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Journal articles on the topic 'Endonucleasi'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Fahmi, Tariq, Xiaoying Wang, Dmitry D. Zhdanov, et al. "DNase I Induces Other Endonucleases in Kidney Tubular Epithelial Cells by Its DNA-Degrading Activity." International Journal of Molecular Sciences 21, no. 22 (2020): 8665. http://dx.doi.org/10.3390/ijms21228665.

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Endonuclease-mediated DNA fragmentation is both an immediate cause and a result of apoptosis and of all other types of irreversible cell death after injury. It is produced by nine enzymes including DNase I, DNase 2, their homologs, caspase-activated DNase (CAD) and endonuclease G (EndoG). The endonucleases act simultaneously during cell death; however, regulatory links between these enzymes have not been established. We hypothesized that DNase I, the most abundant of endonucleases, may regulate other endonucleases. To test this hypothesis, rat kidney tubular epithelial NRK-52E cells were trans

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2

Kamisugi, Y., Y. Ikeda, M. Ohno, M. Minezawa, and K. Fukui. "In situ digestion of barley chromosomes with restriction endonucleases." Genome 35, no. 5 (1992): 793–98. http://dx.doi.org/10.1139/g92-121.

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In situ digestion of barley chromosomes with restriction endonucleases was examined. All the treatments with five restriction endonucleases, MboII, RsaI, HaeIII, HinfI, and DraII, showed various band patterns on the barley chromosomes. Differences were observed in the band patterns produced with different restriction endonucleases. Uneven staining patterns, similar to the band patterns by the endonuclease treatments, also appeared when the chromosomes were treated with the buffer solution without the enzyme. The band patterns observed both with and without the endonucleases were classified int

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3

Petersen, Kamilla Vandsø, Cinzia Tesauro, Marianne Smedegaard Hede, et al. "Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts." Sensors 22, no. 20 (2022): 7763. http://dx.doi.org/10.3390/s22207763.

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Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The m

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4

Shammas, Masood A., Hemant Koley, Sima Shah, et al. "Dysregulated Apurinic/Apyrimidinic Endonucleases (Ape1 and Ape2) Lead to Genetic Instability in Multiple Myeloma." Blood 104, no. 11 (2004): 1418. http://dx.doi.org/10.1182/blood.v104.11.1418.1418.

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Abstract Multiple myeloma (MM) is associated with significant genomic instability. Homologous recombination (HR), which is elevated in MM, is considered to be responsible for this instability. As endonucleases play an important role in mediating HR, here we have evaluated the role of endonuclease in biology and progression of MM. Gene expression profile using Affymetrix U133 array showed &gt; 2 fold elevation of Ape1 or Ape2 or both in 5 of 6 MM cell lines and 12 of 15 patient samples. Immunocytochemistry confirmed upregulation of Ape1 protein in MM cell lines. A Plasmid degradation assay

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5

Landthaler, Markus, Nelson C. Lau, and David A. Shub. "Group I Intron Homing in Bacillus Phages SPO1 and SP82: a Gene Conversion Event Initiated by a Nicking Homing Endonuclease." Journal of Bacteriology 186, no. 13 (2004): 4307–14. http://dx.doi.org/10.1128/jb.186.13.4307-4314.2004.

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ABSTRACT Many group I introns encode endonucleases that promote intron homing by initiating a double-stranded break-mediated homologous recombination event. In this work we describe intron homing in Bacillus subtilis phages SPO1 and SP82. The introns encode the DNA endonucleases I-HmuI and I-HmuII, respectively, which belong to the H-N-H endonuclease family and possess nicking activity in vitro. Coinfections of B. subtilis with intron-minus and intron-plus phages indicate that I-HmuI and I-HmuII are required for homing of the SPO1 and SP82 introns, respectively. The homing process is a gene co

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6

GRISHIN, ALEXANDER, INES FONFARA, ANDREI ALEXEEVSKI, et al. "IDENTIFICATION OF CONSERVED FEATURES OF LAGLIDADG HOMING ENDONUCLEASES." Journal of Bioinformatics and Computational Biology 08, no. 03 (2010): 453–69. http://dx.doi.org/10.1142/s0219720010004665.

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LAGLIDADG family of homing endonucleases are rare-cutting enzymes which recognize long target sequences and are of great interest in genome engineering. Despite advances in homing endonuclease engineering, effective methods of broadening the range of cleaved sequences are still lacking. Here, we present a study of conserved structural features of LAGLIDADG homing endonucleases that might aid further development of such methods. The protein–DNA interface of LAGLIDADG homing endonucleases differs considerably with the particular nuclease, and the analysis of conserved protein–DNA interactions co

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7

Everett, Blake A., Lauren A. Litzau, Kassidy Tompkins, et al. "Crystal structure of the Wheat dwarf virus Rep domain." Acta Crystallographica Section F Structural Biology Communications 75, no. 12 (2019): 744–49. http://dx.doi.org/10.1107/s2053230x19015796.

