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Svetec Miklenić M, Gatalica N, Matanović A, Žunar B, Štafa A, Lisnić B, Svetec IK. Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair (Amst) 2020; 90:102848. [PMID: 32388488 DOI: 10.1016/j.dnarep.2020.102848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 01/01/2023]
Abstract
Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.
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Affiliation(s)
- Marina Svetec Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Nikolina Gatalica
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Angela Matanović
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Bojan Žunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
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2
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Excision of unstable artificial gene-specific inverted repeats mediates scar-free gene deletions in Escherichia coli. Appl Biochem Biotechnol 2014; 175:1858-67. [PMID: 25427592 DOI: 10.1007/s12010-014-1402-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/12/2014] [Indexed: 01/13/2023]
Abstract
Inverted repeat and palindromic sequences have the propensity to form non-beta cruciform structures during DNA replication, leading to perturbations within the genome or plasmid replicon. In this study, the tolerance of the Escherichia coli genome to inverted repeat sequences from 25 to 1200 bp was investigated. Genomic inverted repeats were readily created via the homologous insertion of an overlap extension PCR product containing a gene-specific region of the genome together with thyA coding sequence, creating inverted repeat sequences of various lengths flanking the thyA selection marker in the resulting genome. Inverted repeat sequences below 100 bp were stably propagated, while those above and up to 1200 bp were found to be transiently unstable under auxotrophic thymine selection. Excision efficiency improves with increases of the inverted repeat until 600-800 bp, indicating that the genomic stability of inverted repeat sequences is due to secondary structure formation. Its effectiveness of creating precise and scar-free gene deletions was further demonstrated by deleting a number of genes in E. coli. The procedure can be readily adapted for sequence integration and point mutations in E. coli genome. It also has the potential for applications on other bacteria for efficient gene deletions.
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3
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Voineagu I, Freudenreich CH, Mirkin SM. Checkpoint responses to unusual structures formed by DNA repeats. Mol Carcinog 2009; 48:309-18. [PMID: 19306277 DOI: 10.1002/mc.20512] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA sequences that are prone to adopting non-B DNA secondary structures are associated with hotspots of genomic instability. The fine mechanisms by which alternative DNA structures induce phenomena such as repeat expansions, chromosomal fragility, or gross chromosomal rearrangements are under intensive studies. It is well established that DNA damage checkpoint responses play a crucial role in maintaining a stable genome. It is far less clear, however, whether and how the checkpoint machinery responds to alternative DNA structures. This review discusses the role of the interplay between DNA damage checkpoints and alternative DNA structures in genome maintenance.
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Affiliation(s)
- Irina Voineagu
- Department of Biology, Tufts University, 165 Packard Ave., Medford, MA 02155, USA
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4
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Liu Y, Wang H, Chen Y, Ke CF, Liu M. Supramolecular Aggregates Constructed from Gold Nanoparticles and l-Try-CD Polypseudorotaxanes as Captors for Fullerenes. J Am Chem Soc 2004; 127:657-66. [PMID: 15643890 DOI: 10.1021/ja046294w] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of cyclodextrin-based polypseudorotaxanes (PPRs) were constructed by threading native beta-cyclodextrin or l-tryptophan-modified beta-cyclodextrin onto the amino-terminated PPG chains of different lengths. Subsequently, these PPRs were further assembled to form netlike supramolecular aggregates through the linkage of gold nanoparticles, and the resulting water-soluble Au-PPR aggregates were comprehensively characterized by FT-IR, UV, NMR, fluorescence spectroscopy, powder X-ray diffraction patterning, TG-DTA, and transmission electron microscopy. The results showed that the size and sedimentation rate of the Au-PPR aggregates were mainly dependent on the lengths of the PPG chains. Significantly, the Au-PPR aggregate 8, involving many l-tryptophan residues, showed not only a satisfactory water solubility but also a good capturing ability for fullerenes in aqueous solution. The 8-fullerene conjugate thus formed exhibited a good DNA cleavage ability under light irradiation.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China.
