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Journal articles on the topic 'Plasmid DNA isolation'

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Published: 4 June 2021

Last updated: 13 February 2022

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1

Hardianto, Dudi, Alfik Indarto, and Nurtjahjo Dwi Sasongko. "OPTIMASI METODE LISIS ALKALI UNTUK MENINGKATKAN KONSENTRASI PLASMID." Jurnal Bioteknologi & Biosains Indonesia (JBBI) 2, no. 2 (December 5, 2015): 60. http://dx.doi.org/10.29122/jbbi.v2i2.510.

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Plasmids are extra chromosomal molecules of DNA that replicate autonomously and found in prokaryote and eukaryote cells. There are a number of methods that are used to isolate plasmids, such as alkaline lysis, boiling lysis, using cesium chloride, and chromatography. Amongst the disadvantages in plasmid isolation methods are lengthy time especially when handling a large number of samples, high cost, and low purity. Alkaline lysis is the most popular for plasmid isolation because of its simplicity, relatively low cost, and reproducibility. This method can be accomplished in 50 minutes to one hour. In this research, the alkaline lysis method was developed to obtain suitable plasmid for applications in a molecular biology laboratory. The aim of this research was to reduce contaminants and improve yield of plasmid. The result of isolation of pICZA plasmid in Escherichia coli gave the concentration of 3.3 to 3.8 µg/µL with the purity of 1.99.Keywords: Plasmid isolation, pICZ A, Escherichia coli, rapid, alkaline lysis ABSTRAKPlasmid merupakan molekul DNA ekstrakromosomal yang bereplikasi secara mandiri dan ditemukan dalam sel prokariot dan eukariot. Banyak metode yang digunakan untuk isolasi plasmid, seperti: lisis alkali, lisis dengan pemanasan, penggunaan sesium klorida, dan kromatografi. Kelemahan beberapa metode isolasi DNA adalah waktu isolasi yang lama terutama saat isolasi plasmid dalam jumlah banyak, mahal dan kemurniannya yang rendah. Metode lisis alkali merupakan metode yang sangat umum untuk isolasi plasmid karena mudah dilakukan, relatif murah, dan reprodusibilitas. Metode ini dapat dilakukan dalam 50 menit sampai 1 jam. Pada penelitian ini dikembangkan metode lisis alkali untuk memperoleh plasmid yang sesuai untuk penggunaan di laboratorium biologi molekuler. Tujuan dari penelitian ini adalah untuk mengurangi jumlah kontaminan dan meningkatkan konsentrasi plasmid. Hasil isolasi plasmid pICZA dalam Escherichia coli mempunyai konsentrasi antara 3,3 sampai 3,8 µg/µL dan kemurniannya 1,99.Kata Kunci: Isolasi plasmid, pICZ A, Escherichia coli, cepat, lisis alkali

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2

Kniazeva, Marina. "TRIzol for plasmid DNA isolation." Technical Tips Online 2, no. 1 (January 1997): 76–77. http://dx.doi.org/10.1016/s1366-2120(08)70040-0.

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3

Srutkowska, S., G. Konopa, and G. Wegrzyn. "A method for isolation of plasmid DNA replication intermediates from unsynchronized bacterial cultures for electron microscopy analysis." Acta Biochimica Polonica 45, no. 1 (March 31, 1998): 233–40. http://dx.doi.org/10.18388/abp.1998_4305.

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Electron microscopy is a powerful technique for analysis of DNA replication intermediates. However, isolation of replicating DNA molecules from living cells is tricky and difficult, especially in the case of small DNA molecules (such as bacterial plasmids) whose initiation of replication is not easily synchronized. Here a relatively simple and rapid method for efficient isolation of replicating plasmid molecules from unsynchronized Escherichia coli cultures is described. The efficiency of this procedure is high enough for electron microscopy analysis of plasmid replication intermediates appearing in living cells in normal growth conditions. Under optimal conditions, using standard procedures of isolation of plasmid DNA, it is possible to achieve a content of only as few as 0.02 percent of replication intermediates in a plasmid DNA sample. The described method allowed us to enrich up to 100-fold the fraction of replication intermediates suitable for microscopic analysis among all plasmid molecules.

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4

Kusnadi, Mr, Diana Rochintaniawaty, and Diah Kusumawaty. "MENGEMBANGKAN KEMAMPUAN MAHASISWA PENDIDIKAN BIOLOGI DALAM MENGISOLASI PLASMID BAKTERI SEBAGAI PENGAYAAN PRAKTIKUM MIKROBIOLOGI." Jurnal Pengajaran Matematika dan Ilmu Pengetahuan Alam 6, no. 2 (December 8, 2005): 27. http://dx.doi.org/10.18269/jpmipa.v6i2.346.

