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Krefft D, Papkov A, Prusinowski M, Zylicz-Stachula A, Skowron PM. Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity. BMC Genomics 2018; 19:361. [PMID: 29751745 PMCID: PMC5948728 DOI: 10.1186/s12864-018-4748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Background Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irreproducibility and under-representation of some DNA segments. The DNA fragmentation tool would be a gentle enzymatic method, offering cleavage frequency high enough to eliminate DNA fragments distribution bias and allow for easy control of partial digests. Only three such frequently cleaving natural restriction endonucleases (REases) were discovered: CviJI, SetI and FaiI. Therefore, we have previously developed two artificial enzymatic specificities, cleaving DNA approximately every ~ 3-bp: TspGWI/sinefungin (SIN) and TaqII/SIN. Results In this paper we present the third developed specificity: TthHB27I/SIN(SAM) - a new genomic tool, based on Type IIS/IIC/IIG Thermus-family REases-methyltransferases (MTases). In the presence of dimethyl sulfoxide (DMSO) and S-adenosyl-L-methionine (SAM) or its analogue SIN, the 6-bp cognate TthHB27I recognition sequence 5’-CAARCA-3′ is converted into a combined 3.2–3.0-bp ‘site’ or its statistical equivalent, while a cleavage distance of 11/9 nt is retained. Protocols for various modes of limited DNA digestions were developed. Conclusions In the presence of DMSO and SAM or SIN, TthHB27I is transformed from rare 6-bp cutter to a very frequent one, approximately 3-bp. Thus, TthHB27I/SIN(SAM) comprises a new tool in the very low-represented segment of such prototype REases specificities. Moreover, this modified TthHB27I enzyme is uniquely suited for controlled DNA fragmentation, due to partial DNA cleavage, which is an inherent feature of the Thermus-family enzymes. Such tool can be used for quasi-random libraries generation as well as for other DNA manipulations, requiring high frequency cleavage and uniform distribution of cuts along DNA. Electronic supplementary material The online version of this article (10.1186/s12864-018-4748-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Aliaksei Papkov
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Prusinowski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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Cortés-Gutiérrez EI, López-Fernández C, Fernández JL, Dávila-Rodríguez MI, Johnston SD, Gosálvez J. Interpreting sperm DNA damage in a diverse range of mammalian sperm by means of the two-tailed comet assay. Front Genet 2014; 5:404. [PMID: 25505901 PMCID: PMC4245925 DOI: 10.3389/fgene.2014.00404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 11/01/2014] [Indexed: 11/29/2022] Open
Abstract
Key ConceptsThe two-dimensional Two-Tailed Comet assay (TT-comet) protocol is a valuable technique to differentiate between single-stranded (SSBs) and double-stranded DNA breaks (DSBs) on the same sperm cell. Protein lysis inherent with the TT-comet protocol accounts for differences in sperm protamine composition at a species-specific level to produce reliable visualization of sperm DNA damage. Alkaline treatment may break the sugar–phosphate backbone in abasic sites or at sites with deoxyribose damage, transforming these lesions into DNA breaks that are also converted into ssDNA. These lesions are known as Alkali Labile Sites “ALSs.” DBD–FISH permits the in situ visualization of DNA breaks, abasic sites or alkaline-sensitive DNA regions. The alkaline comet single assay reveals that all mammalian species display constitutive ALS related with the requirement of the sperm to undergo transient changes in DNA structure linked with chromatin packing. Sperm DNA damage is associated with fertilization failure, impaired pre-and post- embryo implantation and poor pregnancy outcome. The TT is a valuable tool for identifying SSBs or DSBs in sperm cells with DNA fragmentation and can be therefore used for the purposes of fertility assessment.
