101
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Andreev SL, Buneva VN, Nevinsky GA. How human IgGs against DNA recognize oligonucleotides and DNA. J Mol Recognit 2016; 29:596-610. [PMID: 27558754 DOI: 10.1002/jmr.2559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 11/10/2022]
Abstract
In the literature, there are no available data on how anti-DNA antibodies recognize DNA. In the present work, to study the molecular mechanism of DNA recognition by antibodies, we have used anti-DNA IgGs from blood sera of patients with multiple sclerosis. A stepwise increase in ligand complexity approach was used to estimate the relative contributions of virtually every nucleotide unit of different single- (ss) and double-stranded (ds) oligonucleotides to their affinity for IgG fraction having high affinity to DNA-cellulose. DNA-binding site disposed on the heavy chain demonstrates higher affinity to different dNMPs (Kd = 0.63μM-3.8μM) than the site located on the light chain (28μM-170μM). The heavy and light chains interact independently forming relatively strong contacts with 2 to 4 nucleotides of short homo- and hetero-d(pN)2-9 . Then the increase in the affinity of different d(pN)n became minimal, and at n ≥ 8 to 9, all dependencies reached plateaus: approximately 3.2nM to 20nM and approximately 200nM to 460nM for the heavy and light chains, respectively. A similar situation was observed for different ribooligonucleotides, in which their affinity is 6-fold to 100-fold lower than that for d(pN)n . Transition from ss to ds d(pN)n leads to a moderate increase in affinity of ligands to DNA-binding site of heavy chains, while light chains demonstrate the same affinity for ss and ds d(pN)n . Long supercoiled DNA interacts with both heavy and light chains with affinity of approximately 10-fold higher than that for short oligonucleotides. The thermodynamic models were constructed to describe the interactions of IgGs light and heavy chains with DNA.
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Affiliation(s)
- Sergey L Andreev
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Valentina N Buneva
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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102
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Johnson PM, Gucinski GC, Garza-Sánchez F, Wong T, Hung LW, Hayes CS, Goulding CW. Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei. J Biol Chem 2016; 291:19387-400. [PMID: 27445337 DOI: 10.1074/jbc.m116.736074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 12/23/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition. CDI(+) bacteria deploy large CdiA effector proteins, which carry variable C-terminal toxin domains (CdiA-CT). CDI(+) cells also produce CdiI immunity proteins that specifically neutralize cognate CdiA-CT toxins to prevent auto-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiI(E479) toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CT(E479) tRNase domain contains a core α/β-fold that is characteristic of PD(D/E)XK superfamily nucleases. Unexpectedly, the closest structural homolog of CdiA-CT(E479) is another CDI toxin domain from B. pseudomallei 1026b. Although unrelated in sequence, the two B. pseudomallei nuclease domains share similar folds and active-site architectures. By contrast, the CdiI(E479) and CdiI(1026b) immunity proteins share no significant sequence or structural homology. CdiA-CT(E479) and CdiA-CT(1026b) are both tRNases; however, each nuclease cleaves tRNA at a distinct position. We used a molecular docking approach to model each toxin bound to tRNA substrate. The resulting models fit into electron density envelopes generated by small-angle x-ray scattering analysis of catalytically inactive toxin domains bound stably to tRNA. CdiA-CT(E479) is the third CDI toxin found to have structural homology to the PD(D/E)XK superfamily. We propose that CDI systems exploit the inherent sequence variability and active-site plasticity of PD(D/E)XK nucleases to generate toxin diversity. These findings raise the possibility that many other uncharacterized CDI toxins may belong to the PD(D/E)XK superfamily.
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Affiliation(s)
| | | | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and
| | - Timothy Wong
- From the Departments of Molecular Biology and Biochemistry and
| | - Li-Wei Hung
- the Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Christopher S Hayes
- the Biomolecular Science and Engineering Program and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and
| | - Celia W Goulding
- From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California at Irvine, Irvine, California 92697,
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103
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Weigele P, Raleigh EA. Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chem Rev 2016; 116:12655-12687. [PMID: 27319741 DOI: 10.1021/acs.chemrev.6b00114] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the DNA of cellular organisms and viruses from all domains of life. Bacterial viruses (bacteriophages) are a particularly rich but still underexploited source of such modified variant nucleotides. The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and protective functions. In prokaryotes, modified bases appear primarily to be part of an arms race between bacteriophages (and other genomic parasites) and their hosts, although, as in eukaryotes, some modifications have been adapted to convey epigenetic information. The first half of this review catalogs the identification and diversity of DNA modifications found in bacteria and bacteriophages. What is known about the biogenesis, context, and function of these modifications are also described. The second part of the review places these DNA modifications in the context of the arms race between bacteria and bacteriophages. It focuses particularly on the defense and counter-defense strategies that turn on direct recognition of the presence of a modified base. Where modification has been shown to affect other DNA transactions, such as expression and chromosome segregation, that is summarized, with reference to recent reviews.
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Affiliation(s)
- Peter Weigele
- Chemical Biology, New England Biolabs , Ipswich, Massachusetts 01938, United States
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104
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Electrochemical biosensor modified with dsDNA monolayer for restriction enzyme activity determination. Bioelectrochemistry 2016; 109:63-9. [DOI: 10.1016/j.bioelechem.2016.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/28/2016] [Accepted: 01/31/2016] [Indexed: 11/22/2022]
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105
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Möncke-Buchner E, Szczepek M, Bokelmann M, Heinemann P, Raftery MJ, Krüger DH, Reuter M. Sin Nombre hantavirus nucleocapsid protein exhibits a metal-dependent DNA-specific endonucleolytic activity. Virology 2016; 496:67-76. [PMID: 27261891 DOI: 10.1016/j.virol.2016.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 01/09/2023]
Abstract
We demonstrate that the nucleocapsid protein of Sin Nombre hantavirus (SNV-N) has a DNA-specific endonuclease activity. Upon incubation of SNV-N with DNA in the presence of magnesium or manganese, we observed DNA digestion in sequence-unspecific manner. In contrast, RNA was not affected under the same conditions. Moreover, pre-treatment of SNV-N with RNase before DNA cleavage increased the endonucleolytic activity. Structure-based protein fold prediction using known structures from the PDB database revealed that Asp residues in positions 88 and 103 of SNV-N show sequence similarity with the active site of the restriction endonuclease HindIII. Crystal structure of HindIII predicts that residues Asp93 and Asp108 are essential for coordination of the metal ions required for HindIII DNA cleavage. Therefore, we hypothesized that homologous residues in SNV-N, Asp88 and Asp103, may have a similar function. Replacing Asp88 and Asp103 by alanine led to an SNV-N protein almost completely abrogated for endonuclease activity.