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This learning cycle focused on developing of Biology education student’s performance in bacteria DNA-plasmid isolation as well as using gel electrophroresis. The aim of the study was to improve student’s performance in operating equipment used in plasmid isolation such as: micropipettes, microsentrifuge, vortex, shaker-incubator, gel electrophoresis, and UV Trans- illuminator camera. Beside that students were also trained to DNA-plasmid isolation base on standard procedure, so students could identify the form of plasmid via the use of gel electrophoresis. This study was conducted in 2 cycle learning processes as an enrichment of microbiology activity, which associated with molecular microbes genetics. Using observation sheet did evaluation. The study revealed that biology education students had good performance in isolating the plasmid and all group were succeed to isolate the plasmid. Beside that there were increased in knowledge ability especially associated with molecular microbes genetics subject, which achievment gain average was 18,3% (Class A) and 35,4% (class B). The DNA isolation activity in microbiology learning shared high contribution as well as increasing of knowledge achievment and performance ability.Keyword: DNA-plasmid, gel electrophoresis, isolation, learning cycle

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5

Williams, Laura E., Chris Detter, Kerrie Barry, Alla Lapidus, and Anne O. Summers. "Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing." Applied and Environmental Microbiology 72, no. 7 (July 2006): 4899–906. http://dx.doi.org/10.1128/aem.00354-06.

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ABSTRACT Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for effective preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli, Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for construction of high-coverage libraries, as shown by sequencing five native plasmids ranging in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on mobile genetic element biology derived from these sequences. Adaptation of this BAC method for large plasmid isolation removes one major technical hurdle to expanding our knowledge of the natural plasmid gene pool.

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6

Sobecky, Patricia A., Tracy J. Mincer, Michelle C. Chang, Aresa Toukdarian, and Donald R. Helinski. "Isolation of Broad-Host-Range Replicons from Marine Sediment Bacteria." Applied and Environmental Microbiology 64, no. 8 (August 1, 1998): 2822–30. http://dx.doi.org/10.1128/aem.64.8.2822-2830.1998.

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ABSTRACT Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888–895, 1997). In the present study we isolated 1.8- to 2.3-kb fragments that contain functional replication origins from one relatively large (30-kb) and three small (<10-kb) naturally occurring plasmids present in different marine isolates. 16S rRNA sequence analyses indicated that the four plasmid-bearing marine isolates belonged to the α and γ subclasses of the classProteobacteria. Three of the marine sediment isolates are related to the γ-3 subclass organisms Vibrio splendidusand Vibrio fischeri, while the fourth isolate may be related to Roseobacter litoralis. Sequence analysis of the plasmid replication regions revealed the presence of features common to replication origins of well-characterized plasmids from clinical bacterial isolates, suggesting that there may be similar mechanisms for plasmid replication initiation in the indigenous plasmids of gram-negative marine sediment bacteria. In addition to replication inEscherichia coli DH5α and C2110, the host ranges of the plasmid replicons, designated repSD41, repSD121, repSD164, and repSD172, extended to marine species belonging to the generaAchromobacter, Pseudomonas,Serratia, and Vibrio. While sequence analysis of repSD41 and repSD121 revealed considerable stretches of homology between the two fragments, these regions do not display incompatibility properties against each other. The replication origin repSD41 was detected in 5% of the culturable plasmid-bearing marine sediment bacterial isolates, whereas the replication origins repSD164 and repSD172 were not detected in any plasmid-bearing bacteria other than the parental isolates. Microbial community DNA extracted from samples collected in November 1995 and June 1997 and amplified by PCR yielded positive signals when they were hybridized with probes specific for repSD41 and repSD172 replication sequences. In contrast, replication sequences specific for repSD164 were not detected in the DNA extracted from marine sediment microbial communities.

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7

Rosenshine, Ilan, and Moshe Mevarech. "Isolation and partial characterization of plasmids found in three Halobacterium volcanii isolates." Canadian Journal of Microbiology 35, no. 1 (January 1, 1989): 92–95. http://dx.doi.org/10.1139/m89-014.

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Three new isolates of Halobacterium volcanii were screened for the presence of plasmids. Each of the different isolates was found to contain one plasmid. These plasmids do not show any homology to each other, nor to the previously isolated plasmid pHV2. Partial restriction maps of these plasmids were determined. One of the plasmids contains chromosomal repetitive sequences as judged by the existence of homologous sequences in the chromosomal DNA of the three isolates. Using the protoplast fusion technique, we showed that at least one of the newly isolated plasmids is compatible with pHV2.Key words: Halobacterium volcanii, archaebacterium, plasmids.

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8

Asmundson, Roderick V., and William J. Kelly. "Isolation and characterization of plasmid DNA fromRuminococcus." Current Microbiology 16, no. 2 (March 1987): 97–100. http://dx.doi.org/10.1007/bf01588178.

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9

Erickson, J. R., and M. Johnston. "Direct cloning of yeast genes from an ordered set of lambda clones in Saccharomyces cerevisiae by recombination in vivo." Genetics 134, no. 1 (May 1, 1993): 151–57. http://dx.doi.org/10.1093/genetics/134.1.151.

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Abstract We describe a technique that facilitates the isolation of yeast genes that are difficult to clone. This technique utilizes a plasmid vector that rescues lambda clones as yeast centromere plasmids. The source of these lambda clones is a set of clones whose location in the yeast genome has been determined by L. Riles et al. in 1993. The Escherichia coli-yeast shuttle plasmid carries URA3, ARS4 and CEN6, and contains DNA fragments from the lambda vector that flank the cloned yeast insert. When yeast is cotransformed with linearized plasmid and lambda clone DNA, Ura+ transformants are obtained by a recombination event between the lambda clone and the plasmid vector that generates an autonomously replicating plasmid containing the cloned yeast DNA sequences. Genes whose genetic map positions are known can easily be identified and recovered in this plasmid by testing only those lambda clones that map to the relevant region of the yeast genome for their ability to complement the mutant phenotype. This technique facilitates the isolation of yeast genes that resist cloning either because (1) they are underrepresented in yeast genomic libraries amplified in E. coli, (2) they provide phenotypes that are too marginal to allow selection of the gene by genetic complementation or (3) they provide phenotypes that are laborious to score. We demonstrate the utility of this technique by isolating three genes, GAL83, SSN2 and MAK7, each of which presents one of these problems for cloning.