Sperm DNA damage is associated with fertilization failure, impaired pre-and post- embryo implantation and poor pregnancy outcome. A series of methodologies to assess DNA damage in spermatozoa have been developed but most are unable to differentiate between single-stranded DNA breaks (SSBs) and double-stranded DNA breaks (DSBs) on the same sperm cell. The two-dimensional Two-Tailed Comet assay (TT-comet) protocol highlighted in this review overcomes this limitation and emphasizes the importance in accounting for the difference in sperm protamine composition at a species-specific level for the appropriate preparation of the assay. The TT-comet is a modification of the original comet assay that uses a two dimensional electrophoresis to allow for the simultaneous evaluation of DSBs and SSBs in mammalian spermatozoa. Here we have compiled a retrospective overview of how the TT-comet assay has been used to investigate the structure and function of sperm DNA across a diverse range of mammalian species (eutheria, metatheria, and prototheria). When conducted as part of the TT-comet assay, we illustrate (a) how the alkaline comet single assay has been used to help understand the constitutive and transient changes in DNA structure associated with chromatin packing, (b) the capacity of the TT-comet to differentiate between the presence of SSBs and DSBs (c) and the possible implications of SSBs or DSBs for the assessment of infertility.
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Affiliation(s)
- Elva I Cortés-Gutiérrez
- Department of Genetics, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social Monterrey, México
| | | | - José Luis Fernández
- Section of Genetics-INIBIC, Hospital Teresa Herrera, Complejo Hospitalario Universitario A Coruña A Coruña, Spain
| | - Martha I Dávila-Rodríguez
- Department of Genetics, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social Monterrey, México
| | - Stephen D Johnston
- School of Agriculture and Food Science, The University of Queensland Gatton, QLD, Australia
| | - Jaime Gosálvez
- Unit of Genetics, Department of Biology, Universidad Autónoma de Madrid Madrid, Spain
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Meaden P. DNA FINGERPRINTING OF BREWERS' YEAST: CURRENT PERSPECTIVES. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1990.tb01027.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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SCHOFIELD MILESA, ROWE SIMONM, HAMMOND JOHNRM, MOLZAHN STUARTW, QUAIN DAVIDE. DIFFERENTIATION OF BREWERY YEAST STRAINS BY DNA FINGERPRINTING. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1995.tb00850.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency. Biotechniques 2011; 50:397-406. [PMID: 21781040 DOI: 10.2144/000113685] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 05/04/2011] [Indexed: 11/23/2022] Open
Abstract
The type IIS/IIC restriction endonuclease TspGWI recognizes the sequence 5'-ACGGA-3', cleaving DNA 11/9 nucleotides downstream. Here we show that sinefungin, a cofactor analog of S-adenosyl methionine, induces a unique type of relaxation in DNA recognition specificity. In the presence of sinefungin, TspGWI recognizes and cleaves at least 12 degenerate variants of the original recognition sequence that vary by single base pair changes from the original 5-bp restriction site with only a single degeneracy per variant appearing to be allowed. In addition, sinefungin was found to have a stimulatory effect on cleavage at these nondegenerate TspGWI recognition sites, irrespective of their number or the DNA topology. Interestingly, no fixed "core" could be identified among the new recognition sequences. Theoretically, TspGWI cleaves DNA every 1024 bp, while sinefungin-induced activity cleaves every 78.8 bp, corresponding to a putative 3-bp long recognition site. Thus, the combination of sinefungin and TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should prove useful in DNA cloning methodologies.
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6
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Enciso M, Sarasa J, Agarwal A, Fernández JL, Gosálvez J. A two-tailed Comet assay for assessing DNA damage in spermatozoa. Reprod Biomed Online 2009; 18:609-16. [PMID: 19549437 DOI: 10.1016/s1472-6483(10)60003-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
DNA fragmentation is considered an important parameter of semen quality, and of significant value as a predictor of male fertility. Poor quality chromatin is closely associated with, and highly indicative of, some fertility problems. Many methodologies to assess DNA fragmentation in spermatozoa are available, but they are all unable to differentiate between single-stranded DNA breaks (SSB) and double-stranded DNA breaks (DSB) in the same sperm cell. The two-tailed Comet assay (2T-Comet) protocol overcomes this limitation. A modification of the original Comet assay was developed for the simultaneous evaluation of DNA SSB and DSB in human spermatozoa. The 2T-Comet assay is a fast, sensitive, and reliable procedure for the quantification and characterization of DNA damage in spermatozoa. It is an innovative method for assessing sperm DNA integrity, which has important implications for human fertility and andrological pathology.