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Affiliation(s)
- Elisabeth Möncke-Buchner
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michal Szczepek
- Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Marcel Bokelmann
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Patrick Heinemann
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin J Raftery
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H Krüger
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Monika Reuter
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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106
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Parente Carvalho C, Norouzy A, Ribeiro V, Nau WM, Pischel U. Cucurbiturils as supramolecular inhibitors of DNA restriction by type II endonucleases. Org Biomol Chem 2016; 13:2866-9. [PMID: 25581012 DOI: 10.1039/c4ob02122c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cucurbiturils (CB6 and CB7) were shown to inhibit the enzymatically catalyzed restriction of plasmids and linear DNA. This effect can be inverted by supramolecular masking of the macrocycles through competitive complexation with polyamines. These experiments provide supramolecular control of biocatalytic processes.
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Affiliation(s)
- Cátia Parente Carvalho
- CIQSO-Center for Research in Sustainable Chemistry and Department of Chemical Engineering, Physical Chemistry and Organic Chemistry, University of Huelva, Campus El Carmen s/n, E-21071 Huelva, Spain.
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107
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Yacoub E, Ben Abdelmoumen Mardassi B. Mm19, a Mycoplasma meleagridis Major Surface Nuclease that Is Related to the RE_AlwI Superfamily of Endonucleases. PLoS One 2016; 11:e0152171. [PMID: 27010566 PMCID: PMC4807054 DOI: 10.1371/journal.pone.0152171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/09/2016] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma meleagridis infection is widespread in turkeys, causing poor growth and feathering, airsacculitis, osteodystrophy, and reduction in hatchability. Like most mycoplasma species, M. meleagridis is characterized by its inability to synthesize purine and pyrimidine nucleotides de novo. Consistent with this intrinsic deficiency, we here report the cloning, expression, and characterization of a M. meleagridis gene sequence encoding a major surface nuclease, referred to as Mm19. Mm19 consists of a 1941-bp ORF encoding a 646-amino-acid polypeptide with a predicted molecular mass of 74,825 kDa. BLASTP analysis revealed a significant match with the catalytic/dimerization domain of type II restriction enzymes of the RE_AlwI superfamily. This finding is consistent with the genomic location of Mm19 sequence, which dispalys characteristics of a typical type II restriction-modification locus. Like intact M. meleagridis cells, the E. coli-expressed Mm19 fusion product was found to exhibit a nuclease activity against plasmid DNA, double-stranded DNA, single-stranded DNA, and RNA. The Mm19-associated nuclease activity was consistently enhanced with Mg2+ divalent cations, a hallmark of type II restriction enzymes. A rabbit hyperimmune antiserum raised against the bacterially expressed Mm19 strongly reacted with M. meleagridis intact cells and fully neutralized the surface-bound nuclease activity. Collectively, the results show that M. meleagridis expresses a strong surface-bound nuclease activity, which is the product of a single gene sequence that is related to the RE_AlwI superfamily of endonucleases.
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Affiliation(s)
- Elhem Yacoub
- Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis, El Manar, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis, El Manar, Tunisia
- * E-mail:
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108
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Kurian P, Dunston G, Lindesay J. How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases. J Theor Biol 2016; 391:102-12. [PMID: 26682627 PMCID: PMC4746125 DOI: 10.1016/j.jtbi.2015.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 10/29/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.
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Affiliation(s)
- P Kurian
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA.
| | - G Dunston
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA
| | - J Lindesay
- Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA
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109
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Liu Z, Lei C, Deng H, Lu G, Huang Y, Yao S. Sensitive and versatile fluorescent enzymatic assay of nucleases and DNA methyltransferase based on a supercharged fluorescent protein. RSC Adv 2016. [DOI: 10.1039/c6ra02711c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ScGFP-based platform takes advantage of the DNA length-dependent binding affinity between ScGFP and DNA for multiple DNA enzyme detection including nucleases and DNA MTase.
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Affiliation(s)
- Zhuoliang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Honghua Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Guoyan Lu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
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110
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Zautner AE, Goldschmidt AM, Thürmer A, Schuldes J, Bader O, Lugert R, Groß U, Stingl K, Salinas G, Lingner T. SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. BMC Genomics 2015; 16:1088. [PMID: 26689587 PMCID: PMC4687069 DOI: 10.1186/s12864-015-2317-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori. RESULTS Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %. CONCLUSIONS Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori. The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.
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Affiliation(s)
- Andreas E Zautner
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
| | - Anne-Marie Goldschmidt
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Andrea Thürmer
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Jörg Schuldes
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Raimond Lugert
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment (BfR), Department of Biological Safety - National Reference Laboratory for Campylobacter, D-12277, Berlin, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
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111
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Rusinov I, Ershova A, Karyagina A, Spirin S, Alexeevski A. Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes. BMC Genomics 2015; 16:1084. [PMID: 26689194 PMCID: PMC4687349 DOI: 10.1186/s12864-015-2288-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/11/2015] [Indexed: 01/10/2023] Open
Abstract
Background Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. Results Only Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called ‘orthodox’ here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of 1774 studied cases. It is known that prokaryotes can acquire and lose R-M systems. Thus it is possible to talk about the lifespan of an R-M system in a genome. We have shown that the recognition site avoidance correlates with the lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in host genomes for a long time are avoided more often (up to 100 % in certain cohorts) than the sites of recently acquired ones. We also found cases of site avoidance in absence of the corresponding R-M systems in the genome. An analysis of closely related bacteria shows that such avoidance can be a trace of lost R-M systems. Sites of Type I, IIС/G, IIM, III, and IV R-M systems are not avoided in vast majority of cases. Conclusions The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. Presence of an R-M system without an underrepresentation of its site may indicate that the R-M system was acquired recently. At the same time, a significant underrepresentation of a site may be a sign of presence of the corresponding R-M system in this organism or in its ancestors for a long time. The drastic difference between site avoidance for orthodox Type II R-M systems and R-M systems of other types can be explained by a higher rate of specificity changes or a less self-toxicity of the latter. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2288-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Rusinov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Anna Ershova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Anna Karyagina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Gamaleya Center of Epidemiology and Microbiology, Moscow, 123098, Russia. .,Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Sergey Spirin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
| | - Andrei Alexeevski
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow, 117281, Russia.
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112
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Xiao X, Wu T, Gu F, Zhao M. Generation of artificial sequence-specific nucleases via a preassembled inert-template. Chem Sci 2015; 7:2051-2057. [PMID: 29899930 PMCID: PMC5968549 DOI: 10.1039/c5sc04398k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/07/2015] [Indexed: 02/01/2023] Open
Abstract
Sequence specific nucleases are important tools for processing nucleic acids in a predictable way. Herein, we demonstrate a conceptually new approach for generating sequence-specific nucleases via a preassembled inert-template (PAIT). A fairly stable DNase I/inert-DNA complex was prepared with a customized sequence specificity for a target DNA which contains a sequence complementary to the inert-DNA template. The complex could efficiently cleave the targeted sequence within either a long double-stranded DNA or a single-stranded DNA without affecting other unrelated DNA strands. The discrimination factor against single-base mismatch strands within a 14 nt target region was as high as 25.3. The strategy was also successfully applied to RNase A. Our findings may hold great potential for the development of a number of new powerful enzymatic tools.