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10

Nakashima, Nobutaka, and Tomohiro Tamura. "Isolation and Characterization of a Rolling-Circle-Type Plasmid from Rhodococcus erythropolis and Application of the Plasmid to Multiple-Recombinant-Protein Expression." Applied and Environmental Microbiology 70, no. 9 (September 2004): 5557–68. http://dx.doi.org/10.1128/aem.70.9.5557-5568.2004.

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ABSTRACT We isolated, sequenced, and characterized the cryptic plasmid pRE8424 from Rhodococcus erythropolis DSM8424. Plasmid pRE8424 is a 5,987-bp circular plasmid; it carries six open reading frames and also contains cis-acting elements, specifically a single-stranded origin and a double-stranded origin, which are characteristic of rolling-circle-replication plasmids. Experiments with pRE8424 derivatives carrying a mutated single-stranded origin sequence showed that single-stranded DNA intermediates accumulated in the cells because of inefficient conversion from single-stranded DNA to double-stranded DNA. This result indicates that pRE8424 belongs to the pIJ101/pJV1 family of rolling-circle-replication plasmids. Expression vectors that are functional in several Rhodococcus species were constructed by use of the replication origin from pRE8424. We previously reported a cryptic plasmid, pRE2895, from R. erythropolis, which may replicate by a θ-type mechanism, like ColE2 plasmids. The new expression vectors originating from pRE8424 were compatible with those derived from pRE2895. Coexpression experiments with these compatible expression vectors indicated that the plasmids are suitable for the simultaneous expression of multiple recombinant proteins.

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11

Zhang, Ran, Ana Zeng, Ping Fang, and Zhongjun Qin. "Characterization of Replication and Conjugation of Streptomyces Circular Plasmids pFP1 and pFP11 and Their Ability To Propagate in Linear Mode with Artificially Attached Telomeres." Applied and Environmental Microbiology 74, no. 11 (April 4, 2008): 3368–76. http://dx.doi.org/10.1128/aem.00402-08.

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ABSTRACT Many Streptomyces species harbor circular plasmids (8 to 31 kb) as well as linear plasmids (12 to 1,700 kb). We report the characterization of two newly detected circular plasmids, pFP11 (35,139 bp) and pFP1 (39,360 bp). As on linear plasmids, their replication loci comprise repA genes and adjacent iterons, to which RepA proteins bind specifically in vitro. Plasmids containing the minimal iterons plus the repA locus of pFP11 were inherited extremely unstably; par and additional loci were required for stable inheritance. Surprisingly, plasmids containing replication loci from pFP11 or Streptomyces circular plasmid SCP2 but not from pFP1, SLP1, or pIJ101 propagated in a stable linear mode when the telomeres of a linear plasmid were attached. These results indicate bidirectional replication for pFP11 and SCP2. Both pFP11 and pFP1 contain, for plasmid transfer, a major functional traB gene (encoding a DNA translocase typical for Streptomyces plasmids) as well as, surprisingly, a putative traA gene (encoding a DNA nickase, characteristic of single-stranded DNA transfer of gram-negative plasmids), but this did not appear to be functional, at least in isolation.

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12

van Elsas, Jan Dirk, Brian B. McSpadden Gardener, Anneke C. Wolters, and Eric Smit. "Isolation, Characterization, and Transfer of Cryptic Gene-Mobilizing Plasmids in the Wheat Rhizosphere." Applied and Environmental Microbiology 64, no. 3 (March 1, 1998): 880–89. http://dx.doi.org/10.1128/aem.64.3.880-889.1998.

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ABSTRACT A set of self-transmissible plasmids with IncQ plasmid-mobilizing capacity was isolated by triparental exogenous isolation from the wheat rhizosphere with an Escherichia coli IncQ plasmid host and a Ralstonia eutropha recipient. Three plasmids of 38 to 45 kb, denoted pIPO1, pIPO2, and pIPO3, were selected for further study. No selectable traits (antibiotic or heavy-metal resistance) were identified in these plasmids. The plasmids were characterized by replicon typing via PCR and hybridization with replicon-specific probes and other hybridizations. pIPO1 and pIPO3 were similar to each other, whereas pIPO2 was different. None of these plasmids belonged to any known incompatibility group. pIPO2 was selected for further work, and a mini-Tn5-tet transposon was inserted to confer selectability. Plasmid pIPO2 had a broad IncQ plasmid mobilization and self-transfer range among the alpha, beta, and gamma subclasses of theProteobacteria but did not show productive transfer to gram-positive bacteria. Plasmid pIPO2 mobilized IncQ plasmid pIE723 from Pseudomonas fluorescens to diverse indigenous proteobacteria in the rhizosphere of field-grown wheat. Transfer of pIE723 to indigenous bacteria was not observed in the absence of added pIPO2. A specific PCR primer system and a probe were developed for the detection of pIPO2-type plasmids in soil and rhizosphere. Analysis of soil DNA provided evidence for the presence of pIPO2 in inoculated wheat rhizosphere soil in the field study, as well as in the rhizosphere of uninoculated wheat plants growing in soil microcosms. The system failed to identify major reservoirs of pIPO2 in a variety of other soils.