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Affiliation(s)
- Maria Enciso
- Departamento de Biología, Universidad Autónoma de Madrid, Spain.
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7
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Skowron PM, Swaminathan N, McMaster K, George D, Van Etten JL, Mead DA. Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella. Gene X 1995; 157:37-41. [PMID: 7607522 DOI: 10.1016/0378-1119(94)00564-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The gene (cviJIR) encoding the two/three-base R.CviJI eukaryotic restriction endonuclease (ENase) from IL-3A virus-infected Chlorella was cloned into Escherichia coli. A high frequency of DNA cleavage by R.CviJI required overexpression of the gene encoding the M.CviJI methyltransferase prior to cloning the gene for the ENase. Both genes were sequenced and their organization was determined to be in head-to-tail order. The open reading frame coding for R.CviJI can potentially translate a 41.4-kDa protein; however, in the E. coli host, a truncated version of the enzyme is produced (32.5 kDa). The recombinant ENase does not exhibit ATP-induced 'star' activity (R.CviJI cleaves at RGCY, while R.CviJI* also cleaves at RGCR and YGCY, but not at YGCR), as is characteristic for native R.CviJI. The very high frequency of DNA cleavage by R.CviJI* was exploited in the development of a quasi-random shotgun library method. R.CviJI*-generated oligodeoxyribonucleotides were applied to improve certain molecular biology applications, i.e., DNA labeling, detection, high-resolution restriction mapping, amplification and epitope mapping.
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Affiliation(s)
- P M Skowron
- Molecular Biology Resources Inc., Milwaukee, WI 53210, USA
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8
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McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1994; 22:3640-59. [PMID: 7937074 PMCID: PMC308336 DOI: 10.1093/nar/22.17.3640] [Citation(s) in RCA: 300] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes.
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Affiliation(s)
- M McClelland
- California Institute of Biological Research, La Jolla 92037
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9
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Swaminathan N, George D, McMaster K, Szablewski J, Van Etten JL, Mead DA. Restriction generated oligonucleotides utilizing the two base recognition endonuclease CviJI*. Nucleic Acids Res 1994; 22:1470-5. [PMID: 8190639 PMCID: PMC308007 DOI: 10.1093/nar/22.8.1470] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The conversion of an anonymous DNA sample into numerous oligonucleotides is enzymatically feasible using an unusual restriction endonuclease, CviJI. Depending on reaction conditions, CviJI is capable of digesting DNA at a two or three base recognition sequence. CviJI normally cleaves RGCY sites between the G and C to leave blunt ends. Under 'relaxed' conditions CviJI* cleaves RGCY, and RGCR/YGCY, but not YGCR sites. In theory, CviJI* restriction of pUC19 (2686 bp) should produce 157 fragments, 75% of which are smaller than 20 bp. Instead, 96% of the CviJI* fragments were 18-56 bp long and none of the fragments were smaller than 18 bp. Thermal denaturation of these fragments generates sequence specific oligonucleotides homologous for the cognate template. The enzymatic conversion of anonymous DNA into sequence specific oligomers has implications for several conventional and novel molecular biology procedures.