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Affiliation(s)
- Xianjin Xiao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Feidan Gu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
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113
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Davidovich C, Cech TR. The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2. RNA (NEW YORK, N.Y.) 2015; 21:2007-22. [PMID: 26574518 PMCID: PMC4647455 DOI: 10.1261/rna.053918.115] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Among chromatin modifying factors shown to be recruited and regulated by long noncoding RNAs (lncRNAs), PRC2 is one of the most studied. Mammalian PRC2 binds thousands of RNAs in vivo, and it is becoming a model system for the recruitment of chromatin modifying factors by RNA. Yet, well-defined PRC2-binding motifs within target RNAs have been elusive. From the protein side, PRC2 RNA-binding subunits contain no known RNA-binding domains, complicating functional studies. Here we provide a critical review of existing models for the recruitment of PRC2 to chromatin by RNAs. This discussion may also serve researchers who are studying the recruitment of other chromatin modifiers by lncRNAs.
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Affiliation(s)
- Chen Davidovich
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Thomas R Cech
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
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114
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Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S, Gao YQ. DNA Structural Correlation in Short and Long Ranges. J Phys Chem B 2015; 119:13980-90. [PMID: 26439165 DOI: 10.1021/acs.jpcb.5b06217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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115
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Cleavage of DNA containing 5-fluorocytosine or 5-fluorouracil by type II restriction endonucleases. Bioorg Med Chem 2015; 23:6885-90. [PMID: 26463367 DOI: 10.1016/j.bmc.2015.09.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/25/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022]
Abstract
A systematic study of the cleavage of DNA sequences containing 5-fluorocytosine or 5-fluorouracil by type II restriction endonucleases (REs) was performed and the results compared with the same sequences containing natural pyrimidine bases, uracil or 5-methylcytosine. The results show that some REs recognize fluorine as a hydrogen on cytosine and cleave the corresponding sequences where the presence of m5dC leads to blocking of the cleavage. However, on uracil, the same REs recognize the F as a methyl surrogate and cleave the sequences which are not cleaved if uracil is incorporated instead of thymine. These results are interesting for understanding the recognition of DNA sequences by REs and for manipulation of the specific DNA cutting.
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116
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Mačková M, Boháčová S, Perlíková P, Poštová Slavětínská L, Hocek M. Polymerase Synthesis and Restriction Enzyme Cleavage of DNA Containing 7-Substituted 7-Deazaguanine Nucleobases. Chembiochem 2015; 16:2225-36. [PMID: 26382079 DOI: 10.1002/cbic.201500315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 01/06/2023]
Abstract
Previous studies of polymerase synthesis of base-modified DNAs and their cleavage by restriction enzymes have mostly related only to 5-substituted pyrimidine and 7-substituted 7-deazaadenine nucleotides. Here we report the synthesis of a series of 7-substituted 7-deazaguanine 2'-deoxyribonucleoside 5'-O-triphosphates (dG(R) TPs), their use as substrates for polymerase synthesis of modified DNA and the influence of the modification on their cleavage by type II restriction endonucleases (REs). The dG(R) TPs were generally good substrates for polymerases but the PCR products could not be visualised on agarose gels by intercalator staining, due to fluorescence quenching. The presence of 7-substituted 7-deazaguanine residues in recognition sequences of REs in most cases completely blocked the cleavage.
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Affiliation(s)
- Michaela Mačková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic.
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117
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Mondragón E, Maher LJ. RNA aptamer inhibitors of a restriction endonuclease. Nucleic Acids Res 2015; 43:7544-55. [PMID: 26184872 PMCID: PMC4551934 DOI: 10.1093/nar/gkv702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/29/2015] [Indexed: 11/18/2022] Open
Abstract
Restriction endonucleases (REases) recognize and cleave short palindromic DNA sequences, protecting bacterial cells against bacteriophage infection by attacking foreign DNA. We are interested in the potential of folded RNA to mimic DNA, a concept that might be applied to inhibition of DNA-binding proteins. As a model system, we sought RNA aptamers against the REases BamHI, PacI and KpnI using systematic evolution of ligands by exponential enrichment (SELEX). After 20 rounds of selection under different stringent conditions, we identified the 10 most enriched RNA aptamers for each REase. Aptamers were screened for binding and specificity, and assayed for REase inhibition. We obtained eight high-affinity (Kd ∼12-30 nM) selective competitive inhibitors (IC50 ∼20-150 nM) for KpnI. Predicted RNA secondary structures were confirmed by in-line attack assay and a 38-nt derivative of the best anti-KpnI aptamer was sufficient for inhibition. These competitive inhibitors presumably act as KpnI binding site analogs, but lack the primary consensus KpnI cleavage sequence and are not cleaved by KpnI, making their potential mode of DNA mimicry fascinating. Anti-REase RNA aptamers could have value in studies of REase mechanism and may give clues to a code for designing RNAs that competitively inhibit DNA binding proteins including transcription factors.
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Affiliation(s)
- Estefanía Mondragón
- Neurobiology of Disease track, Mayo Graduate School, 200 First St SW, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905, USA
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118
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Malina J, Hannon MJ, Brabec V. Iron(II) supramolecular helicates condense plasmid DNA and inhibit vital DNA-related enzymatic activities. Chemistry 2015; 21:11189-95. [PMID: 26103944 DOI: 10.1002/chem.201501307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/06/2022]
Abstract
The dinuclear iron(II) supramolecular helicates [Fe2 L3 ]Cl4 (L=C25 H20 N4 ) bind to DNA through noncovalent (i.e., hydrogen-bonding, electrostatic) interactions and exhibit antimicrobial and anticancer effects. In this study, we show that the helicates condense plasmid DNA with a much higher potency than conventional DNA-condensing agents. Notably, molecules of DNA in the presence of the M enantiomer of [Fe2 L3 ]Cl4 do not form intermolecular aggregates typically formed by other condensing agents, such as spermidine or spermine. The helicates inhibit the activity of several DNA-processing enzymes, such as RNA polymerase, DNA topoisomerase I, deoxyribonuclease I, and site-specific restriction endonucleases. However, the results also indicate that the DNA condensation induced by the helicates does not play a crucial role in these inhibition reactions. The mechanisms for the inhibitory effects of [Fe2 L3 ]Cl4 helicates on DNA-related enzymatic activities have been proposed.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Kralovopolska 135, 612 65 Brno (Czech Republic)
| | - Michael J Hannon
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT (UK)
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Kralovopolska 135, 612 65 Brno (Czech Republic).
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119
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2'-O-methyl nucleotide modified DNA substrates influence the cleavage efficiencies of BamHI and BglII. J Biosci 2015; 39:621-30. [PMID: 25116617 DOI: 10.1007/s12038-014-9466-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Induction of endonucleolytic DNA cleavage is an essential event that links the initiating stimuli to the final effects of cells. The cleavage efficiency and thus the final yield could be affected by many factors, including structures of DNA substrates, composite structures of enzymes-substrates or enzymes-nucleic analogs and so on. However, it is not clear whether a nucleotide derivative-substituted in DNA substrates can influence the efficiency of enzymatic cleavage. To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl modified nucleotides (OMeN) to modify DNA substrates of isocaudemers BamHI and BglII in this study, and used FRET assay as an efficient method for analysis of enzyme cleavage. Experimental results demonstrated that OMeN-substituted recognition sequences influenced the cleavage rates significantly in a position-dependent manner. OMeN substitutions can reduce the cleavage as expected. Surprisingly, OMeN substitutions can also enhance the cleavage rates. The kinetics parameters of Vmax and Km have been obtained by fitting the Michaelis-Menten kinetic equation. These 2'- OMe nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property could enrich our understanding about the endonuclease cleavage mechanism and enhance our ability to regulate the enzymatic cleavage efficiency for applications in synthetic biology.