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5
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Pan X, Leach DR. The roles of mutS, sbcCD and recA in the propagation of TGG repeats in Escherichia coli. Nucleic Acids Res 2000; 28:3178-84. [PMID: 10931934 PMCID: PMC108438 DOI: 10.1093/nar/28.16.3178] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A 24 triplet TGG.CCA repeat array shows length- and orientation-dependent propagation when present in the plasmid pUC18. When TGG(24) is present as template for leading-strand synthesis, plasmid recovery is normal in all strains tested. However, when it acts as template for lagging-strand synthesis, plasmid propagation is seriously compromised. Plasmids carrying deletions in the 5' side of this sequence can be isolated and products carrying 15 TGG triplets do not significantly interfere with plasmid propagation. Mutations in sbcCD, mutS and recA significantly improve the recovery of plasmids with TGG(24) on the lagging-strand template. These findings suggest that TGG(24) can fold into a structure that can interfere with DNA replication in vivo but that TGG(15) cannot. Furthermore, since the presence of the MutS and SbcCD proteins are required for propagation interference, it is likely that stabilisation of mismatched base pairs and secondary structure cleavage are implicated. In contrast, there is no correlation of triplet repeat expansion and deletion instability with predicted DNA folding. These results argue for a dissociation of the factors affecting DNA fragility from those affecting trinucleotide repeat expansion-contraction instability.
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Affiliation(s)
- X Pan
- Institute of Cell and Molecular Biology, The University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
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6
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Cromie GA, Millar CB, Schmidt KH, Leach DR. Palindromes as substrates for multiple pathways of recombination in Escherichia coli. Genetics 2000; 154:513-22. [PMID: 10655207 PMCID: PMC1460955 DOI: 10.1093/genetics/154.2.513] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A 246-bp imperfect palindrome has the potential to form hairpin structures in single-stranded DNA during replication. Genetic evidence suggests that these structures are converted to double-strand breaks by the SbcCD nuclease and that the double-strand breaks are repaired by recombination. We investigated the role of a range of recombination mutations on the viability of cells containing this palindrome. The palindrome was introduced into the Escherichia coli chromosome by phage lambda lysogenization. This was done in both wt and sbcC backgrounds. Repair of the SbcCD-induced double-strand breaks requires a large number of proteins, including the components of both the RecB and RecF pathways. Repair does not involve PriA-dependent replication fork restart, which suggests that the double-strand break occurs after the replication fork has passed the palindrome. In the absence of SbcCD, recombination still occurs, probably using a gap substrate. This process is also PriA independent, suggesting that there is no collapse of the replication fork. In the absence of RecA, the RecQ helicase is required for palindrome viability in a sbcC mutant, suggesting that a helicase-dependent pathway exists to allow replicative bypass of secondary structures.
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Affiliation(s)
- G A Cromie
- Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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7
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Ahmed A, Podemski L. Observations on template switching during DNA replication through long inverted repeats. Gene X 1998; 223:187-94. [PMID: 9858727 DOI: 10.1016/s0378-1119(98)00159-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The bacterial Tn5 transposon consists of a pair of long inverted repeats flanking a central region that carries genes for antibiotic resistance. An analysis of DNA replication through Tn5 by two-dimensional gel electrophoresis has revealed two interesting features: (i) a spike representing X-shaped molecules, and (ii) a spot representing a barrier on the arc of Y-shaped replication intermediates. The electrophoretic behavior of various restriction fragments derived from this region indicates that the X molecules contain two linear Tn5 fragments joined together by a cross connection (Holliday junction). However, their formation is recA independent. The junction seems to connect the right inverted repeat of one fragment to the left inverted repeat of the other. The structure of the X molecules suggests that they could be formed by template switching when synthesis of the leading strand enters the right inverted repeat. One possible mechanism is that switching occurs at the center of a transient cruciform structure. A similar switching event, occurring when synthesis of the leading strand enters the left inverted repeat, could give rise to the barrier. These results imply that the inviability of palindromic DNA, which has previously been attributed to the slowing down of replication, may actually be caused by frequent template switching.