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The Rep domain of Wheat dwarf virus (WDV Rep) is an HUH endonuclease involved in rolling-circle replication. HUH endonucleases coordinate a metal ion to enable the nicking of a specific ssDNA sequence and the subsequent formation of an intermediate phosphotyrosine bond. This covalent protein–ssDNA adduct makes HUH endonucleases attractive fusion tags (HUH-tags) in a diverse number of biotechnological applications. Solving the structure of an HUH endonuclease in complex with ssDNA will provide critical information about ssDNA recognition and sequence specificity, thus enabling rationally engine

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8

Bultmann, H., and R. Mezzanotte. "Characterization and origin of extrachromosomal DNA granules in Sarcophaga bullata." Journal of Cell Science 88, no. 3 (1987): 327–34. http://dx.doi.org/10.1242/jcs.88.3.327.

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We have used endonuclease treatment in situ, followed by Giemsa or ethidium bromide staining, for mapping repetitive sequences on the chromosomes of the flesh fly Sarcophaga bullata and thus for studying extrachromosomal DNA granules in this species. All three restriction enzymes employed (HaeIII, A1uI and HindIII) show the same cytological effects, except for a single interstitial band. In both polytene and mitotic chromosomes, chromatin resistant to these endonucleases presumably includes at least three endonucleases presumably includes at least three previously unrecognized buoyant density

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9

Jordano-Raya, Marina, Cristina Beltrán-Melero, M. Dolores Moreno-Recio, et al. "Complementary Functions of Plant AP Endonucleases and AP Lyases during DNA Repair of Abasic Sites Arising from C:G Base Pairs." International Journal of Molecular Sciences 22, no. 16 (2021): 8763. http://dx.doi.org/10.3390/ijms22168763.

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Abasic (apurinic/apyrimidinic, AP) sites are ubiquitous DNA lesions arising from spontaneous base loss and excision of damaged bases. They may be processed either by AP endonucleases or AP lyases, but the relative roles of these two classes of enzymes are not well understood. We hypothesized that endonucleases and lyases may be differentially influenced by the sequence surrounding the AP site and/or the identity of the orphan base. To test this idea, we analysed the activity of plant and human AP endonucleases and AP lyases on DNA substrates containing an abasic site opposite either G or C in

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10

Carnes, Jason, Carmen Zelaya Soares, Carey Wickham, and Kenneth Stuart. "Endonuclease Associations with Three Distinct Editosomes in Trypanosoma brucei." Journal of Biological Chemistry 286, no. 22 (2011): 19320–30. http://dx.doi.org/10.1074/jbc.m111.228965.

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Three distinct editosomes, typified by mutually exclusive KREN1, KREN2, or KREN3 endonucleases, are essential for mitochondrial RNA editing in Trypanosoma brucei. The three editosomes differ in substrate endoribonucleolytic cleavage specificity, which may reflect the vast number of editing sites that need insertion or deletion of uridine nucleotides (Us). Each editosome requires the single RNase III domain in each endonuclease for catalysis. Studies reported here show that the editing endonucleases do not form homodimeric domains, and may therefore function as intermolecular heterodimers, perh

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11

Birkholz, Erica A., Chase J. Morgan, Thomas G. Laughlin, et al. "An intron endonuclease facilitates interference competition between coinfecting viruses." Science 385, no. 6704 (2024): 105–12. http://dx.doi.org/10.1126/science.adl1356.

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Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. In this work, we studied intron-encoded homing endonuclease gp210 in bacteriophage ΦPA3 and found that it contributes to viral competition by interfering with the replication of a coinfecting phage, ΦKZ. We show that gp210 targets a specific sequence in ΦKZ, which prevents the assembly of progeny viruses. This work demonstrates how a

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12

Anzai, N., H. Kawabata, T. Hirama, et al. "Types of nuclear endonuclease activity capable of inducing internucleosomal DNA fragmentation are completely different between human CD34+ cells and their granulocytic descendants." Blood 86, no. 3 (1995): 917–23. http://dx.doi.org/10.1182/blood.v86.3.917.917.

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Abstract A hallmark of apoptosis is internucleosomal DNA fragmentation resulting from the activation of endonucleases. We characterized the endonuclease activity of human myeloid cell nuclei that cleaved their own nuclear chromatin to oligonucleosomal length fragments. Polymorphonuclear leukocytes (PMNs) of normal peripheral blood contained both Ca2+/Mg(2+)- dependent and DNase II-like acidic endonuclease activities in their nuclei. Immature myeloid cells of normal bone marrow at various stages of granulocytic maturation had similar nuclease activities. In contrast, a clear difference was show

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13

Anzai, N., H. Kawabata, T. Hirama, et al. "Types of nuclear endonuclease activity capable of inducing internucleosomal DNA fragmentation are completely different between human CD34+ cells and their granulocytic descendants." Blood 86, no. 3 (1995): 917–23. http://dx.doi.org/10.1182/blood.v86.3.917.bloodjournal863917.