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120
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Sharov AA, Vehkavaara T. Protosemiosis: agency with reduced representation capacity. BIOSEMIOTICS 2015; 8:103-123. [PMID: 25937852 PMCID: PMC4414345 DOI: 10.1007/s12304-014-9219-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Life has semiotic nature; and as life forms differ in their complexity, functionality, and adaptability, we assume that forms of semiosis also vary accordingly. Here we propose a criterion to distinguish between the primitive kind of semiosis, which we call "protosemiosis" (following Prodi) from the advanced kind of semiosis, or "eusemiosis". In protosemiosis, agents associate signs directly with actions without considering objects, whereas in eusemiosis, agents associate signs with objects and only then possibly with actions. Protosemiosis started from the origin of life, and eusemiosis started when evolving agents acquired the ability to track and classify objects. Eusemiosis is qualitatively different from protosemiosis because it can not be reduced to a small number of specific signaling pathways. Proto-signs can be classified into proto-icons that signal via single specific interaction, proto-indexes that combine several functions, and proto-symbols that are processed by a universal subagent equipped with a set of heritable adapters. Prefix "proto" is used here to characterize signs at the protosemiotic level. Although objects are not recognized by protosemiotic agents, they can be reliably reconstructed by human observers. In summary, protosemiosis is a primitive kind of semiosis that supports "know-how" without "know-what". Without studying protosemiosis, the biosemiotics theory would be incomplete.
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Affiliation(s)
- Alexei A. Sharov
- Genetics Laboratory, National Institute on Aging, Baltimore, USA
| | - Tommi Vehkavaara
- School of Social Sciences and Humanities, University of Tampere, 33014 University of Tampere, Finland
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121
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Wons E, Mruk I, Kaczorowski T. Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes. J Appl Genet 2015; 56:539-546. [PMID: 25787880 DOI: 10.1007/s13353-015-0279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 01/18/2023]
Abstract
RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops. Their susceptibility to modification by DNA-specific or RNA-specific enzymes is, thus, a biologically relevant question, which, in addition, has possible biotechnological implications. In this study, we investigated the activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI, M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the β-group of adenine N6-methyltransferases and recognize the palindromic DNA sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the addition of agents that generally relax specificity, such as dimethyl sulfoxide (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated. The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge, the first report that demonstrates such activity by prokaryotic DNA methyltransferases. Possible applications of these findings in a laboratory practice are also discussed.
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Affiliation(s)
- Ewa Wons
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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122
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Jurkowski TP, Ravichandran M, Stepper P. Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity. Clin Epigenetics 2015; 7:18. [PMID: 25741388 PMCID: PMC4347971 DOI: 10.1186/s13148-015-0044-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/12/2015] [Indexed: 01/14/2023] Open
Abstract
Epigenetics is currently one of the hottest topics in basic and biomedical research. However, to date, most of the studies have been descriptive in nature, designed to investigate static distribution of various epigenetic modifications in cells. Even though tremendous amount of information has been collected, we are still far from the complete understanding of epigenetic processes, their dynamics or even their direct effects on local chromatin and we still do not comprehend whether these epigenetic states are the cause or the consequence of the transcriptional profile of the cell. In this review, we try to define the concept of synthetic epigenetics and outline the available genome targeting technologies, which are used for locus-specific editing of epigenetic signals. We report early success stories and the lessons we have learned from them, and provide a guide for their application. Finally, we discuss existing limitations of the available technologies and indicate possible areas for further development.
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Affiliation(s)
- Tomasz P Jurkowski
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Mirunalini Ravichandran
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Peter Stepper
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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123
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Qin Y, Ma Y, Jin X, Zhang L, Ye G, Zhao S. A sensitive fluorescence turn-on assay of bleomycin and nuclease using WS2 nanosheet as an effective sensing platform. Anal Chim Acta 2015; 866:84-89. [PMID: 25732696 DOI: 10.1016/j.aca.2015.01.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/30/2015] [Indexed: 11/17/2022]
Abstract
As an important antitumor drug, bleomycin (BLM) is widely used in the treatment of a variety of cancers. In addition, nucleases play a crucial role in DNA replication, recombination and repair which are associated with cancer development. Thus, the development of BLM and nuclease detection methods is of great significance in cancer therapy and related biological mechanism research. Here, a WS2 nanosheet-based turn-on fluorescent sensing platform for simple, fast and sensitive detection of BLM and nuclease was reported. WS2 nanosheet exhibits different affinity toward ssDNA with different length and excellent fluorescence quenching ability. A fluorescein (FAM)-labeled long ssDNA could be adsorbed on the surface of WS2 nanosheet and the fluorescence was therefore quenched. In the presence of BLM·Fe(II) or S1 nuclease (a ssDNA-specific nuclease which was used as a model enzyme), an irreversible scission of long ssDNA was underwent through the BLM-induced oxidation cleavage or S1 nuclease-induced enzymatic hydrolysis. Short FAM-linked oligonucleotide fragments which could not be adsorbed on the nanosheet surface were then produced, resulting in a weak fluorescence quenching after mixing WS2 nanosheets. Thus, the fluorescence signal was restored. The proposed sensor displays a wide linear range and a high sensitivity with a detection limit of 0.3 nM for BLM and 0.01 U mL(-1) for S1 nuclease. It also exhibits a good performance in complex biological samples. This method not only provides a strategy for BLM or S1 nuclease assay but also offers a potential application in biomedical and clinical study.
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Affiliation(s)
- Yingfeng Qin
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China
| | - Yefei Ma
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China
| | - Xue Jin
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China
| | - Liangliang Zhang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China.
| | - Gaojie Ye
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources of Education Ministry, Guangxi Normal University, Guilin 541004, China.