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Affiliation(s)
- A Ahmed
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9,
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8
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Connelly JC, Kirkham LA, Leach DR. The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA. Proc Natl Acad Sci U S A 1998; 95:7969-74. [PMID: 9653124 PMCID: PMC20913 DOI: 10.1073/pnas.95.14.7969] [Citation(s) in RCA: 185] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hairpin structures can inhibit DNA replication and are intermediates in certain recombination reactions. We have shown that the purified SbcCD protein of Escherichia coli cleaves a DNA hairpin. This cleavage does not require the presence of a free (3' or 5') DNA end and generates products with 3'-hydroxyl and 5'-phosphate termini. Electron microscopy of SbcCD has revealed the "head-rod-tail" structure predicted for the SMC (structural maintenance of chromosomes) family of proteins, of which SbcC is a member. This work provides evidence consistent with the proposal that SbcCD cleaves hairpin structures that halt the progress of the replication fork, allowing homologous recombination to restore DNA replication.
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Affiliation(s)
- J C Connelly
- Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, United Kingdom
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9
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Pearson CE, Zorbas H, Price GB, Zannis-Hadjopoulos M. Inverted repeats, stem-loops, and cruciforms: significance for initiation of DNA replication. J Cell Biochem 1996; 63:1-22. [PMID: 8891900 DOI: 10.1002/(sici)1097-4644(199610)63:1%3c1::aid-jcb1%3e3.0.co;2-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inverted repeats occur nonrandomly in the DNA of most organisms. Stem-loops and cruciforms can form from inverted repeats. Such structures have been detected in pro- and eukaryotes. They may affect the supercoiling degree of the DNA, the positioning of nucleosomes, the formation of other secondary structures of DNA, or directly interact with proteins. Inverted repeats, stem-loops, and cruciforms are present at the replication origins of phage, plasmids, mitochondria, eukaryotic viruses, and mammalian cells. Experiments with anti-cruciform antibodies suggest that formation and stabilization of cruciforms at particular mammalian origins may be associated with initiation of DNA replication. Many proteins have been shown to interact with cruciforms, recognizing features like DNA crossovers, four-way junctions, and curved/bent DNA of specific angles. A human cruciform binding protein (CBP) displays a novel type of interaction with cruciforms and may be linked to initiation of DNA replication.
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Affiliation(s)
- C E Pearson
- McGill Cancer Centre, McGill University, Montréal, Quebec, Canada
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10
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Pearson CE, Zorbas H, Price GB, Zannis-Hadjopoulos M. Inverted repeats, stem-loops, and cruciforms: Significance for initiation of DNA replication. J Cell Biochem 1996. [DOI: 10.1002/(sici)1097-4644(199610)63:1<1::aid-jcb1>3.0.co;2-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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11
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Leach DR. Cloning and characterization of DNAs with palindromic sequences. GENETIC ENGINEERING 1996; 18:1-11. [PMID: 8785115 DOI: 10.1007/978-1-4899-1766-9_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D R Leach
- Institute of Cell and Molecular Biology, University of Edinburgh
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12
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Leach DR. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 1994; 16:893-900. [PMID: 7840768 DOI: 10.1002/bies.950161207] [Citation(s) in RCA: 206] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Long DNA palindromes pose a threat to genome stability. This instability is primarily mediated by slippage on the lagging strand of the replication fork between short directly repeated sequences close to the ends of the palindrome. The role of the palindrome is likely to be the juxtaposition of the directly repeated sequences by intra-strand base-pairing. This intra-strand base-pairing, if present on both strands, results in a cruciform structure. In bacteria, cruciform structures have proved difficult to detect in vivo, suggesting that if they form, they are either not replicated or are destroyed. SbcCD, a recently discovered exonuclease of Escherichia coli, is responsible for preventing the replication of long palindromes. These observations lead to the proposal that cells may have evolved a post-replicative mechanism for the elimination and/or repair of large DNA secondary structures.