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A hallmark of apoptosis is internucleosomal DNA fragmentation resulting from the activation of endonucleases. We characterized the endonuclease activity of human myeloid cell nuclei that cleaved their own nuclear chromatin to oligonucleosomal length fragments. Polymorphonuclear leukocytes (PMNs) of normal peripheral blood contained both Ca2+/Mg(2+)- dependent and DNase II-like acidic endonuclease activities in their nuclei. Immature myeloid cells of normal bone marrow at various stages of granulocytic maturation had similar nuclease activities. In contrast, a clear difference was shown in the

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14

Karvelis, Tautvydas, Giedrius Gasiunas, and Virginijus Siksnys. "Programmable DNA cleavage in vitro by Cas9." Biochemical Society Transactions 41, no. 6 (2013): 1401–6. http://dx.doi.org/10.1042/bst20130164.

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The ternary Cas9–crRNA–tracrRNA complex (Cas9t) of the Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) system functions as an Mg2+-dependent RNA-directed DNA endonuclease that locates its DNA target guided by the crRNA (CRISPR RNA) in the tracrRNA–crRNA structure and introduces a double-strand break at a specific site in DNA. The simple modular organization of Cas9t, where specificity for the DNA target is encoded by a small crRNA and the cleavage reaction is executed by the Cas9 endonuclease, provides a versatile platform for the engineering

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15

Takai, Ken, and Koki Horikoshi. "Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool." Applied and Environmental Microbiology 65, no. 12 (1999): 5586–89. http://dx.doi.org/10.1128/aem.65.12.5586-5589.1999.

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ABSTRACT Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible

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16

Daley, James M., Chadi Zakaria, and Dindial Ramotar. "The endonuclease IV family of apurinic/apyrimidinic endonucleases." Mutation Research/Reviews in Mutation Research 705, no. 3 (2010): 217–27. http://dx.doi.org/10.1016/j.mrrev.2010.07.003.

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17

Yang, Zhi-Hui, Ji-Xiang Huang, and Yi-Jian Yao. "Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example." Applied and Environmental Microbiology 73, no. 24 (2007): 7947–58. http://dx.doi.org/10.1128/aem.00842-07.

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ABSTRACT A molecular method based on PCR-restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) ribosomal DNA sequences was designed to rapidly identify fungal species, with members of the genus Pleurotus as an example. Based on the results of phylogenetic analysis of ITS sequences from Pleurotus, a PCR-RFLP endonuclease autoscreening (PRE Auto) program was developed to screen restriction endonucleases for discriminating multiple sequences from different species. The PRE Auto program analyzes the endonuclease recognition sites and calculates the sizes of

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18

Davletgildeeva, Anastasiia T., Alexandra A. Kuznetsova, Darya S. Novopashina, et al. "Comparative Analysis of Exo- and Endonuclease Activities of APE1-like Enzymes." International Journal of Molecular Sciences 23, no. 5 (2022): 2869. http://dx.doi.org/10.3390/ijms23052869.

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Apurinic/apyrimidinic (AP)-endonucleases are multifunctional enzymes that are required for cell viability. AP-endonucleases incise DNA 5′ to an AP-site; can recognize and process some damaged nucleosides; and possess 3′-phosphodiesterase, 3′-phosphatase, and endoribonuclease activities. To elucidate the mechanism of substrate cleavage in detail, we analyzed the effect of mono- and divalent metal ions on the exo- and endonuclease activities of four homologous APE1-like endonucleases (from an insect (Rrp1), amphibian (xAPE1), fish (zAPE1), and from humans (hAPE1)). It was found that the enzymes

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19

Jones, Rhian, Sana Lessoued, Kristina Meier, et al. "Structure and function of the Toscana virus cap-snatching endonuclease." Nucleic Acids Research 47, no. 20 (2019): 10914–30. http://dx.doi.org/10.1093/nar/gkz838.

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Abstract Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important human pathogens such as Rift Valley fever virus (RVFV). Here, we carried out a structural and functional characterization of the TOSV cap-snatching endonuclease, an N terminal domain of the viral polymerase (L protein) that provides capped 3′OH primers for transcription. W

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20

Engebretson, Jeff J., and Craig L. Moyer. "Fidelity of Select Restriction Endonucleases in Determining Microbial Diversity by Terminal-Restriction Fragment Length Polymorphism." Applied and Environmental Microbiology 69, no. 8 (2003): 4823–29. http://dx.doi.org/10.1128/aem.69.8.4823-4829.2003.