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124
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Głów D, Pianka D, Sulej AA, Kozłowski ŁP, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM. Sequence-specific cleavage of dsRNA by Mini-III RNase. Nucleic Acids Res 2015; 43:2864-73. [PMID: 25634891 PMCID: PMC4357697 DOI: 10.1093/nar/gkv009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ribonucleases (RNases) play a critical role in RNA processing and degradation by hydrolyzing phosphodiester bonds (exo- or endonucleolytically). Many RNases that cut RNA internally exhibit substrate specificity, but their target sites are usually limited to one or a few specific nucleotides in single-stranded RNA and often in a context of a particular three-dimensional structure of the substrate. Thus far, no RNase counterparts of restriction enzymes have been identified which could cleave double-stranded RNA (dsRNA) in a sequence-specific manner. Here, we present evidence for a sequence-dependent cleavage of long dsRNA by RNase Mini-III from Bacillus subtilis (BsMiniIII). Analysis of the sites cleaved by this enzyme in limited digest of bacteriophage Φ6 dsRNA led to the identification of a consensus target sequence. We defined nucleotide residues within the preferred cleavage site that affected the efficiency of the cleavage and were essential for the discrimination of cleavable versus non-cleavable dsRNA sequences. We have also determined that the loop α5b-α6, a distinctive structural element in Mini-III RNases, is crucial for the specific cleavage, but not for dsRNA binding. Our results suggest that BsMiniIII may serve as a prototype of a sequence-specific dsRNase that could possibly be used for targeted cleavage of dsRNA.
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Affiliation(s)
- Dawid Głów
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Dariusz Pianka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Agata A Sulej
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Łukasz P Kozłowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Justyna Czarnecka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Grzegorz Chojnowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Krzysztof J Skowronek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
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125
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Xu Q, Zhang Y, Zhang CY. A triple-color fluorescent probe for multiple nuclease assays. Chem Commun (Camb) 2015; 51:9121-4. [DOI: 10.1039/c5cc02177d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.
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Affiliation(s)
- Qinfeng Xu
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Yihong Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
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126
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Ma DL, Lu L, Lin S, He B, Leung CH. A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity. J Mater Chem B 2015; 3:348-352. [DOI: 10.1039/c4tb01569j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A G-triplex luminescent switch-on probe for the detection of nuclease activity.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Bingyong He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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127
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Heffelfinger C, Fragoso CA, Moreno MA, Overton JD, Mottinger JP, Zhao H, Tohme J, Dellaporta SL. Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics 2014. [PMID: 25406744 DOI: 10.1186/1471‐2164‐15‐979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those involving genetic mapping, breeding, and population genomics. We have modified the GBS technology in a number of ways. Custom, enzyme specific adaptors have been replaced with standard Illumina adaptors compatible with blunt-end restriction enzymes. Multiplexing is achieved through a dual barcoding system, and bead-based library preparation protocols allows for in-solution size selection and eliminates the need for columns and gels. RESULTS A panel of eight restriction enzymes was selected for testing on B73 maize and Nipponbare rice genomic DNA. Quality of the data was demonstrated by identifying that the vast majority of reads from each enzyme aligned to restriction sites predicted in silico. The link between enzyme parameters and experimental outcome was demonstrated by showing that the sequenced portion of the genome was adaptable by selecting enzymes based on motif length, complexity, and methylation sensitivity. The utility of the new GBS protocol was demonstrated by correctly mapping several in a maize F2 population resulting from a B73×Country Gentleman test cross. CONCLUSIONS This technology is readily adaptable to different genomes, highly amenable to multiplexing and compatible with over forty commercially available restriction enzymes. These advancements represent a major improvement in genotyping technology by providing a highly flexible and scalable GBS that is readily implemented for studies on genome-wide variation.
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Affiliation(s)
| | | | | | | | | | | | | | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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128
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Heffelfinger C, Fragoso CA, Moreno MA, Overton JD, Mottinger JP, Zhao H, Tohme J, Dellaporta SL. Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics 2014; 15:979. [PMID: 25406744 PMCID: PMC4253001 DOI: 10.1186/1471-2164-15-979] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022] Open
Abstract
Background Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those involving genetic mapping, breeding, and population genomics. We have modified the GBS technology in a number of ways. Custom, enzyme specific adaptors have been replaced with standard Illumina adaptors compatible with blunt-end restriction enzymes. Multiplexing is achieved through a dual barcoding system, and bead-based library preparation protocols allows for in-solution size selection and eliminates the need for columns and gels. Results A panel of eight restriction enzymes was selected for testing on B73 maize and Nipponbare rice genomic DNA. Quality of the data was demonstrated by identifying that the vast majority of reads from each enzyme aligned to restriction sites predicted in silico. The link between enzyme parameters and experimental outcome was demonstrated by showing that the sequenced portion of the genome was adaptable by selecting enzymes based on motif length, complexity, and methylation sensitivity. The utility of the new GBS protocol was demonstrated by correctly mapping several in a maize F2 population resulting from a B73 × Country Gentleman test cross. Conclusions This technology is readily adaptable to different genomes, highly amenable to multiplexing and compatible with over forty commercially available restriction enzymes. These advancements represent a major improvement in genotyping technology by providing a highly flexible and scalable GBS that is readily implemented for studies on genome-wide variation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-979) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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129
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Song C, Zhang Q, Han GM, Du YC, Kong DM. A facile fluorescence method for endonuclease detection using exonuclease III-aided signal amplification of a molecular beacon. RSC Adv 2014. [DOI: 10.1039/c4ra09676b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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130
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Barbaro BA, Lukacsovich T, Agrawal N, Burke J, Bornemann DJ, Purcell JM, Worthge SA, Caricasole A, Weiss A, Song W, Morozova OA, Colby DW, Marsh JL. Comparative study of naturally occurring huntingtin fragments in Drosophila points to exon 1 as the most pathogenic species in Huntington's disease. Hum Mol Genet 2014; 24:913-25. [PMID: 25305076 DOI: 10.1093/hmg/ddu504] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although Huntington's disease is caused by the expansion of a CAG triplet repeat within the context of the 3144-amino acid huntingtin protein (HTT), studies reveal that N-terminal fragments of HTT containing the expanded PolyQ region can be produced by proteolytic processing and/or aberrant splicing. N-terminal HTT fragments are also prevalent in postmortem tissue, and expression of some of these fragments in model organisms can cause pathology. This has led to the hypothesis that N-terminal peptides may be critical modulators of disease pathology, raising the possibility that targeting aberrant splicing or proteolytic processing may present attractive therapeutic targets. However, many factors can contribute to pathology, including genetic background and differential expression of transgenes, in addition to intrinsic differences between fragments and their cellular effects. We have used Drosophila as a model system to determine the relative toxicities of different naturally occurring huntingtin fragments in a system in which genetic background, transgene expression levels and post-translational proteolytic processing can be controlled. These studies reveal that among the naturally occurring N-terminal HTT peptides, the exon 1 peptide is exceptionally pathogenic and exhibits unique structural and biophysical behaviors that do not appear to be incremental changes compared with other fragments. If this proves correct, efforts to specifically reduce the levels of exon 1 peptides or to target toxicity-influencing post-translational modifications that occur with the exon 1 context are likely to have the greatest impact on pathology.