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13

Giovannini, R., and R. Freitag. "Continuous isolation of plasmid DNA by annular chromatography." Biotechnology and Bioengineering 77, no. 4 (January 4, 2002): 445–54. http://dx.doi.org/10.1002/bit.10149.

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14

Kanatani, Kazuo, Kazushi Yoshida, Takatsugu Tahara, Hirosumi Miura, Masaru Sakamoto, and Masao Oshimura. "Isolation and Characterization of Plasmid DNA inLactobacillus acidophilus." Agricultural and Biological Chemistry 55, no. 8 (August 1991): 2051–156. http://dx.doi.org/10.1080/00021369.1991.10870929.

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15

Gardner, Murray N., Shelly M. Deane, and Douglas E. Rawlings. "Isolation of a New Broad-Host-Range IncQ-Like Plasmid, pTC-F14, from the Acidophilic Bacterium Acidithiobacillus caldus and Analysis of the Plasmid Replicon." Journal of Bacteriology 183, no. 11 (June 1, 2001): 3303–9. http://dx.doi.org/10.1128/jb.183.11.3303-3309.2001.

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ABSTRACT A moderately thermophilic (45 to 50°C), highly acidophilic (pH 1.5 to 2.5), chemolithotrophic Acidithiobacillus caldusstrain, f, was isolated from a biooxidation process used to treat nickel ore. Trans-alternating field electrophoresis analysis of total DNA from the A. caldus cells revealed two plasmids of approximately 14 and 45 kb. The 14-kb plasmid, designated pTC-F14, was cloned and shown by replacement of the cloning vector with a kanamycin resistance gene to be capable of autonomous replication inEscherichia coli. Autonomous replication was also demonstrated in Pseudomonas putida andAgrobacterium tumefaciens LBA 4404, which suggested that pTC-F14 is a broad-host-range plasmid. Sequence analysis of the pTC-F14 replicon region revealed five open reading frames and a replicon organization like that of the broad-host-range IncQ plasmids. Three of the open reading frames encoded replication proteins which were most closely related to those of IncQ-like plasmid pTF-FC2 (amino acid sequence identities: RepA, 81%; RepB, 78%; RepC, 74%). However, the two plasmids were fully compatible and pTC-F14 represents a new IncQ-like plasmid replicon. Surprisingly, asymmetrical incompatibility was found with the less closely related IncQ plasmid R300B derivative pKE462 and the IncQ-like plasmid derivative pIE1108. Analysis of the pTC-F14 oriV region revealed five direct repeats consisting of three perfectly conserved 22-bp iterons flanked by iterons of 23 and 21 bp. Plasmid pTC-F14 had a copy number of 12 to 16 copies per chromosome in both E. coli, and A. caldus. The rep gene products of pTC-F14 and pTF-FC2 were unable to functionally complement each other'soriV regions, but replication occurred when the genes for each plasmid's own RepA, RepB, and RepC proteins were provided intrans. Two smaller open reading frames were found between the repB and repA genes of pTC-F14, which encode proteins with high amino acid sequence identity (PasA, 81%; PasB, 72%) to the plasmid addiction system of pTF-FC2. This is the second time a plasmid stability system of this type has been found on an IncQ-like plasmid.

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Tereza, Sovová, Křížová Barbora, Drábková Lenka, and Ovesná Jaroslava. "Detection of PCR inhibition in food and feed with a synthetic plasmid." Czech Journal of Food Sciences 35, No. 2 (April 29, 2017): 160–64. http://dx.doi.org/10.17221/374/2016-cjfs.

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We present a successful use of the plasmid inhibition detection and DNA isolation protocol optimisation for four food/feed samples in qPCR analysis of the sequence coding for chloroplast tRNA-Leu: two meat meal samples and two samples made of cranberries (jam and dried fruit). The quantitative real-time polymerase chain reaction (qPCR) can be inhibited by various substances and the DNA content in the sample can be underestimated. It is necessary to identify the PCR inhibition and choose an optimal DNA isolation protocol to correctly evaluate the sample. In a previous study, we have developed an assay using plasmid DNA carrying a non-homologous random sequence identifying possible inhibitors in qPCR in food/feed samples. The plasmid assay allowed to effectively reveal the PCR inhibition in all of the different sample matrices and to choose an optimal DNA isolation protocol.

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17

KANATANI, Kazuo, Kazushi YOSHIDA, Takatsugu TAHARA, Hirosumi MIURA, Masaru SAKAMOTO, and Masao OSHIMURA. "Isolation and Characterization of Plasmid DNA in Lactobacillus acidophilus." Agricultural and Biological Chemistry 55, no. 8 (1991): 2051–56. http://dx.doi.org/10.1271/bbb1961.55.2051.

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18

Roeder, Thomas, Derk Görich, Niklas P. Roeder, and Iris Bruchhaus. "Isolation of ultrapure supercoiled plasmid-DNA using preparative electrophoresis." Electrophoresis 19, no. 10 (July 1998): 1575–76. http://dx.doi.org/10.1002/elps.1150191009.