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ABSTRACT An evaluation of 18 DNA restriction endonucleases for use in terminal-restriction fragment length polymorphism (T-RFLP) analysis was performed by using richness and density indices in conjunction with computer simulations for 4,603 bacterial small-subunit rRNA gene sequences. T-RFLP analysis has become a commonly used method for screening environmental samples for precursory identification and community comparison studies due to its precision and high-throughput capability. The accuracy of T-RFLP analysis for describing a community has not yet been thoroughly evaluated. In this study,

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Tocchini-Valentini, Giuseppe D., and Glauco P. Tocchini-Valentini. "Archaeal tRNA-Splicing Endonuclease as an Effector for RNA Recombination and Novel Trans-Splicing Pathways in Eukaryotes." Journal of Fungi 7, no. 12 (2021): 1069. http://dx.doi.org/10.3390/jof7121069.

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We have characterized a homodimeric tRNA endonuclease from the euryarchaeota Ferroplasma acidarmanus (FERAC), a facultative anaerobe which can grow at temperatures ranging from 35 to 42 °C. This enzyme, contrary to the eukaryal tRNA endonucleases and the homotetrameric Methanocaldococcus jannaschii (METJA) homologs, is able to cleave minimal BHB (bulge–helix–bulge) substrates at 30 °C. The expression of this enzyme in Schizosaccharomyces pombe (SCHPO) enables the use of its properties as effectors by inserting BHB motif introns into hairpin loops normally seen in mRNA transcripts. In addition,

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Bilto, Iman M., Tuhin K. Guha, Alvan Wai, and Georg Hausner. "Three new active members of the I-OnuI family of homing endonucleases." Canadian Journal of Microbiology 63, no. 8 (2017): 671–81. http://dx.doi.org/10.1139/cjm-2017-0067.

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In vitro characterization of 3 LAGLIDADG-type homing endonucleases (HEs) (I-CcaI, I-CcaII, and I-AstI) that belong to the I-OnuI family showed that they are functional HEs that cleave their respective cognate target sites. These endonucleases are encoded within group ID introns and appear to be orthologues that have inserted into 3 different mitochondrial genes: rns, rnl, and cox3. The endonuclease activity of I-CcaI was tested using various substrates, and its minimum DNA recognition sequence was estimated to be 26 nt. This set of HEs may provide some insight into how these types of mobile el

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23

Bakhrat, Anya, Melissa S. Jurica, Barry L. Stoddard, and Dina Raveh. "Homology Modeling and Mutational Analysis of Ho Endonuclease of Yeast." Genetics 166, no. 2 (2004): 721–28. http://dx.doi.org/10.1093/genetics/166.2.721.

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Abstract Ho endonuclease is a LAGLIDADG homing endonuclease that initiates mating-type interconversion in yeast. Ho is encoded by a free-standing gene but shows 50% primary sequence similarity to the intein (protein-intron encoded) PI-SceI. Ho is unique among LAGLIDADG endonucleases in having a 120-residue C-terminal putative zinc finger domain. The crystal structure of PI-SceI revealed a bipartite enzyme with a protein-splicing domain (Hint) and intervening endonuclease domain. We made a homology model for Ho on the basis of the PI-SceI structure and performed mutational analysis of putative

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Turkki, Vesa, Diana Schenkwein, Oskari Timonen, Tiia Husso, Hanna P. Lesch, and Seppo Ylä-Herttuala. "Lentiviral Protein Transduction with Genome-Modifying HIV-1 Integrase-I-PpoI Fusion Proteins: Studies on Specificity and Cytotoxicity." BioMed Research International 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/379340.

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Rare-cutting endonucleases, such as the I-PpoI, can be used for the induction of double strand breaks (DSBs) in genome editing and targeted integration based on homologous recombination. For therapeutic approaches, the specificity and the pattern of off-target effects are of high importance in these techniques. For its applications, the endonuclease needs to be transported into the target cell nucleus, where the mechanism of transport may affect its function. Here, we have studied the lentiviral protein transduction of the integrase (IN)-PpoI fusion protein using thecis-packaging method. In ge

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25

Shammas, Masood A., Hemanta Koley, Paola Neri, et al. "Molecular Basis of Genomic Instability and Progression in Multiple Myeloma: Potential Role of Apurinic (Apyrimidinic) Endonuclease." Blood 106, no. 11 (2005): 1561. http://dx.doi.org/10.1182/blood.v106.11.1561.1561.

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Abstract Genetic instability is a prominent feature of most cancers including multiple myeloma (MM) and is responsible for ongoing accrual of mutational changes which may lead to development of drug resistance and metastasis. The molecular basis for the generation of genetic diversity in MM is therefore extremely important to understand carcinogenesis and to identify novel targets for treatment. As genomic rearrangements require excision of DNA, we hypothesized that an elevated endonuclease activity may induce recombination and subsequent genomic instability in cancer cells. We developed a pla

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26

Whetstone, C. A., J. G. Wheeler, and D. E. Reed. "Investigation of possible vaccine-induced epizootics of infectious bovine rhinotracheitis, using restriction endonuclease analysis of viral DNA." American Journal of Veterinary Research 47, no. 8 (1986): 1789–95. https://doi.org/10.2460/ajvr.1986.47.08.1789.