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Affiliation(s)
- D R Leach
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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13
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Chalker AF, Okely EA, Davison A, Leach DR. The effects of central asymmetry on the propagation of palindromic DNA in bacteriophage lambda are consistent with cruciform extrusion in vivo. Genetics 1993; 133:143-8. [PMID: 8436264 PMCID: PMC1205305 DOI: 10.1093/genetics/133.2.143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The propagation of lambda phages carrying long perfect palindromes has been compared with that of phages carrying imperfect palindromes with small regions of central asymmetry. The perfect palindromes confer a more deleterious phenotype than those with central asymmetry and the severity of the phenotype declines with the length of asymmetry in the range from O to 27 base pairs. These results argue that a center-dependent reaction is involved in the phenotypic effects of palindromic DNA sequences, consistent with the idea that cruciform extrusion occurs in vivo.
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Affiliation(s)
- A F Chalker
- Institute of Cell and Molecular Biology, University of Edinburgh, Scotland
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14
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Orlowski R, Miller G. Single-stranded structures are present within plasmids containing the Epstein-Barr virus latent origin of replication. J Virol 1991; 65:677-86. [PMID: 1846191 PMCID: PMC239807 DOI: 10.1128/jvi.65.2.677-686.1991] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Epstein-Barr virus (EBV) latent origin of plasmid replication (oriP) contains two essential regions, a family of repeats with 20 imperfect copies of a 30-bp sequence and a dyad symmetry element with four similar 30-bp repeats. Each of the repeats has an internal palindromic sequence and can bind EBNA 1, a protein that together with oriP constitutes the only viral element necessary for EBV maintenance and replication. Using single-strand-specific nucleases, we have probed plasmids containing oriP-derived sequences for the presence of secondary structural elements. Multiple single-stranded structures were detected within the oriP region. Of the two essential elements of oriP, the family of repeats seemed to extrude these structures at a much higher frequency than did sequences within the dyad symmetry region. Though negative supercoiling was found to stabilize the single-stranded structures, they showed significant stability even after linearization of the oriP plasmids. Two major single-stranded structures detected involved approximately 12 bp of DNA. These loci could be transiently unwound regions that form because of negative supercoiling and the high A + T content of this region of DNA, or they could be cruciform structures extruded within the palindromic sequences of oriP that may be important sites for protein-DNA interactions in the EBV oriP.
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Affiliation(s)
- R Orlowski
- Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510-8064
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Abstract
We have examined the frequency with which identical deletions are formed in different chromosomal contexts. A panel of six mutant bla genes containing palindrome/direct repeat structures were moved from pBR322 to three locations: at lambda att, at chromosomal lac, and at F'lac. Deletion of the palindromes and one of the direct repeats results in reversion to Ampr. The frequency of deletion for all alleles declines beyond the reduction in copy number when they are moved from the multicopy plasmid environment to a single-copy chromosome. The magnitude of the declines varies in an allele-specific and location-specific manner. Our data support the hypothesis that context can influence the frequency of mutation independent of the immediate DNA sequence.
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Affiliation(s)
- T Kazic
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110
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16
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Hyrien O. Large inverted duplications in amplified DNA of mammalian cells form hairpins in vitro upon DNA extraction but not in vivo. Nucleic Acids Res 1989; 17:9557-69. [PMID: 2602136 PMCID: PMC335197 DOI: 10.1093/nar/17.23.9557] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
I have analysed the duplex-to-hairpin transition of large inverted duplications with a short asymmetric center which are found in the amplified DNA of two mammalian cell lines resistant to cytotoxic drugs. Psoralen crosslinking experiments establish that this transition does not occur in vivo, but takes place in a significant portion of the palindromes during genomic DNA purification, at the phenol-chloroform extraction step. The introduction of single strand nicks in the DNA by gamma irradiation prior to its purification does not prevent hairpin formation but instead facilitates it. These results show that the rate-limiting step of the duplex-to-hairpin transition does not require negative supercoiling, and that transient melting of large segments of cellular DNA occurs during phenol-chloroform extraction. I also show, and discuss the fact, that only cellular DNA, and not cloned palindromic DNA, is able to undergo hairpin formation by this mechanism. These results bear practical implications for the study of inverted repeated DNA sequences in eukaryotic cells.
