, no. 2 (February 1, 2000): 179–85. http://dx.doi.org/10.4315/0362-028x-63.2.179.

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Changes in the temporal and spatial patterns of strain distribution for the foodborne pathogen Listeria monocytogenes were studied by ribotyping using the Qualicon Riboprinter system. Ribotype patterns were obtained by using the restriction enzymes EcoRI and PvuII for 72 isolates of L. monocytogenes recovered from smoked salmon samples over a period of 3 years. Each pattern was classified both by comparison to a pattern library and by comparison among the 72 isolate patterns. Eleven EcoRI-based ribogroups and 16 PvuII groups were identified. Eight of the 11 EcoRI ribogroups were found in isolates obtained over a period of &gt;12 months, and 75% of the EcoRI ribogroups that were found in more than one food sample were distributed nationally. Within the set of isolates, there were 26 instances where more than one isolate was obtained from a single food sample. In 35% of these instances, the co-isolates produced different ribotype patterns, indicating that multiple strains of L. monocytogenes commonly coexist in the same environment. Overall, these data indicate that the population of L. monocytogenes consists of a number of widely dispersed strains with little geographic or temporal stratification.
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38

Chen, J., C. J. Chang, and R. L. Jarret. "Plasmids from Xylella fastidiosa strains." Canadian Journal of Microbiology 38, no. 9 (September 1, 1992): 993–95. http://dx.doi.org/10.1139/m92-161.

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Plasmids were observed from three strains of Xylella fastidiosa. A restriction map of a plasmid, pXFPW1 of 1.3 kb, isolated from Xyl. fastidiosa strain PWT-22, causing periwinkle wilt disease, was constructed using EcoRI, HaeIII, HinfI, MspI, StyI, and TaqI fragments. No restriction site for BamHI, BglI, DraI, EcoRV, HindIII, PstI, SalI, NcoI, or XbaI was evident. Studies based on the intensity of ethidium bromide staining indicated that there are at least 60 copies of pXFPW1 per genome. pXFPW1 shares a high degree homology with two other plasmids from strains PD82-21 and mul1, the pathogens of Pierce's disease of grapevine and mulberry leaf scorch disease, respectively. Key words: Xylella fastidiosa, plasmids.
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39

Hawse, A., R. A. Collins, and F. E. Nargang. "Behavior of the [mi-3] mutation and conversion of polymorphic mtDNA markers in heterokaryons of Neurospora crassa." Genetics 126, no. 1 (September 1, 1990): 63–72. http://dx.doi.org/10.1093/genetics/126.1.63.

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Abstract We have examined the behavior of the [mi-3] mitochondrial mutation and two physical mtDNA markers in heterokaryotic cultures of Neurospora crassa. Previous workers showed that a 1.2-kilobase insertion in the larger polymorphic form of EcoRI-5 restriction fragment is a site of high frequency and rapid unidirectional gene conversion. We have confirmed this observation and determined by DNA sequence analysis that the insertion in the EcoRI-5 fragment corresponds precisely to an optional intron that contains a long open reading frame in the ND1 gene. Thus, the conversion of the short, intron-lacking, form of EcoRI-5 to the longer, intron-containing, form may be analogous to the unidirectional gene conversion events catalyzed by intron-encoded proteins in other organisms. The resolution of two polymorphic forms of the mtDNA EcoRI-9 restriction fragment in our heterokaryons differs from that observed previously and suggests that this locus is not a site of gene conversion in our heterokaryon pair. The size polymorphism of the EcoRI-9 fragments is due to a tandemly reiterated 78-base-pair sequence which occurs two times in the short form and three times in the long form. One copy of the repeat unit and 66 base pairs following it have been duplicated from the ND2 gene which is located about 30 kilobases distant on the mtDNA. In contrast to the [poky] mitochondrial mutant, which was completely dominant over wild-type mitochondria in heterokaryons, the [mi-3] mutant was recovered in only seven of twenty heterokaryons after ten cycles of conidiation and subculturing. The resolution of the [mi-3] or wild-type phenotype in heterokaryons may depend solely on random factors such as allele input frequency, drift, and segregation rather than specific dominant or suppressive effects.
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40

Morozov, I. V., V. P. Mishin, S. M. Zelenin, V. S. Popova, and A. P. Mertvetsov. "Nucleotide sequence of the rat liver tyrosine amlnotransferas'e gene EcoRI-fragment." Biopolymers and Cell 6, no. 3 (May 20, 1990): 95–96. http://dx.doi.org/10.7124/bc.000275.

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41

Ariga, H., Z. Tsuchihashi, M. Naruto, and M. Yamada. "Cloned mouse DNA fragments can replicate in a simian virus 40 T antigen-dependent system in vivo and in vitro." Molecular and Cellular Biology 5, no. 3 (March 1985): 563–68. http://dx.doi.org/10.1128/mcb.5.3.563-568.1985.