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SUMMARY Viral DNA was extracted from each of 14 modified-live (ml) bovine herpesvirus 1 vaccines, representing all of the ml infectious bovine rhinotracheitis virus (ibrv) vaccines licensed by the US Department of Agriculture for use in cattle. Restriction endonucleases Pst I and Bgl II were used to establish restriction enzyme patterns for the vaccinal viruses. Viral DNA from isolates obtained from 6 field samples of ibrv (1 from Colorado, 1 from West Virginia, 3 from Wisconsin, 1 from South Dakota) were digested with restriction endonucleases, and patterns were compared to evaluate the role

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27

Carlson, Karin, and Aud Ȗvervatin. "BACTERIOPHAGE T4 ENDONUCLEASES II AND IV, OPPOSITELY AFFECTED BY dCMP HYDROXYMETHYLASE ACTIVITY, HAVE DIFFERENT ROLES IN THE DEGRADATION AND IN THE RNA POLYMERASE-DEPENDENT REPLICATION OF T4 CYTOSINE-CONTAINING DNA." Genetics 114, no. 3 (1986): 669–85. http://dx.doi.org/10.1093/genetics/114.3.669.

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ABSTRACT Bacteriophage T4 mutants defective in gene 56 (dCTPase) synthesize DNA where cytosine (Cyt) partially or completely replaces hydroxymethylcytosine (HmCyt). This Cyt-DNA is degraded in vivo by T4 endonucleases II and IV, and by the exonuclease coded or controlled by genes 46 and 47.—Our results demonstrate that T4 endonuclease II is the principal enzyme initiating degradation of T4 Cyt-DNA. The activity of endonuclease IV, but not that of endonuclease II, was stimulated in the presence of a wild-type dCMP hydroxymethylase, also when no HmCyt was incorporated into phage DNA, suggesting

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Rahman, Md Maminur, Mohiuddin Mohiuddin, Islam Shamima Keka, et al. "Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination." Journal of Biological Chemistry 295, no. 51 (2020): 17460–75. http://dx.doi.org/10.1074/jbc.ra120.013521.

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Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null ML

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Welch, S. G., and R. A. D. Williams. "Two thermostable type II restriction endonucleases from Icelandic strains of the genus Thermus: Tsp4C I (ACN/GT), a novel type II restriction endonuclease, and Tsp8E I, an isoschizomer of the mesophilic enzyme Bgl I (GCCNNNN/NGGC)." Biochemical Journal 309, no. 2 (1995): 595–99. http://dx.doi.org/10.1042/bj3090595.

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Sixteen isolates of thermophilic bacteria from the genus Thermus, isolated from neutral and alkaline hot water springs in the southwest region of Iceland, were tested for the presence of restriction endonucleases. Extracts from five of the isolates showed evidence of the presence of restriction endonuclease activity by producing discrete nucleotide fragments when incubated at 65 degrees C with lambda phage DNA. Two of the isolates (Tsp4C and Tsp8E) were found to have particularly high levels of restriction endonuclease activity, and the respective enzymes from these two Thermus isolates were p

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Gosálvez, J., C. López-Fernández, and V. Goyanes. "Detection of cryptic bands by AluI in eukaryotic chromosomes." Genome 32, no. 4 (1989): 672–75. http://dx.doi.org/10.1139/g89-497.

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Selective digestion of fixed chromatin with the restriction endonuclease AluI (which cuts the sequence AG CT) uncovers a specific and repeatable pattern of bands within the euchromatin of two species of grasshoppers and of the L929 mouse cell line, which are not detectable by means of other banding techniques such as C-bands, specific fluorochromes, or other restriction endonucleases. It is tentatively suggested that this chromatin represents a special class of repetitive DNA embedded in the euchromatin, not containing the AluI restriction site to the same extent as in euchromatin and not asso

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Zhang, Chunlin, and K. V. Nagaraja. "Differentiation of avian adenovirus type-II strains by restriction endonuclease fingerprinting." American Journal of Veterinary Research 50, no. 9 (1989): 1466–70. https://doi.org/10.2460/ajvr.1989.50.09.1466.