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19

Domenico, P., J. L. Marx, P. E. Schoch, and B. A. Cunha. "Rapid plasmid DNA isolation from mucoid gram-negative bacteria." Journal of Clinical Microbiology 30, no. 11 (1992): 2859–63. http://dx.doi.org/10.1128/jcm.30.11.2859-2863.1992.

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20

Todorova, Kristina, Vihren Kolev, Genoveva Nacheva, and Ivan G. Ivanov. "Isolation of Plasmid DNA by Adsorption on Glass Fibers." Biotechnology & Biotechnological Equipment 16, no. 1 (January 2002): 145–47. http://dx.doi.org/10.1080/13102818.2002.10819170.

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21

Imperio, Tatiana, Roberto Bargagli, and Laura Marri. "Detection of IncP replicon-specific regions in DNA from Antarctic microbiota." Open Life Sciences 2, no. 3 (September 1, 2007): 378–84. http://dx.doi.org/10.2478/s11535-007-0025-y.

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AbstractPlasmids capable of horizontal transfer contribute to the adaptability of bacteria, as they may provide genes that enable their hosts to cope with different selective pressures. Only limited information is available on plasmids from Antarctic habitats, and up until now surveys have only used traditional methods of endogenous plasmid isolation. The method based on primer systems, designed on the basis of published sequences for plasmids from different incompatibility (Inc) groups, is appropriate to detect the replicon-specific regions of corresponding plasmids in cultured bacteria, or in total community DNA, which share sufficient DNA similarity with reference plasmids at the amplified regions. In this study, we applied broad-host-range plasmid-specific primers to DNA from microbial samples collected at six different locations in Northern Victoria Land (Antarctica). DNA preparations were used as targets for PCR (polymerase chain reaction) amplification with primers for the IncP (trfA2) and IncQ (oriV ) groups. PCR products were Southern blotted and hybridized with PCR-derived probes for trfA2 and oriV regions. This approach detected the occurrence of IncP-specific sequences in eight out of fifteen DNA samples, suggesting a gene-mobilizing capacity within the original habitats.

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Schwarz, J. J., and P. B. Berget. "The isolation and sequence of missense and nonsense mutations in the cloned bacteriophage P22 tailspike protein gene." Genetics 121, no. 4 (April 1, 1989): 635–49. http://dx.doi.org/10.1093/genetics/121.4.635.

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Abstract Twenty-seven new mutations in the structural gene for the Salmonella typhimurium bacteriophage P22 tailspike protein have been isolated, mapped using a powerful plasmid-based genetic system and their DNA sequence changes determined. The mutations were generated by hydroxylamine treatment of the cloned gene on a plasmid expression vector. Assaying the activity of the tailspike protein produced from this plasmid and screening for plasmid mutants were accomplished by the in situ complementation of P22 capsids imbedded in soft agar to produce infectious phage. Deletion mutations in the cloned gene have been constructed by a two step procedure involving oligonucleotide linker insertion and in vitro deletion by restriction endonuclease digestion. The deletions, whose physical endpoints were determined by DNA sequencing, define 12 genetic and physical intervals into which the new mutations were mapped by marker rescue experiments. These deletions were transferred to phage P22 by recombination and used to map mutations carried on plasmids. Following mapping, the nucleotide change for each of the mutations was determined by DNA sequencing. The majority were absolute missense mutations although both amber and ochre nonsense mutations were also identified in the protein coding portion of the gene. The suppression pattern of the nonsense mutations was determined on several nonsense suppressors. Four of the mutations cause severely depressed levels of tailspike protein expression from both the cloned gene on the plasmid expression vector and from P22 phage carrying these mutations. These mutations were identified as nucleotide changes in what is probably the P22 late operon transcription terminator which immediately follows the tailspike protein coding sequence.

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Iswara, Arya, and Sri Sinto Dewi. "Bacterial Plasmids Profile from Escherichia coli Resistant to Metronidazole and Nalidixic Acid." El-Hayah 6, no. 1 (September 19, 2017): 23. http://dx.doi.org/10.18860/elha.v6i1.4079.

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bacteria that cause an illness. Antibiotic treatments to a patient have a purpose to eliminate the pathogen bacteria. Bacteria resistance to antibiotic was influenced by the intensity of antibiotic treatment in a region, the uncontrolled antibiotics treatments would increase the antibiotic resistance of bacteria. Plasmids was an extrachromosomal DNA that encodes a functional protein that would eliminate the antibiotic activity. Plasmid is the determinant of bacteria sensitivity to antibiotics. In this case it would be important to find out the bacterial plasmid profile on the E.coli resistant to metronidazole and nalidixic acid antibiotics. This research was using four different sample from faces of diarrhea, ice block, waters from well, and ketchup to cultivate the E. coli. lasmid isolation method was carried out by lyses alkali method. Plasmid profile of the E. coli that resistant to metronidazole and nalidixic acid antibiotics and analyzed using electrophoresis on 1% agarose. E. coli plasmid DNA profile was observed as a fluorescent DNA band in ultraviolet rays. In result, isolated plasmids from bacteria that resistant to antibiotics metronidazole and nalidixic acid having similar size approximately 500 bp, different from bacteria that sensitive to antibiotics metronidazole and nalidixic acid has a smaller size in region of 100 bp.