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Affiliation(s)
- O Hyrien
- Unité de Génétique Somatique, UA CNRS, Institut Pasteur, Paris, France
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17
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Naom IS, Morton SJ, Leach DR, Lloyd RG. Molecular organization of sbcC, a gene that affects genetic recombination and the viability of DNA palindromes in Escherichia coli K-12. Nucleic Acids Res 1989; 17:8033-45. [PMID: 2530497 PMCID: PMC334945 DOI: 10.1093/nar/17.20.8033] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The sbcC gene product of Escherichia coli interferes with the growth of a lambda red gam phage carrying a long palindrome in its DNA. This phenotype was used to identify recombinant plasmids harbouring the wild-type gene and to isolate sbcC mutant derivatives carrying Tn1000 insertions. Analysis of these plasmids located sbcC between proC and phoR at a slightly different position from that reported before (Lloyd, R.G. and Buckman, C. 1985, J. Bacteriol. 164, 836-844). Nucleotide sequencing revealed that the gene spans a DNA segment of 3.3 kb that encodes a poorly expressed protein of 118 kDa and which lies downstream of a gene of unknown function that encodes a polypeptide of 45 kDa. The amino acid sequence of SbcC contains a nucleotide binding fold similar to that in RecB and other recombination proteins.
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Affiliation(s)
- I S Naom
- Department of Genetics, University of Nottingham, Queens Medical Centre, UK
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18
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Saing KM, Orii H, Tanaka Y, Yanagisawa K, Miura A, Ikeda H. Formation of deletion in Escherichia coli between direct repeats located in the long inverted repeats of a cellular slime mold plasmid: participation of DNA gyrase. MOLECULAR & GENERAL GENETICS : MGG 1988; 214:1-5. [PMID: 2852300 DOI: 10.1007/bf00340170] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We constructed a recombinant plasmid containing the 2.1 kb HindIII fragment of plasmid pDG1, isolated from the cellular slime mold (Dictyostelium sp. strain GA11), and using pAG60 as cloning vector. We found that deletions of the recombinant plasmid took place frequently in Escherichia coli wild-type cells. However, the deletion was not observed when the plasmid was introduced into a strain that was an isogenic temperature-sensitive mutant of the gyrA gene. These results suggest that E. coli DNA gyrase is involved in the mechanisms of the deletion formation. It was shown that the 1.0 kb deletant derived from the 2.1 kb HindIII insert was produced by elimination of a 1.1 kb region. Sequence analysis of the deletants showed that cutting and rejoining took place between two out of the six nearly perfect direct repeats [21 bp palindromic sequences; AAAAAA(T/C)GGC(G/C)GCC(A/G)TTTTTT], located near the distal ends of the inverted repeats, preserving one copy of the repeats. These sequences consist of local short inverted repeats, where cutting and rejoining occur at one of the two regions.
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Affiliation(s)
- K M Saing
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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19
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Woodcock DM, Crowther PJ, Diver WP, Graham M, Bateman C, Baker DJ, Smith SS. RglB facilitated cloning of highly methylated eukaryotic DNA: the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase. Nucleic Acids Res 1988; 16:4465-82. [PMID: 2837736 PMCID: PMC336642 DOI: 10.1093/nar/16.10.4465] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In vitro methylation of Bluescribe plasmid DNA (pBS) with human placental DNA methyltransferase to 6% 5-methylcytosine (mC) reduced transformation efficiencies in rglB+ host strains C600 and DS410 by almost 2 orders of magnitude. By contrast, the rglB- derivative of DS410 showed no reduction in transformation efficiency with methylation while the rglB- derivative of C600 was partially tolerant to methylation. Further, we show that the 1.8 kilobase (kb) and 1.2 kb KpnI fragments derived from the human L1 repeat have respectively 18.3% and 2.3% mC in vivo. Using these hyper- and hypo-methylated genomic segments ligated into the pBS plasmid, transformants with the highly methylated 1.8 kb L1 insert were recovered at 17 to 40 fold higher frequency with the rglB- host strains than with the rglB+ hosts. In addition, recombinant phage (lambda 2001) containing inserts of plant genomic DNA with 26.7% mC (from Petunia hybrida) when plated on rglB- hosts gave titres up to 222 times higher than on the rglB+ strains.
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Affiliation(s)
- D M Woodcock
- Molecular Science Group, Peter MacCallum Cancer Institute, Melbourne, Victoria, Australia
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