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SUMMARY Three serologically indistinguishable viruses from the avian adenovirus type-II splenomegaly virus of chickens, marble spleen disease virus of pheasants, and hemorrhagic enteritis virus of turkeys, were analyzed by restriction endonuclease fingerprinting. The dna from these viruses were examined with 6 restriction endonucleases (Bgl II, EcoRI, HindIII, Hha I, Xho I, and BamHI). Markedly different dna cleavage patterns were found in these virus isolates with all the 5 enzymes, except with BamHI, suggesting genetic differences between isolates of adenovirus type II. Restriction endonucle

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Seligman, Lenny M., Kathryn M. Stephens, Jeremiah H. Savage, and Raymond J. Monnat. "Genetic Analysis of the Chlamydomonas reinhadtii I-CreI Mobile Intron Homing System in Escherichia coli." Genetics 147, no. 4 (1997): 1653–64. http://dx.doi.org/10.1093/genetics/147.4.1653.

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Abstract We have developed and used a genetic selection system in Escherichia coli to study functional requirements for homing site recognition and cleavage by a representative eukaryotic mobile intron endonuclease. The homing endonuclease, I-CreI, was originally isolated from the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. I-CreI homing site mutants contained base pair substitutions or single base deletions that altered the rate of homing site cleavage and/or product release. I-CreI endonuclease mutants fell into six phenotypic classes that differed in in vivo activit

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Plessis, A., A. Perrin, J. E. Haber, and B. Dujon. "Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus." Genetics 130, no. 3 (1992): 451–60. http://dx.doi.org/10.1093/genetics/130.3.451.

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Abstract The Saccharomyces cerevisiae mitochondrial endonuclease I-SceI creates a double-strand break as the initiating step in the gene conversional transfer of the omega+ intron to omega- DNA. We have expressed a galactose-inducible synthetic I-SceI gene in the nucleus of yeast that also carries the I-SceI recognition site on a plasmid substrate. We find that the galactose-induced I-SceI protein can be active in the nucleus and efficiently catalyze recombination. With a target plasmid containing direct repeats of the Escherichia coli lacZ gene, one copy of which is interrupted by a 24-bp cut

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Barbado, Casimiro, Dolores Córdoba-Cañero, Rafael R. Ariza, and Teresa Roldán-Arjona. "Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis." Proceedings of the National Academy of Sciences 115, no. 5 (2018): E916—E924. http://dx.doi.org/10.1073/pnas.1719497115.

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Abasic (apurinic/apyrimidinic, AP) sites in DNA arise from spontaneous base loss or by enzymatic removal during base excision repair. It is commonly accepted that both classes of AP site have analogous biochemical properties and are equivalent substrates for AP endonucleases and AP lyases, although the relative roles of these two types of enzymes are not well understood. We provide here genetic and biochemical evidence that, in Arabidopsis, AP sites generated by spontaneous loss of N7-methylguanine (N7-meG) are exclusively repaired through an AP endonuclease-independent pathway initiated by FP

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MAK, C. H., Y. Y. Y. CHUNG, and R. C. KO. "Single-stranded endonuclease activity in the excretory–secretory products of Trichinella spiralis and Trichinella pseudospiralis." Parasitology 120, no. 5 (2000): 527–33. http://dx.doi.org/10.1017/s0031182099005879.

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A novel acidic extracellular single-stranded endonuclease was demonstrated for the first time in the excretory–secretory (E–S) products of 2 species of Trichinella. Unlike the double-stranded endonuclease reported earlier, the single-stranded molecule is divalent cation independent and is detected in both T. spiralis and T. pseudospiralis E–S products. It hydrolysed single-stranded DNA and RNA at comparable rates. The single-stranded endonuclease was sensitive to inhibition by Zn2+ and to high concentrations of NaCl. Zymographic analysis indicated that it was encoded by at least 3 peptides of

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Tomanicek, Stephen J., Ronny C. Hughes, Joseph D. Ng, and Leighton Coates. "Structure of the endonuclease IV homologue fromThermotoga maritimain the presence of active-site divalent metal ions." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 9 (2010): 1003–12. http://dx.doi.org/10.1107/s1744309110028575.

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The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5′-phosphodiester bond at an AP site to generate a free 3′-hydroxyl group and a 5′-terminal sugar phosphate using their AP nuclease activity. Specifically,Thermotoga maritimaendonuclease IV

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Wuitschick, Jeffrey D., Paul R. Lindstrom, Alison E. Meyer, and Kathleen M. Karrer. "Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains." Eukaryotic Cell 3, no. 3 (2004): 685–94. http://dx.doi.org/10.1128/ec.3.3.685-694.2004.

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ABSTRACT Three insertion elements were previously found in a family of germ line-limited mobile elements, the Tlr elements, in the ciliate Tetrahymena. Each of the insertions contains an open reading frame (ORF). Sequence analysis of the deduced proteins encoded by the elements suggests that they are homing endonucleases. The genes are designated TIE1-1, TIE2-1, and TIE3-1 for Tetrahymena insertion-homing endonuclease. The endonuclease motif occupies the amino terminal half of each TIE protein. The C-terminal regions of the proteins are similar to the APETELA2 DNA binding domain of plant trans

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Lutz, Thomas, Kiersten Flodman, Alyssa Copelas, et al. "A protein architecture guided screen for modification dependent restriction endonucleases." Nucleic Acids Research 47, no. 18 (2019): 9761–76. http://dx.doi.org/10.1093/nar/gkz755.