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Rishi, A. K., and D. P. McManus. "Genomic cloning of human Echinococcus granulosus DNA: isolation of recombinant plasmids and their use as genetic markers in strain characterization." Parasitology 94, no. 2 (April 1987): 369–83. http://dx.doi.org/10.1017/s0031182000054020.

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SUMMARYA small, size selected (0·5–5·0Kbp) genomic DNA library has been constructed in the bacterial plasmid pAT153 using DNA extracted from a human isolate (Kenyan origin) of the hydatid disease organism, Echinococcus granulosus. A panel of taeniid cestode DNAs has been used in conjunction with hybridization and restriction-enzyme analysis to identify in the library two recombinant plasmids with Echinococcus-specific inserts and a single recombinant plasmid (coded pEG18) with a DNA fragment unique for E. granulosus. These, and other recombinant plasmids with E. granulosus DNA inserts, have been used in restriction endonuclease, Southern transfer and hybridization analysis to independently and repro-ducibly discriminate between the UK horse and sheep strains of E. granulosus; these probes may well prove of value for characterizing isolates from other endemic areas. The feasibility of using a cloned DNA fragment as the basis of a simple field test for distinguishing eggs of E. granulosus from those of other taeniid cestodes is discussed. The recombinant insert (approximately 2·3 Kbp in size) of pEG18 has a low copy number - estimated at approximately 26 - and it may not be sufficiently sensitive for practical use as a DNA probe in the identification of small numbers of E. granulosus eggs by molecular hybridization.

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Zhou, Aiwu, Xueyuan Jiang, and Xianxiu Xu. "Improved Alkaline Lysis Method for Rapid Isolation of Plasmid DNA." BioTechniques 23, no. 4 (October 1997): 592–94. http://dx.doi.org/10.2144/97234bm06.

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26

Schallinger, Luke E., John E. Gray, L. Winola Wagner, Sue Knowlton, and Joseph J. Kirkland. "Preparative isolation of plasmid DNA with sedimentation field flow fractionation." Journal of Chromatography B: Biomedical Sciences and Applications 342 (January 1985): 67–77. http://dx.doi.org/10.1016/s0378-4347(00)84489-8.

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27

HE, X., H. HUO, K. WANG, W. TAN, P. GONG, and J. GE. "Plasmid DNA isolation using amino-silica coated magnetic nanoparticles (ASMNPs)." Talanta 73, no. 4 (October 15, 2007): 764–69. http://dx.doi.org/10.1016/j.talanta.2007.04.056.

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Chowdhury, K. "One step 'miniprep' method for the isolation of plasmid DNA." Nucleic Acids Research 19, no. 10 (May 25, 1991): 2792. http://dx.doi.org/10.1093/nar/19.10.2792.

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Serghini, M. A., C. Ritzenthaler, and L. Pinck. "A rapid and efficient ‘miniprep’ for isolation of plasmid DNA." Nucleic Acids Research 17, no. 9 (1989): 3604. http://dx.doi.org/10.1093/nar/17.9.3604.

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30

Herman, R. E., and L. L. McKay. "Isolation and partial characterization of plasmid DNA from Streptococcus thermophilus." Applied and Environmental Microbiology 50, no. 4 (1985): 1103–6. http://dx.doi.org/10.1128/aem.50.4.1103-1106.1985.

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31

Eldem, Turkan, Pelin Yargan, and Ozgen Koseoglu Eser. "Optimization in isolation and purification of plasmid DNA (pAcGFP1-N1)." Current Opinion in Biotechnology 22 (September 2011): S125. http://dx.doi.org/10.1016/j.copbio.2011.05.406.

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32

Soltysiak, Maximillian P. M., Rebecca S. Meaney, Samir Hamadache, Preetam Janakirama, David R. Edgell, and Bogumil J. Karas. "Trans-Kingdom Conjugation within Solid Media from Escherichia coli to Saccharomyces cerevisiae." International Journal of Molecular Sciences 20, no. 20 (October 21, 2019): 5212. http://dx.doi.org/10.3390/ijms20205212.

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Conjugation is a bacterial mechanism for DNA transfer from a donor cell to a wide range of recipients, including both prokaryotic and eukaryotic cells. In contrast to conventional DNA delivery techniques, such as electroporation and chemical transformation, conjugation eliminates the need for DNA extraction, thereby preventing DNA damage during isolation. While most established conjugation protocols allow for DNA transfer in liquid media or on a solid surface, we developed a procedure for conjugation within solid media. Such a protocol may expand conjugation as a tool for DNA transfer to species that require semi-solid or solid media for growth. Conjugation within solid media could also provide a more stable microenvironment in which the conjugative pilus can establish and maintain contact with recipient cells for the successful delivery of plasmid DNA. Furthermore, transfer in solid media may enhance the ability to transfer plasmids and chromosomes greater than 100 kbp. Using our optimized method, plasmids of varying sizes were tested for transfer from Escherichia coli to Saccharomyces cerevisiae. We demonstrated that there was no significant change in conjugation frequency when plasmid size increased from 56.5 to 138.6 kbp in length. Finally, we established an efficient PCR-based synthesis protocol to generate custom conjugative plasmids.