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Affiliation(s)
- Brett A Barbaro
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Tamas Lukacsovich
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Namita Agrawal
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA, Department of Zoology, University of Delhi, Delhi 110007, India
| | - John Burke
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Doug J Bornemann
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Judith M Purcell
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Shane A Worthge
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | | | | | - Wan Song
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA
| | - Olga A Morozova
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - David W Colby
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, University of California, Irvine 92697, USA,
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131
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Mačková M, Pohl R, Hocek M. Polymerase synthesis of DNAs bearing vinyl groups in the major groove and their cleavage by restriction endonucleases. Chembiochem 2014; 15:2306-12. [PMID: 25179889 DOI: 10.1002/cbic.201402319] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Indexed: 01/12/2023]
Abstract
DNA molecules containing 5-vinyluracil, 5-vinylcytosine, or 7-deaza-7-vinyladenine were prepared by polymerase incorporation of the corresponding vinyl-modified 2'-deoxyribonucleoside triphosphates, and the influence of the vinyl group in the major groove of DNA on the cleavage by diverse type II restriction endonucleases (REs) was studied. The presence of 5-vinyluracil was tolerated by most of the REs, whereas only some REs were able to cleave sequences containing 7-deaza-7-vinyladenine. The enzyme ScaI was found to cleave DNA containing 5-vinylcytosine efficiently but not DNA containing the related 5-ethynylcytosine. All other REs failed to cleave sequences containing any cytosine modifications.
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Affiliation(s)
- Michaela Mačková
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
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132
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Stryjewska A, Kiepura K, Librowski T, Lochyński S. Biotechnology and genetic engineering in the new drug development. Part II. Monoclonal antibodies, modern vaccines and gene therapy. Pharmacol Rep 2014; 65:1086-101. [PMID: 24399705 DOI: 10.1016/s1734-1140(13)71467-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 05/13/2013] [Indexed: 12/01/2022]
Abstract
Monoclonal antibodies, modern vaccines and gene therapy have become a major field in modern biotechnology, especially in the area of human health and fascinating developments achieved in the past decades are impressive examples of an interdisciplinary interplay between medicine, biology and engineering. Among the classical products from cells one can find viral vaccines, monoclonal antibodies, and interferons, as well as recombinant therapeutic proteins. Gene therapy opens up challenging new areas. In this review, a definitions of these processes are given and fields of application and products, as well as the future prospects, are discussed.
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Affiliation(s)
- Agnieszka Stryjewska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, PL 50-370 Wrocław, Poland. ;
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133
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Stryjewska A, Kiepura K, Librowski T, Lochyński S. Biotechnology and genetic engineering in the new drug development. Part I. DNA technology and recombinant proteins. Pharmacol Rep 2014; 65:1075-85. [PMID: 24399704 DOI: 10.1016/s1734-1140(13)71466-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 05/13/2013] [Indexed: 11/17/2022]
Abstract
Pharmaceutical biotechnology has a long tradition and is rooted in the last century, first exemplified by penicillin and streptomycin as low molecular weight biosynthetic compounds. Today, pharmaceutical biotechnology still has its fundamentals in fermentation and bioprocessing, but the paradigmatic change affected by biotechnology and pharmaceutical sciences has led to an updated definition. The biotechnology revolution redrew the research, development, production and even marketing processes of drugs. Powerful new instruments and biotechnology related scientific disciplines (genomics, proteomics) make it possible to examine and exploit the behavior of proteins and molecules. Recombinant DNA (rDNA) technologies (genetic, protein, and metabolic engineering) allow the production of a wide range of peptides, proteins, and biochemicals from naturally nonproducing cells. This technology, now approximately 25 years old, is becoming one of the most important technologies developed in the 20(th) century. Pharmaceutical products and industrial enzymes were the first biotech products on the world market made by means of rDNA. Despite important advances regarding rDNA applications in mammalian cells, yeasts still represent attractive hosts for the production of heterologous proteins. In this review we describe these processes.
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Affiliation(s)
- Agnieszka Stryjewska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, PL 50-370 Wrocław, Poland. ;
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134
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Ordinario DD, Burke AM, Phan L, Jocson JM, Wang H, Dickson MN, Gorodetsky AA. Sequence specific detection of restriction enzymes at DNA-modified carbon nanotube field effect transistors. Anal Chem 2014; 86:8628-33. [PMID: 25137193 DOI: 10.1021/ac501441d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein-DNA interactions play a central role in many cellular processes, and their misregulation has been implicated in a number of human diseases. Thus, there is a pressing need for the development of analytical strategies for interrogating the binding of proteins to DNA. Herein, we report the electrical monitoring of a prototypical DNA-binding protein, the PvuII restriction enzyme, at microfluidic-encapsulated, DNA-modified carbon nanotube field effect transistors. Our integrated platform enables the sensitive, sequence specific detection of PvuII at concentrations as low as 0.5 pM in a volume of 0.025 μL (corresponding to ~7500 proteins). These figures of merit compare favorably to state of the art values reported for alternative fluorescent and electrical assays. The overall detection strategy represents a step toward the massively parallel electrical monitoring, identification, and quantification of protein-DNA interactions at arrayed nanoscale devices.
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Affiliation(s)
- David D Ordinario
- Department of Chemical Engineering and Materials Science, University of California, Irvine , Irvine, California 92697, United States
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135
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Booth MJ, Raiber EA, Balasubramanian S. Chemical methods for decoding cytosine modifications in DNA. Chem Rev 2014; 115:2240-54. [PMID: 25094039 PMCID: PMC4378238 DOI: 10.1021/cr5002904] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michael J Booth
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Eun-Ang Raiber
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Shankar Balasubramanian
- †Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom.,‡Cambridge Institute, Li Ka Shing Centre, Cancer Research U.K., Robinson Way, Cambridge, CB2 0RE United Kingdom.,§School of Clinical Medicine, The University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0SP United Kingdom
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136
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Harteis S, Schneider S. Making the bend: DNA tertiary structure and protein-DNA interactions. Int J Mol Sci 2014; 15:12335-63. [PMID: 25026169 PMCID: PMC4139847 DOI: 10.3390/ijms150712335] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 12/11/2022] Open
Abstract
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout") as well as the intrinsic DNA structure ("shape recognition"). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics.
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Affiliation(s)
- Sabrina Harteis
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
| | - Sabine Schneider
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
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137
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Bouhaddou M, Birtwistle MR. Dimerization-based control of cooperativity. MOLECULAR BIOSYSTEMS 2014; 10:1824-32. [PMID: 24736836 PMCID: PMC4060435 DOI: 10.1039/c4mb00022f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cooperativity of ligand-receptor binding influences the input-output behavior of a biochemical system and thus is an important determinant of its physiological function. Canonically, such cooperativity is understood in terms of ligand-receptor binding affinity, where an initial binding event changes the affinity for subsequent binding events. Here, we demonstrate that dimerization-a simple yet pervasive signaling motif across biology-can have significant control over cooperativity and even dominate over the canonical mechanism. Through an exhaustive parameter sensitivity analysis of a general kinetic model for signal-mediated dimerization, we show that quantitative modulation of dimerization processes can reinforce, eliminate, and even reverse cooperativity imposed by the canonical allosteric ligand-receptor binding affinity mechanism. The favored accumulation of stoichiometrically asymmetric dimers (those with ligand-receptor stoichiometry of 1 : 2) is a major determinant of dimerization-based cooperativity control. However, simulations demonstrate that favoring accumulation of such stoichiometrically asymmetric dimers can either increase or decrease cooperativity, and thus the quantitative relationship between stoichiometrically asymmetric dimers and cooperativity is highly dependent on the parameter values of the particular system of interest. These results suggest that the dimerization motif provides a novel mechanism for both generating and quantitatively tuning cooperativity that, due to the ubiquity of dimerization motifs in biochemical systems, may play a major role in a host of biological functions. Thus, the canonical, allosteric view of cooperativity is incomplete without considering dimerization effects, which is of particular importance as dimerization is often a necessary feature of the allosteric mechanism.