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Mouse liver DNA was cut out with BamHI and cloned into YIp5, which contained the URA3 gene of Saccharomyces cerevisiae in pBR322. Of the several plasmids isolated, two plasmids, pMU65 and pMU111, could transform S. cerevisiae from the URA- to the URA+ phenotype and could replicate autonomously within the transformant, indicating that mouse DNA fragments present in pMU65 or pMU111 contain autonomously replicating sequences (ARS) for replication in S. cerevisiae. Furthermore, to determine the correlation between ARS function in yeast cells and that in much higher organisms, we tried to challenge these plasmids with the simian virus 40 (SV40) DNA replication system. Of the two plasmids tested, the EcoRI-BglII region of pMU65 could be hybridized with a chemically synthesized 13-nucleotide fragment corresponding to the origin region of SV40 DNA. Both pMU65 (the EcoRI-BglII region cloned in pBR322) and its subclone pMU65EB could replicate semiconservatively, and initiation of DNA replication started from the EcoRI-BglII region when the replicating activity of these plasmids was tested in the in vitro SV40 DNA replication system we have established before. Furthermore, pMU65 and pMU65EB could replicate autonomously within monkey Cos cells which produce SV40 T antigen constitutively. These results show that a 2.5-kilobase fragment of the EcoRI-BglII region in pMU65 contains the ARS needed for replication in the SV40 DNA replication system.
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42

Ariga, H., Z. Tsuchihashi, M. Naruto, and M. Yamada. "Cloned mouse DNA fragments can replicate in a simian virus 40 T antigen-dependent system in vivo and in vitro." Molecular and Cellular Biology 5, no. 3 (March 1985): 563–68. http://dx.doi.org/10.1128/mcb.5.3.563.

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Mouse liver DNA was cut out with BamHI and cloned into YIp5, which contained the URA3 gene of Saccharomyces cerevisiae in pBR322. Of the several plasmids isolated, two plasmids, pMU65 and pMU111, could transform S. cerevisiae from the URA- to the URA+ phenotype and could replicate autonomously within the transformant, indicating that mouse DNA fragments present in pMU65 or pMU111 contain autonomously replicating sequences (ARS) for replication in S. cerevisiae. Furthermore, to determine the correlation between ARS function in yeast cells and that in much higher organisms, we tried to challenge these plasmids with the simian virus 40 (SV40) DNA replication system. Of the two plasmids tested, the EcoRI-BglII region of pMU65 could be hybridized with a chemically synthesized 13-nucleotide fragment corresponding to the origin region of SV40 DNA. Both pMU65 (the EcoRI-BglII region cloned in pBR322) and its subclone pMU65EB could replicate semiconservatively, and initiation of DNA replication started from the EcoRI-BglII region when the replicating activity of these plasmids was tested in the in vitro SV40 DNA replication system we have established before. Furthermore, pMU65 and pMU65EB could replicate autonomously within monkey Cos cells which produce SV40 T antigen constitutively. These results show that a 2.5-kilobase fragment of the EcoRI-BglII region in pMU65 contains the ARS needed for replication in the SV40 DNA replication system.
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43

Liu, Yaoping, and Ichizo Kobayashi. "Negative Regulation of the EcoRI Restriction Enzyme Gene Is Associated with Intragenic Reverse Promoters." Journal of Bacteriology 189, no. 19 (July 6, 2007): 6928–35. http://dx.doi.org/10.1128/jb.00127-07.

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ABSTRACT Type II restriction-modification systems are expected to possess mechanisms for tight regulation of their expression to suppress the potential of lethal attack on their host bacteria when they establish and maintain themselves within them. Although the EcoRI restriction enzyme has been well characterized, regulation of its expression is still poorly understood. In this study, mutational analysis with lacZ gene fusion and primer extension assay identified a promoter for the transcription of the ecoRIR gene. Further analyses revealed that an intragenic region containing two overlapping reverse promoter-like elements acted as a negative regulator for ecoRIR gene expression. The activity of these putative reverse promoters was verified by transcriptional gene fusion, primer extension and in vitro transcription. Mutations in these reverse promoters resulted in increased gene expression in both translational and transcriptional gene fusions. An RNase protection assay revealed that the transcript level of the wild type relative to that of the reverse promoter mutant at the downstream regions was much lower than the level at the upstream regions. This suggests that these reverse promoter-like elements affect their downstream transcript level. The possible mechanisms of this kind of negative regulation, in addition to their possible biological roles, are discussed.
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44

Vilhelmsdotter, S., and H. Luthman. "Two EcoRI RFLPs at the GLUT2 locus." Nucleic Acids Research 18, no. 20 (1990): 6175. http://dx.doi.org/10.1093/nar/18.20.6175-a.

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45

Miller, D. L., D. Smailus, and P. J. Goodfellow. "An EcoRI RFLP at the D10S103 locus." Nucleic Acids Research 18, no. 20 (1990): 6177. http://dx.doi.org/10.1093/nar/18.20.6177.

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46

Kinzler, K. W., and B. Vogelstein. "EcoRI polymorphism within theGLIgene (chromosome 12q13.3–14.1)." Nucleic Acids Research 18, no. 9 (1990): 2834. http://dx.doi.org/10.1093/nar/18.9.2834.

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47

Børglum, A. D., A. Byskov, M. V. Cubellis, and T. A. Kruse. "An EcoRI polymorphism for the PLAUR gene." Nucleic Acids Research 19, no. 23 (1991): 6661. http://dx.doi.org/10.1093/nar/19.23.6661-a.

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48

Patel, P., G. I. Bell, R. C. Turner, and J. S. Wainscoat. "Two EcoRI RFLPs at the GLUT2 locus." Nucleic Acids Research 18, no. 16 (1990): 4956. http://dx.doi.org/10.1093/nar/18.16.4956-a.

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49

Hoefsloot, L. H., M. Hoogeveek-Westerveld, H. Sakuraba, Y. Suzuki, B. A. Oostra, and A. J. J. Reuser. "HindIII/EcoRI polymorphism in the GAA gene." Nucleic Acids Research 18, no. 19 (1990): 5921. http://dx.doi.org/10.1093/nar/18.19.5921.

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50

Reich, Norbert O., and Neda Mashhoon. "Kinetic mechanism of the EcoRI DNA methyltransferase." Biochemistry 30, no. 11 (March 19, 1991): 2933–39. http://dx.doi.org/10.1021/bi00225a029.

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