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Zheng, Bo, Haruyoshi Tomita, Takako Inoue, and Yasuyoshi Ike. "Isolation of VanB-Type Enterococcus faecalis Strains from Nosocomial Infections: First Report of the Isolation and Identification of the Pheromone-Responsive Plasmids pMG2200, Encoding VanB-Type Vancomycin Resistance and a Bac41-Type Bacteriocin, and pMG2201, Encoding Erythromycin Resistance and Cytolysin (Hly/Bac)." Antimicrobial Agents and Chemotherapy 53, no. 2 (November 24, 2008): 735–47. http://dx.doi.org/10.1128/aac.00754-08.

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ABSTRACT Eighteen identical VanB-type Enterococcus faecalis isolates that were obtained from different hospitalized patients were examined for their drug resistance and plasmid DNAs. Of the 18 strains, 12 strains exhibited resistance to erythromycin (Em), gentamicin (Gm), kanamycin (Km), tetracycline (Tc), and vancomycin (Van) and produced cytolysin (Hly/Bac) and a bacteriocin (Bac) active against E. faecalis strains. Another six of the strains exhibited resistance to Gm, Km, Tc, and Van and produced a bacteriocin. Em and Van resistance was transferred individually to E. faecalis FA2-2 strains at a frequency of about 10−4 per donor cell by broth mating. The Em-resistant transconjugants and the Van-resistant transconjugants harbored a 65.7-kbp plasmid and a 106-kbp plasmid, respectively. The 106-kbp and 65.7-kbp plasmids isolated from the representative E. faecalis NKH15 strains were designated pMG2200 and pMG2201, respectively. pMG2200 conferred vancomycin resistance and bacteriocin activity on the host strain and responded to the synthetic pheromone cCF10 for pCF10, while pMG2201 conferred erythromycin resistance and cytolysin activity on its host strain and responded to the synthetic pheromone cAD1 for pAD1. The complete DNA sequence of pMG2200 (106,527 bp) showed that the plasmid carried a Tn1549-like element encoding vanB2-type resistance and the Bac41-like bacteriocin genes of pheromone-responsive plasmid pYI14. The plasmid contained the regulatory region found in pheromone-responsive plasmids and encoded the genes prgX and prgQ, which are the key negative regulatory elements for plasmid pCF10. pMG2200 also encoded TraE1, a key positive regulator of plasmid pAD1, indicating that pMG2200 is a naturally occurring chimeric plasmid that has a resulting prgX-prgQ-traE1 genetic organization in the regulatory region of the pheromone response. The functional oriT region and the putative relaxase gene of pMG2200 were identified and found to differ from those of pCF10 and pAD1. The putative relaxase of pMG2200 was classified as a member of the MOBMG family, which is found in pheromone-independent plasmid pHTβ of the pMG1-like plasmids. This is the first report of the isolation and characterization of a pheromone-responsive highly conjugative plasmid encoding vanB resistance.

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SUN, NAI-EN, BAO-HE SHEN, JUN-MA ZHOU, JING YUAN, XIAN-XIU XU, DE-XU ZHU, and KIA-KI HAN. "An Efficient Method for Large-Scale Isolation of Plasmid DNAs by Heat-Alkali Co-Denaturation." DNA and Cell Biology 13, no. 1 (January 1994): 83–86. http://dx.doi.org/10.1089/dna.1994.13.83.

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35

Malatinkova, Eva, Maja Kiselinova, Pawel Bonczkowski, Wim Trypsteen, Peter Messiaen, Jolien Vermeire, Bruno Verhasselt, Karen Vervisch, Linos Vandekerckhove, and Ward De Spiegelaere. "Accurate Quantification of Episomal HIV-1 Two-Long Terminal Repeat Circles by Use of Optimized DNA Isolation and Droplet Digital PCR." Journal of Clinical Microbiology 53, no. 2 (December 10, 2014): 699–701. http://dx.doi.org/10.1128/jcm.03087-14.

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Episomal HIV-1 two-long terminal repeat (2-LTR) circles are considered markers for ongoing viral replication. Two sample processing procedures were compared to accurately quantify 2-LTR in patients by using droplet digital PCR (ddPCR). Here, we show that plasmid isolation with a spiked non-HIV plasmid for normalization enables more accurate 2-LTR quantification than genomic DNA isolation.

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Krysan, P. J., S. B. Haase, and M. P. Calos. "Isolation of human sequences that replicate autonomously in human cells." Molecular and Cellular Biology 9, no. 3 (March 1989): 1026–33. http://dx.doi.org/10.1128/mcb.9.3.1026.

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We have isolated a heterogeneous collection of human genomic sequences which replicate autonomously when introduced into human cells. The novel strategy for the isolation of these sequences involved cloning random human DNA fragments into a defective Epstein-Barr virus vector. This vector alone was unable to replicate in human cells, but appeared to provide for the nuclear retention of linked DNA. The human sequences persist in a long-term replication assay (greater than 2 months) in the presence of the viral nuclear retention sequences. Using a short-term (4-day) assay, we showed that the human sequences are able to replicate in the absence of all viral sequences. The plasmids bearing human sequences were shown to replicate based on the persistence of MboI-sensitive plasmid DNA in the long-term assay and the appearance of DpnI-resistant DNA in the short-term assay. The human sequences were shown to be responsible for the replication activity and may represent authentic human origins of replication.