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10
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Nelson M, Raschke E, McClelland M. Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1993; 21:3139-54. [PMID: 8392715 PMCID: PMC309743 DOI: 10.1093/nar/21.13.3139] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- M Nelson
- California Institute of Biological Research, La Jolla 92037
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11
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Williamson MR, Doherty JP, Woodcock DM. Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli. Gene X 1993; 124:37-44. [PMID: 8382656 DOI: 10.1016/0378-1119(93)90759-v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have tested whether, and to what extent, recombinant clones from DNA segments with 5-methylation of cytosines recovered in methylation-restrictive (mcr+) hosts contain mutations. We constructed a model system in which the tetracycline-resistance-encoding gene (tet) from pBR322 was cloned into the plasmid pGEM3Zf+. The central region of tet was removed from the construct, methylated in vitro and then religated back into the unmethylated remainder of the construct. The central region of tet was either (1) methylated with a combination of four bacterial methyltransferases (M.AluI, M.HaeIII, M.HpaII plus M.HhaI) or (2) methylated with M.SssI which methylates at all CpG dinucleotides. These two protocols generated theoretical levels of DNA methylation in the central fragment of 10.5% and 33%, respectively. The construct was transformed into a series of isogenic (recA+) bacterial strains that were mcrA+ mcrB+C+, mcrA+ mcrB-C+, mcrA- mcrB+C+, mcrA- mcrB-C+ or mcrA- delta mcrBC, and also into a set of isogenic recA- derivatives of these strains. With the two methylation protocols, there was an average 48- and 141-fold reduction, respectively, in the number of transformants recovered from the recA+ mcr+ hosts compared with a methylation-tolerant host (mcr-). Of the clones recovered in recA+mcr+ hosts, > 20% of clones had an inactivating mutation in tet. The majority of such mutant clones contained deletions that frequently extended into the unmethylated portion of tet and even into the plasmid sequences beyond the end of the polylinker. With the recA- mcr+ hosts, effective restriction was much more stringent, rendering the plasmid containing the methylated segment effectively unclonable.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M R Williamson
- Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
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12
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Gabbara S, Bhagwat A. Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)37006-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Ahuja SK, Ozçelik T, Milatovitch A, Francke U, Murphy PM. Molecular evolution of the human interleukin-8 receptor gene cluster. Nat Genet 1992; 2:31-6. [PMID: 1303245 DOI: 10.1038/ng0992-31] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Interleukin-8 (IL-8) is the prototype for a family of at least eight neutrophil chemoattractants whose genes map to human chromosome 4q13-q21. Two human IL-8 receptors, IL8RA and IL8RB, are known from cDNA cloning; IL8RA is a promiscuous receptor for at least two other related ligands, GRO alpha and NAP-2. We now report cloning of the genes for IL8RA, IL8RB and a recently inactivated pseudogene of receptor A (IL8RAP). These form a cluster of only three genes in the superfamily of G protein-coupled receptors (GPCRs) and map to 2q34-q35. The coevolutionary diversity displayed by the IL-8 ligand-receptor complex--ligand promiscuity for IL-8, receptor promiscuity for IL8RA, gene duplication for both ligands and receptors and gene extinction in the case of IL8RAP--is unprecedented for the GPCR superfamily.
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Affiliation(s)
- S K Ahuja
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
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14
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Fitzgerald MC, Skowron P, Van Etten JL, Smith LM, Mead DA. Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI. Nucleic Acids Res 1992; 20:3753-62. [PMID: 1322530 PMCID: PMC334028 DOI: 10.1093/nar/20.14.3753] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the specificity of this enzyme (CviJI**) yield a quasi-random distribution of DNA fragments from the small molecule pUC19 (2686 base pairs). To quantitatively evaluate the randomness of this fragmentation strategy, a CviJI** digest of pUC19 was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lacZ minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI** restricts PyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation. Advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 micrograms instead of 2-5 micrograms), fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed), and higher cloning efficiencies are obtained (CviJI** digested and column fractionated DNA transforms 3-16 times more efficiently than sonicated, end-repaired, and agarose fractionated DNA).
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Affiliation(s)
- M C Fitzgerald
- Chemistry Department, University of Wisconsin, Madison 53706
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15
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McClelland M, Nelson M. Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res 1992; 20 Suppl:2145-57. [PMID: 1317957 PMCID: PMC333989 DOI: 10.1093/nar/20.suppl.2145] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- M McClelland
- California Institute of Biological Research, La Jolla, CA 92037
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16
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Mead DA, Pey NK, Herrnstadt C, Marcil RA, Smith LM. A universal method for the direct cloning of PCR amplified nucleic acid. Nat Biotechnol 1992; 9:657-63. [PMID: 1367662 DOI: 10.1038/nbt0791-657] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have devised a simple, universal cloning strategy that permits the direct ligation of PCR amplified nucleic acid to a compatible vector preparation. The method does not require that special restriction sites or additional sequences be appended onto the amplification primers, nor the use of restriction endonucleases, modifying enzymes, or any purification procedures. This approach takes advantage of the single 3' deoxyadenylate extension that Thermus aquaticus, Thermus flavus, and Thermococcus litoralis DNA polymerases add to the termini of amplified nucleic acid. A new type of plasmid was constructed that allows the preparation of ends containing a single complementary 3' deoxythymidylate extension. Cloning PCR products by this method is approximately 50 times more efficient than blunt-ended ligation reactions. This direct PCR ligation technique has been engineered in-phase with a truncated lacZ gene to facilitate the discrimination of recombinants from non-recombinants. We have applied this method to directly clone amplified RNA and DNA from as little as 1 microliter of a PCR reaction, without prior modification or purification steps.