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Affiliation(s)
- Mehdi Bouhaddou
- Icahn School of Medicine at Mount Sinai, Department of Pharmacology and Systems Therapeutics, New York, NY 10029, USA.
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138
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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139
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Kronbak R, Ingvardsen CR, Madsen CK, Gregersen PL. A novel approach to the generation of seamless constructs for plant transformation. PLANT METHODS 2014; 10:10. [PMID: 24855486 PMCID: PMC4030040 DOI: 10.1186/1746-4811-10-10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND When creating plant transformation vectors, full control of nucleotides flanking the insert in the final construct may be desirable. Modern ligase-independent methods for DNA-recombination are based on linearization by classical type II restriction endonucleases (REs) alone or in combination with nicking enzymes leaving residual nucleotides behind in the final construct. We here explore the use of type IIS and type IIB REs for vector linearization that combined with sequence and ligase-independent cloning (SLIC) overcomes this problem and promotes seamless gene-insertion in vectors. Providing the basis for a collection of biolistic plant transformation vectors ready to be cloned with different genes-of-interest, we present two vectors, where promoter and terminator are joined by a spacer. During spacer-removal linearization (SRL), type IIS and type IIB REs remove their own recognition sequences from the vector leaving no undesired, short sequences behind. RESULTS We designed two plant transformation vectors prepared for SRL in combination with SLIC, pAUrumII and pAUrumIII, harboring a spacer with recognition sites for a type IIS and IIB RE, respectively. The gene for a green fluorescent protein, gfp, was successfully cloned into both vectors; traces of pAUrumIII, however, contaminated the transformation due to incomplete linearization, an issue not encountered with the type IIS linearized pAUrumII. Both constructs, pAUrumII-gfp and pAUrumIII-gfp, were functional, when tested in vitro on wheat and barley endosperm cells for transient gfp expression. CONCLUSIONS All nucleotides flanking an insert in a biolistic plant transformation vector can be customized by means of SRL in combination with SLIC. Especially type IIS REs promote an efficient cloning result. Based on our findings, we believe that the SRL system can be useful in a series of plant transformation vectors, favoring the presence of functional sequences for optimal expression over redundant cloning-site remnants.
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Affiliation(s)
- Remy Kronbak
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Christina Rønn Ingvardsen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Claus Krogh Madsen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Per Langkjær Gregersen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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140
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Luo Y, Lin L, Bolund L, Sørensen CB. Efficient construction of rAAV-based gene targeting vectors by Golden Gate cloning. Biotechniques 2014; 56:263-8. [PMID: 24806227 DOI: 10.2144/000114169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 02/14/2014] [Indexed: 11/23/2022] Open
Abstract
The recombinant adeno-associated virus (rAAV) has proven to be an efficient and attractive tool for targeted genome engineering. Here we present a novel method employing the Golden Gate cloning strategy for fast and efficient construction of rAAV-based gene knockout or single-nucleotide knockin vectors. Two vectors, pGolden-Neo and pGolden-Hyg, were generated as common assembling modules to confer antibiotic resistance to the targeting vector. To validate the method, we then generated two rAAV-based targeting vectors: pAAV-pTP53-KO and pAAV-hTau(P301L)-KI. Furthermore, we generated a pGolden-AAV plasmid that allows one-step generation of an rAAV-based targeting vector. Our new methodology for rAAV targeting vector assembly is efficient, accurate, time-saving, and cost-effective.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Lin Lin
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Lars Bolund
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark
| | - Charlotte Brandt Sørensen
- Department of Biomedicine, Faculty of Heath, Aarhus University, Aarhus, Denmark; Department of Clinical Medicine, Department of Cardiological Medicine B, Aarhus University, Aarhus, Denmark
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141
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Beck CM, Morse RP, Cunningham DA, Iniguez A, Low DA, Goulding CW, Hayes CS. CdiA from Enterobacter cloacae delivers a toxic ribosomal RNase into target bacteria. Structure 2014; 22:707-18. [PMID: 24657090 DOI: 10.1016/j.str.2014.02.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/11/2014] [Accepted: 02/16/2014] [Indexed: 12/31/2022]
Abstract
Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. CDI(+) cells export large CdiA effector proteins, which carry a variety of C-terminal toxin domains (CdiA-CT). CdiA-CT toxins are specifically neutralized by cognate CdiI immunity proteins to protect toxin-producing cells from autoinhibition. Here, we use structure determination to elucidate the activity of a CDI toxin from Enterobacter cloacae (ECL). The structure of CdiA-CT(ECL) resembles the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis. In accord with this structural homology, we show that CdiA-CT(ECL) uses the same nuclease activity to inhibit bacterial growth. Surprisingly, although colicin E3 and CdiA(ECL) carry equivalent toxin domains, the corresponding immunity proteins are unrelated in sequence, structure, and toxin-binding site. Together, these findings reveal unexpected diversity among 16S rRNases and suggest that these nucleases are robust and versatile payloads for a variety of toxin-delivery platforms.
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Affiliation(s)
- Christina M Beck
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Robert P Morse
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - David A Cunningham
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Angelina Iniguez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - David A Low
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA; Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA; Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA.
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142
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Ikeda S, Tainaka K, Matsumoto K, Shinohara Y, Ode KL, Susaki EA, Ueda HR. Non-enzymatic DNA cleavage reaction induced by 5-ethynyluracil in methylamine aqueous solution and application to DNA concatenation. PLoS One 2014; 9:e92369. [PMID: 24647759 PMCID: PMC3960239 DOI: 10.1371/journal.pone.0092369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 02/21/2014] [Indexed: 11/19/2022] Open
Abstract
DNA can be concatenated by hybridization of DNA fragments with protruding single-stranded termini. DNA cleavage occurring at a nucleotide containing a DNA base analogue is a useful method to obtain DNA with designed protruding termini. Here, we report a novel non-enzymatic DNA cleavage reaction for DNA concatenation. We found that DNA is cleaved at a nucleotide containing 5-ethynyluracil in a methylamine aqueous solution to generate 5′-phosphorylated DNA fragment as a cleavage product. We demonstrated that the reaction can be applied to DNA concatenation of PCR-amplified DNA fragments. This novel non-enzymatic DNA cleavage reaction is a simple practical approach for DNA concatenation.