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Abstract Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featur

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Padron-Barthe, Laura, Chloé Leprêtre, Elisabeth Martin, Marie-France Counis, and Alicia Torriglia. "Conformational Modification of Serpins Transforms Leukocyte Elastase Inhibitor into an Endonuclease Involved in Apoptosis." Molecular and Cellular Biology 27, no. 11 (2007): 4028–36. http://dx.doi.org/10.1128/mcb.01959-06.

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ABSTRACT The best-characterized biochemical feature of apoptosis is degradation of genomic DNA into oligonucleosomes. The endonuclease responsible for DNA degradation in caspase-dependent apoptosis is caspase-activated DNase. In caspase-independent apoptosis, different endonucleases may be activated according to the cell line and the original insult. Among the known effectors of caspase-independent cell death, L-DNase II (LEI [leukocyte elastase inhibitor]-derived DNase II) has been previously characterized by our laboratory. We have thus shown that this endonuclease derives from the serpin su

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Prorok, Paulina, Inga R. Grin, Bakhyt T. Matkarimov, et al. "Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases." Cells 10, no. 7 (2021): 1591. http://dx.doi.org/10.3390/cells10071591.

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It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites an

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Iino, Hitoshi, Kwang Kim, Atsuhiro Shimada, Ryoji Masui, Seiki Kuramitsu, and Kenji Fukui. "Characterization of C- and N-terminal domains of Aquifex aeolicus MutL endonuclease: N-terminal domain stimulates the endonuclease activity of C-terminal domain in a zinc-dependent manner." Bioscience Reports 31, no. 5 (2011): 309–22. http://dx.doi.org/10.1042/bsr20100116.

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DNA MMR (mismatch repair) is an excision repair system that removes mismatched bases generated primarily by failure of the 3′–5′ proofreading activity associated with replicative DNA polymerases. MutL proteins homologous to human PMS2 are the endonucleases that introduce the entry point of the excision reaction. Deficiency in PMS2 function is one of the major etiologies of hereditary non-polyposis colorectal cancers in humans. Although recent studies revealed that the CTD (C-terminal domain) of MutL harbours weak endonuclease activity, the regulatory mechanism of this activity remains unknown.

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Coco, Rosalba Del, Liborio Stuppia, Caterina Cinti, Rita Peila, and Nadir Mario Maraldi. "Ultrastructural banding induced by DraI or HaeIII progressive digestion and in situ nick translation on human chromosomes." Genome 37, no. 6 (1994): 950–56. http://dx.doi.org/10.1139/g94-135.

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Fixed human metaphase chromosomes were progressively digested with DraI or HaeIII restriction enzymes, submitted to in situ nick translation, and observed by transmission electron microscopy to obtain further information on the localization of the endonuclease target sequences and on the conformational changes in chromosomal bands. This approach allows us to detect specific nick translation patterns, namely, G-banding or R-like banding after short DraI and HaeIII endonuclease digestion, respectively. Intermediate banding recognizable as C-negative banding and G + C banding are induced by longe

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Zhou, Wen, Qingtao Lu, Qingwei Li, et al. "PPR-SMR protein SOT1 has RNA endonuclease activity." Proceedings of the National Academy of Sciences 114, no. 8 (2017): E1554—E1563. http://dx.doi.org/10.1073/pnas.1612460114.

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Numerous attempts have been made to identify and engineer sequence-specific RNA endonucleases, as these would allow for efficient RNA manipulation. However, no natural RNA endonuclease that recognizes RNA in a sequence-specific manner has been described to date. Here, we report that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), anArabidopsispentatricopeptide repeat (PPR) protein with a small MutS-related (SMR) domain, has RNA endonuclease activity. We show that the SMR moiety of SOT1 performs the endonucleolytic maturation of 23S and 4.5S rRNA through the PPR domain, specifically recognizing a 1

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Gnügge, Robert, and Lorraine S. Symington. "Efficient DNA double-strand break formation at single or multiple defined sites in the Saccharomyces cerevisiae genome." Nucleic Acids Research 48, no. 20 (2020): e115-e115. http://dx.doi.org/10.1093/nar/gkaa833.