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Affiliation(s)
- D A Mead
- Department of Chemistry, University of Wisconsin, Madison 53706
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17
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Chan JC, Scanlon M, Zhang HZ, Jia LB, Yu DH, Hung MC, French M, Eastman EM. Molecular cloning and characterization of v-mos-activated transformation-associated proteins. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)48401-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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18
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De Feyter R, Gabriel DW. Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum. J Bacteriol 1991; 173:6421-7. [PMID: 1655710 PMCID: PMC208975 DOI: 10.1128/jb.173.20.6421-6427.1991] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In vitro-packaged cosmid libraries of DNA from the bacterium Xanthomonas campestris pv. malvacearum were restricted 200- to 1,000-fold when introduced into Mcr+ strains of Escherichia coli compared with restriction in the Mcr- strain HB101. Restriction was predominantly associated with the mcrBC+ gene in E. coli. A plasmid (pUFR052) encoding the XmaI and XmaIII DNA methylases was isolated from an X. campestris pv. malvacearum library by a screening procedure utilizing Mcr+ and Mcr- E. coli strains. Transfer of plasmids from E. coli strains to X. campestris pv. malvacearum by conjugation was enhanced by up to five orders of magnitude when the donor cells contained pUFR052 as well as the plasmid to be transferred. Subcloning of pUFR052 revealed that at least two regions of the plasmid were required for full modification activity. Use of such modifier plasmids is a simple, novel method that may allow the efficient introduction of genes into any organism in which restriction systems provide a potent barrier to such gene transfer.
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Affiliation(s)
- R De Feyter
- Plant Pathology Department, University of Florida, Gainesville 32611
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Woodcock DM, Crowther PJ, Doherty JP, Linsenmeyer ME, Krüger DH. A sizing artifact of DNA restriction fragments with unusually long single-stranded termini. Gene 1991; 102:79-81. [PMID: 1650735 DOI: 10.1016/0378-1119(91)90542-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The restriction endonucleases (ENases) BstNI (CCATGG) and EcoRII (CCATGG) both cleave DNA at the same time sequences, but only EcoRII produces 5-nucleotide (nt) cohesive ends and is inhibited by 5-methylation of the inner cytosine. The low-Mr fragments in digests of mouse DNA made with these two ENases exhibit different mobilities during agarose-gel electrophoresis. The difference in the mobilities of the BstNI and EcoRII fragments from mouse DNA was not due to closely spaced, differentially methylated sites, or to alternate mechanisms such as circularization of the long cohesive ends of the EcoRII fragments, or to residual bound protein. Rather, it was due to the unusually long 5-nt single-stranded (ss) ends of fragments produced by EcoRII digestion, since the slower mobility of the EcoRII fragments was abolished by treatment with ss-specific nuclease. Similar mobility differences between BstNI and EcoRII fragments which could be removed by ss nuclease were also observed in digests of simian virus 40 DNA.
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Affiliation(s)
- D M Woodcock
- Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
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20
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Nelson M, McClelland M. Site-specific methylation: effect on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res 1991; 19 Suppl:2045-71. [PMID: 1645875 PMCID: PMC331346 DOI: 10.1093/nar/19.suppl.2045] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- M Nelson
- California Institute of Biological Research, La Jolla 92037
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21
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Nelson M, McClelland M. Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res 1989; 17 Suppl:r389-415. [PMID: 2541418 PMCID: PMC334788 DOI: 10.1093/nar/17.suppl.r389] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- M Nelson
- Department of Biochemistry, University of Chicago, IL 60637
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McClelland M, Nelson M. The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases--a review. Gene 1988; 74:291-304. [PMID: 2854811 DOI: 10.1016/0378-1119(88)90305-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M McClelland
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637
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