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Affiliation(s)
- Shuji Ikeda
- Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, Chuo-ku, Kobe, Japan
| | - Kazuki Tainaka
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Katsuhiko Matsumoto
- Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, Chuo-ku, Kobe, Japan
| | - Yuta Shinohara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, Quantitative Biology Center, RIKEN, Chuo-ku, Kobe, Japan; Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, Chuo-ku, Kobe, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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143
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Gutjahr A, Xu SY. Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA. Nucleic Acids Res 2014; 42:e77. [PMID: 24609382 PMCID: PMC4027164 DOI: 10.1093/nar/gku192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
N.ϕGamma is a strand-specific and site-specific DNA nicking enzyme (YCG↓GT or AC↑CGR). Here we describe the isolation of single and double mutants of N.ϕGamma with attenuated activity. The nicking domains (NDs) of E59A and 11 double mutants were fused to the 5mCG-binding domain of MBD2 and generated fusion enzymes that preferentially nick 5mCG-modified DNA. The CG dinucleotide can be modified by C5 methyltransferases (MTases) such as M.SssI, M.HhaI or M.HpaII to create composite sites AC↑YGG N(8-15) 5mCG. We also constructed a fusion enzyme 2xMBD2-ND(N.BceSVIII) targeting more frequent composite sites AS↑YS N(5-12) 5mCG in Mn2+ buffer. 5mCG-dependent nicking requires special digestion conditions in high salt (0.3 M KCl) or in Ni2+ buffer. The fusion enzyme can be used to nick and label 5mCG-modified plasmid and genomic DNAs with fluorescently labeled Cy3-dUTP and potentially be useful for diagnostic applications, DNA sequencing and optical mapping of epigenetic markers. The importance of the predicted catalytic residues D89, H90, N106 and H115 in N.ϕGamma was confirmed by mutagenesis. We found that the wild-type enzyme N.ϕGamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking activity is sub-optimal compared to the activity in Mg2+ buffer.
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Affiliation(s)
- Alice Gutjahr
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shuang-yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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144
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Zhu Z, Guan S, Robinson D, El Fezzazi H, Quimby A, Xu SY. Characterization of cleavage intermediate and star sites of RM.Tth111II. Sci Rep 2014; 4:3838. [PMID: 24452415 PMCID: PMC3899748 DOI: 10.1038/srep03838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/03/2014] [Indexed: 11/09/2022] Open
Abstract
Tth111II is a thermostable Type IIGS restriction enzyme that recognizes DNA sites CAARCA (R = A or G) and cleaves downstream at N11/N9. Here, the tth111IIRM gene was cloned and expressed in E. coli, and Tth111II was purified. The purified enzyme contains internally-bound S-adenosylmethionine (SAM). When the internal SAM was removed, the endonuclease activity was stimulated by adding SAM or its analog sinefungin. The cleavage intermediate is mostly top-strand nicked DNA on a single-site plasmid. Addition of duplex oligos with a cognate site stimulates cleavage activity of the one-site substrate. Tth111II cleaves a two-site plasmid DNA with equal efficiency regardless of site orientation. We propose the top-strand nicking is carried out by a Tth111II monomer and bottom-strand cleavage is carried out by a transient dimer. Tth111II methylates cleavage product-like duplex oligos CAAACAN9, but the modification rate is estimated to be much slower than the top-strand nicking rate. We cloned and sequenced a number of Tth111II star sites which are 1-bp different from the cognate sites. A biochemical pathway is proposed for the restriction and methylation activities of Tth111II.
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Affiliation(s)
- Zhenyu Zhu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Derek Robinson
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Hanna El Fezzazi
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Aine Quimby
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shuang-yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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145
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Ferrandino R, Sidorova N, Rau D. Using single-turnover kinetics with osmotic stress to characterize the EcoRV cleavage reaction. Biochemistry 2014; 53:235-46. [PMID: 24328115 DOI: 10.1021/bi401089y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II restriction endonucleases require metal ions to specifically cleave DNA at canonical sites. Despite the wealth of structural and biochemical information, the number of Mg(2+) ions used for cleavage by EcoRV, in particular, at physiological divalent ion concentrations has not been established. In this work, we employ a single-turnover technique that uses osmotic stress to probe reaction kinetics between an initial specific EcoRV-DNA complex formed in the absence of Mg(2+) and the final cleavage step. With osmotic stress, complex dissociation before cleavage is minimized and the reaction rates are slowed to a convenient time scale of minutes to hours. We find that cleavage occurs by a two-step mechanism that can be characterized by two rate constants. The dependence of these rate constants on Mg(2+) concentration and osmotic pressure gives the number of Mg(2+) ions and water molecules coupled to each kinetic step of the EcoRV cleavage reaction. Each kinetic step is coupled to the binding 1.5-2.5 Mg(2+) ions, the uptake of ∼30 water molecules, and the cleavage of a DNA single strand. We suggest that each kinetic step reflects an independent, rate-limiting conformational change of each monomer of the dimeric enzyme that allows Mg(2+) ion binding. This modified single-turnover protocol has general applicability for metalloenzymes.
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Affiliation(s)
- Rocco Ferrandino
- The Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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146
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Song C, Wang GY, Wang HZ, Wang YJ, Kong DM. Applications of porous organic frameworks (POFs) in detection of nucleic acid and exonuclease I activity. J Mater Chem B 2014; 2:1549-1556. [DOI: 10.1039/c3tb21461c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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147
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A label-free DNA-templated silver nanocluster probe for fluorescence on–off detection of endonuclease activity and inhibition. Biosens Bioelectron 2014; 51:408-12. [DOI: 10.1016/j.bios.2013.07.060] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 01/03/2023]
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148
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Restriction-Modification Systems as a Barrier for Genetic Manipulation of Staphylococcus aureus. Methods Mol Biol 2014; 1373:9-23. [PMID: 25646604 DOI: 10.1007/7651_2014_180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic manipulation is a powerful approach to study fundamental aspects of bacterial physiology, metabolism, and pathogenesis. Most Staphylococcus aureus strains are remarkably difficult to genetically manipulate as they possess strong host defense mechanisms that protect bacteria from cellular invasion by foreign DNA. In S. aureus these bacterial "immunity" mechanisms against invading genomes are mainly associated with restriction-modification systems. To date, prokaryotic restriction-modification systems are classified into four different types (Type I-IV), all of which have been found in the sequenced S. aureus genomes. This chapter describes the roles, classification, mechanisms of action of different types of restriction-modification systems and the recent advances in the biology of restriction and modification in S. aureus.
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149
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Abstract
Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both their own genes and their local genetic environment. The mechanisms that govern the function and evolution of these genetic oddities have been well documented over the past few decades at the genetic, biochemical, and structural levels. This wealth of information has led to the manipulation and reprogramming of the endonucleases and to their exploitation in genome editing for use as therapeutic agents, for insect vector control and in agriculture. In this chapter we summarize the molecular properties of homing endonucleases and discuss their strengths and weaknesses in genome editing as compared to other site-specific nucleases such as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.
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150
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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3-19. [PMID: 24141096 PMCID: PMC3874209 DOI: 10.1093/nar/gkt990] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/24/2013] [Accepted: 10/02/2013] [Indexed: 11/16/2022] Open
Abstract
In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - David T. F. Dryden
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, Leiden, the Netherlands, EaStChemSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK and New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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