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Abstract DNA double-strand breaks (DSBs) are common genome lesions that threaten genome stability and cell survival. Cells use sophisticated repair machineries to detect and heal DSBs. To study DSB repair pathways and associated factors, inducible site-specific endonucleases have proven to be fundamental tools. In Saccharomyces cerevisiae, galactose-inducible rare-cutting endonucleases are commonly used to create a single DSB at a unique cleavage site. Galactose induction requires cell cultivation in suboptimal growth media, which is tedious especially when working with slow growing DSB repair

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von Kanel, Thomas, Dominik Gerber, André Schaller, et al. "Quantitative 1-Step DNA Methylation Analysis with Native Genomic DNA as Template." Clinical Chemistry 56, no. 7 (2010): 1098–106. http://dx.doi.org/10.1373/clinchem.2009.142828.

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Abstract Background: DNA methylation analysis currently requires complex multistep procedures based on bisulfite conversion of unmethylated cytosines or on methylation-sensitive endonucleases. To facilitate DNA methylation analysis, we have developed a quantitative 1-step assay for DNA methylation analysis. Methods: The assay is based on combining methylation-sensitive FastDigest® endonuclease digestion and quantitative real-time PCR (qPCR) in a single reaction. The first step consists of DNA digestion, followed by endonuclease inactivation and qPCR. The degree of DNA methylation is evaluated

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Kwiatek, Agnieszka, Maciej Łuczkiewicz, Katarzyna Bandyra, Daniel C. Stein, and Andrzej Piekarowicz. "Neisseria gonorrhoeae FA1090 Carries Genes Encoding Two Classes of Vsr Endonucleases." Journal of Bacteriology 192, no. 15 (2010): 3951–60. http://dx.doi.org/10.1128/jb.00098-10.

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ABSTRACT A very short patch repair system prevents mutations resulting from deamination of 5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing sequence specificity. We identified two genes encoding Vsr endonucleases V.NgoAXIII and V.NgoAXIV from Neisseria gonorrhoeae FA1090 based on DNA sequence similarity to genes encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in Escherichia coli, the proteins were biochemically characterized and the endonucleolytic activities and specificities of V.NgoAXIII and V.NgoAXIV were

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Batistatou, A., and L. A. Greene. "Aurintricarboxylic acid rescues PC12 cells and sympathetic neurons from cell death caused by nerve growth factor deprivation: correlation with suppression of endonuclease activity." Journal of Cell Biology 115, no. 2 (1991): 461–71. http://dx.doi.org/10.1083/jcb.115.2.461.

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Past studies have shown that serum-free cultures of PC12 cells are a useful model system for studying the neuronal cell death which occurs after neurotrophic factor deprivation. In this experimental paradigm, nerve growth factor (NGF) rescues the cells from death. It is reported here that serum-deprived PC12 cells manifest an endonuclease activity that leads to internucleosomal cleavage of their cellular DNA. This activity is detected within 3 h of serum withdrawal and several hours before any morphological sign of cell degeneration or death. NGF and serum, which promote survival of the cells,

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Zhou, Xiaohong, Maria DeLucia, and Jinwoo Ahn. "SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr)." Journal of Biological Chemistry 291, no. 33 (2016): 16936–47. http://dx.doi.org/10.1074/jbc.m116.721183.

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Evolutionarily conserved structure-selective endonuclease MUS81 forms a complex with EME1 and further associates with another endonuclease SLX4-SLX1 to form a four-subunit complex of MUS81-EME1-SLX4-SLX1, coordinating distinctive biochemical activities of both endonucleases in DNA repair. Viral protein R (Vpr), a highly conserved accessory protein in primate lentiviruses, was previously reported to bind SLX4 to mediate down-regulation of MUS81. However, the detailed mechanism underlying MUS81 down-regulation is unclear. Here, we report that HIV-1 Vpr down-regulates both MUS81 and its cofactor

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Liu, Guang, Zhenyi Zhang, Gong Zhao, Zixin Deng, Geng Wu, and Xinyi He. "Crystallization and preliminary X-ray analysis of the type IV restriction endonuclease ScoMcrA fromStreptomyces coelicolor, which cleaves both Dcm-methylated DNA and phosphorothioated DNA." Acta Crystallographica Section F Structural Biology Communications 71, no. 1 (2015): 57–60. http://dx.doi.org/10.1107/s2053230x14025801.

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ScoMcrA is a type IV modification-dependent restriction endonuclease found in the model strainStreptomyces coelicolor. Unlike type I, II and III restriction endonucleases, which cleave unmodified DNA, type IV restriction endonucleases cleave modified DNA, including methylated, hydroxymethylated, glucosyl-hydroxymethylated and phosphorothioated DNA. ScoMcrA targets both Dcm-methylated DNA and phosphorothioated DNA, and makes double-strand breaks 16–28 nt away from the modified nucleotides or the phosphorothioate links. However, the mechanism by which ScoMcrA recognizes these two entirely differ

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Xu, Shuang-yong, and Yogesh K. Gupta. "Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease." Nucleic Acids Research 41, no. 1 (2012): 378–90. http://dx.doi.org/10.1093/nar/gks1043.

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