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37

Krysan, P. J., S. B. Haase, and M. P. Calos. "Isolation of human sequences that replicate autonomously in human cells." Molecular and Cellular Biology 9, no. 3 (March 1989): 1026–33. http://dx.doi.org/10.1128/mcb.9.3.1026-1033.1989.

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Abstract:

We have isolated a heterogeneous collection of human genomic sequences which replicate autonomously when introduced into human cells. The novel strategy for the isolation of these sequences involved cloning random human DNA fragments into a defective Epstein-Barr virus vector. This vector alone was unable to replicate in human cells, but appeared to provide for the nuclear retention of linked DNA. The human sequences persist in a long-term replication assay (greater than 2 months) in the presence of the viral nuclear retention sequences. Using a short-term (4-day) assay, we showed that the human sequences are able to replicate in the absence of all viral sequences. The plasmids bearing human sequences were shown to replicate based on the persistence of MboI-sensitive plasmid DNA in the long-term assay and the appearance of DpnI-resistant DNA in the short-term assay. The human sequences were shown to be responsible for the replication activity and may represent authentic human origins of replication.

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38

Voo, Kui Shin, and Britta M. Jacobsen. "Rapid Resuspension of Pelleted Bacterial Cells for Miniprep Plasmid DNA Isolation." BioTechniques 24, no. 2 (February 1998): 240–43. http://dx.doi.org/10.2144/98242bm15.

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39

Voskuil, M. I., and G. H. Chambliss. "Rapid isolation and sequencing of purified plasmid DNA from Bacillus subtilis." Applied and Environmental Microbiology 59, no. 4 (1993): 1138–42. http://dx.doi.org/10.1128/aem.59.4.1138-1142.1993.

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40

Yang, Wen K., and Donald C. Henley. "A simple and economical procedure for large-scale plasmid DNA isolation." Nucleic Acids Research 19, no. 9 (1991): 2507. http://dx.doi.org/10.1093/nar/19.9.2507.

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41

Dean, R. G., S. A. Martin, and C. Carver. "Isolation of plasmid DNA from the ruminal bacterium Selenomonas ruminantium HD4." Letters in Applied Microbiology 8, no. 2 (February 1989): 45–48. http://dx.doi.org/10.1111/j.1472-765x.1989.tb00220.x.

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42

Amberg, David C., Daniel J. Burke, and Jeffrey N. Strathern. "Isolation of Plasmid DNA from Yeast Cells: A Ten-Minute Preparation." Cold Spring Harbor Protocols 2006, no. 1 (January 1, 2006): pdb.prot4150. http://dx.doi.org/10.1101/pdb.prot4150.

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43

Sosa-Acosta, J. R., J. A. Silva, L. Fernández-Izquierdo, S. Díaz-Castañón, M. Ortiz, J. C. Zuaznabar-Gardona, and A. M. Díaz-García. "Iron Oxide Nanoparticles (IONPs) with potential applications in plasmid DNA isolation." Colloids and Surfaces A: Physicochemical and Engineering Aspects 545 (May 2018): 167–78. http://dx.doi.org/10.1016/j.colsurfa.2018.02.062.

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44

Brenner, V., I. Holubová, and J. Hubáček. "An efficient method for isolation of plasmid DNA from methylotrophic bacteria." Folia Microbiologica 35, no. 5 (October 1990): 454–55. http://dx.doi.org/10.1007/bf02821415.

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45

Keen, Cheryl L., Simona Mendelovitz, Gerald Cohen, Yair Aharonowitz, and Kenneth L. Roy. "Isolation and characterization of a linear DNA plasmid from Streptomyces clavuligerus." Molecular and General Genetics MGG 212, no. 1 (April 1988): 172–76. http://dx.doi.org/10.1007/bf00322461.

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46

Chowdhury, E. H., and Toshihiro Akaike. "Rapid isolation of high quality, multimeric plasmid DNA using zwitterionic detergent." Journal of Biotechnology 119, no. 4 (October 2005): 343–47. http://dx.doi.org/10.1016/j.jbiotec.2005.05.013.

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47

Somkuti, G. A., and D. H. Steinberg. "General method for plasmid DNA isolation from thermophilic lactic acid bacteria." Journal of Biotechnology 3, no. 5-6 (April 1986): 323–32. http://dx.doi.org/10.1016/0168-1656(86)90013-1.

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48

Bodorová-Urgošíková, J., O. Benada, and P. Tichý. "Large-scale isolation and partial characterization of plasmid DNA fromB. larvae." Folia Microbiologica 37, no. 2 (April 1992): 82–86. http://dx.doi.org/10.1007/bf02836609.

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49

Sauer, Marie-Laure, Brett Kollars, Ryan Geraets, and Fedora Sutton. "Sequential CaCl2, polyethylene glycol precipitation for RNase-free plasmid DNA isolation." Analytical Biochemistry 380, no. 2 (September 2008): 310–14. http://dx.doi.org/10.1016/j.ab.2008.05.044.

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50

Davies, Martin J., James I. Taylor, Niki Sachsinger, and Ian J. Bruce. "Isolation of Plasmid DNA Using Magnetite as a Solid-Phase Adsorbent." Analytical Biochemistry 262, no. 1 (August 1998): 92–94. http://dx.doi.org/10.1006/abio.1998.2743.

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