Alfred Pingoud

Summary

Affiliation: University of Giessen
Country: Germany

Publications

  1. ncbi request reprint Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase
    Sebastian R Scholz
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 42:9288-94. 2003
  2. ncbi request reprint From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes
    George H Silva
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 361:744-54. 2006
  3. pmc Type II restriction endonucleases-a historical perspective and more
    Alfred Pingoud
    Institute of Biochemistry, Justus Liebig University Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 42:7489-527. 2014
  4. pmc Developing a programmed restriction endonuclease for highly specific DNA cleavage
    Kristin Eisenschmidt
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 33:7039-47. 2005
  5. pmc Structure and function of type II restriction endonucleases
    A Pingoud
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 29:3705-27. 2001
  6. ncbi request reprint Precision genome surgery
    Alfred Pingoud
    Institut fuer Biochemie, Fachbereich Biologie und Chemie, Justus Liebig Universitaet, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nat Biotechnol 25:743-4. 2007
  7. ncbi request reprint Type II restriction endonucleases: structure and mechanism
    A Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, 35392, Giessen, Germany
    Cell Mol Life Sci 62:685-707. 2005
  8. ncbi request reprint Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Biol Chem 280:4289-98. 2005
  9. ncbi request reprint PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 329:913-29. 2003
  10. ncbi request reprint Tyr212: a key residue involved in strand discrimination by the DNA mismatch repair endonuclease MutH
    Peter Friedhoff
    Institut für Biochemie FB 08, Justus Liebig Universitat, D 35392 Giessen, Germany
    J Mol Biol 325:285-97. 2003

Collaborators

Detail Information

Publications66

  1. ncbi request reprint Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase
    Sebastian R Scholz
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 42:9288-94. 2003
    ..Our findings provide a first insight into the likely active-site structure and catalytic mechanism of a nuclease involved in the degradation of chromosomal DNA during programmed cell death...
  2. ncbi request reprint From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes
    George H Silva
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 361:744-54. 2006
    ..This novel endonuclease allows speculation regarding specificity of monomeric LAGLIDADG proteins, while it supports the evolutionary genesis of these proteins by a gene duplication event...
  3. pmc Type II restriction endonucleases-a historical perspective and more
    Alfred Pingoud
    Institute of Biochemistry, Justus Liebig University Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 42:7489-527. 2014
    ..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. ..
  4. pmc Developing a programmed restriction endonuclease for highly specific DNA cleavage
    Kristin Eisenschmidt
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 33:7039-47. 2005
    ..Single base pair substitutions in the TFS prevent addressed DNA cleavage by scPvuII-TFO...
  5. pmc Structure and function of type II restriction endonucleases
    A Pingoud
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 29:3705-27. 2001
    ..Cleavage in the two strands usually occurs in a concerted fashion and leads to inversion of configuration at the phosphorus. The products of the reaction are DNA fragments with a 3'-OH and a 5'-phosphate...
  6. ncbi request reprint Precision genome surgery
    Alfred Pingoud
    Institut fuer Biochemie, Fachbereich Biologie und Chemie, Justus Liebig Universitaet, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nat Biotechnol 25:743-4. 2007
  7. ncbi request reprint Type II restriction endonucleases: structure and mechanism
    A Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, 35392, Giessen, Germany
    Cell Mol Life Sci 62:685-707. 2005
    ..A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature...
  8. ncbi request reprint Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Biol Chem 280:4289-98. 2005
    ..This is the first example of a relatively close evolutionary link between Type II restriction enzymes of widely different specificities...
  9. ncbi request reprint PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 329:913-29. 2003
    ..These results are discussed in an evolutionary context...
  10. ncbi request reprint Tyr212: a key residue involved in strand discrimination by the DNA mismatch repair endonuclease MutH
    Peter Friedhoff
    Institut für Biochemie FB 08, Justus Liebig Universitat, D 35392 Giessen, Germany
    J Mol Biol 325:285-97. 2003
    ..This demonstrates that Tyr212 is an important, if not the only amino acid residue in MutH for sensing the methylation status of the DNA...
  11. ncbi request reprint DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change
    Ann Josée Noël
    Institute for Biochemistry, Justus Liebig University, D 35392 Giessen, Germany
    J Biol Chem 279:6794-804. 2004
    ....
  12. ncbi request reprint Interaction of DNA fragmentation factor (DFF) with DNA reveals an unprecedented mechanism for nuclease inhibition and suggests that DFF can be activated in a DNA-bound state
    Christian Korn
    Institute of Biochemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
    J Biol Chem 280:6005-15. 2005
    ..In transfected HeLa cells transiently expressed DFF associates with chromatin, suggesting that DFF could be activated during apoptosis in a DNA-bound state...
  13. ncbi request reprint Chimeras of the homing endonuclease PI-SceI and the homologous Candida tropicalis intein: a study to explore the possibility of exchanging DNA-binding modules to obtain highly specific endonucleases with altered specificity
    Shawn Steuer
    Justus Liebig Universitat, Institut für Biochemie FB08, Heinrich Buff Ring 58, 35392 Giessen, Germany
    Chembiochem 5:206-13. 2004
    ..This flexibility in DNA recognition should, in principle, allow endonucleases to be produced with new specificities useful for genome engineering...
  14. ncbi request reprint Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis
    Patrick Schafer
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 338:217-28. 2004
    ....
  15. ncbi request reprint Mechanism of DNA cleavage by the DNA/RNA-non-specific Anabaena sp. PCC 7120 endonuclease NucA and its inhibition by NuiA
    G Meiss
    Institut fur Biochemie, FB08, Justus Liebig Universitat, Heinrich Buff Ring 58, Giessen, D 35392, Germany
    J Mol Biol 297:521-34. 2000
    ..Based on these results a mechanism of DNA cleavage by NucA and its inhibition by NuiA is proposed...
  16. ncbi request reprint The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat
    Uwe Pieper
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 41:5245-54. 2002
    ....
  17. doi request reprint Chemical rescue of active site mutants of S. pneumoniae surface endonuclease EndA and other nucleases of the HNH family by imidazole
    Marika Midon
    Institute of Biochemistry FB 08, Justus Liebig University Giessen, Heinrich Buff Ring 58, 35392 Giessen, Germany
    Chembiochem 13:713-21. 2012
    ..pneumoniae to escape the innate immune response...
  18. doi request reprint Redesigning the single-chain variant of the restriction endonuclease PvuII by circular permutation
    Benno Schierling
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    FEBS Lett 586:1736-41. 2012
    ..Three circularly permuted variants of scPvuII were obtained that all maintain the specific endonucleolytic activity of scPvuII...
  19. ncbi request reprint Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII
    Vera Pingoud
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Mol Biosyst 1:135-41. 2005
    ..This result confirms previously published conclusions drawn on the basis of a mutational analysis of SsoII. The methodology that was employed here can be used in principle to identify the DNA binding site of any protein...
  20. pmc Controlling the enzymatic activity of a restriction enzyme by light
    Benno Schierling
    Institute of Biochemistry, Justus Liebig University, Giessen, Germany
    Proc Natl Acad Sci U S A 107:1361-6. 2010
    ..The change in activity is achieved in seconds, is fully reversible, and, in the case analyzed, is due to a change in V(max) rather than K(m)...
  21. ncbi request reprint An efficient method for the preparation of long heteroduplex DNA as substrate for mismatch repair by the Escherichia coli MutHLS system
    Evangelos Thomas
    Institut fur Biochemie, Justus Liebig Universitat, Giessen, Germany
    Biol Chem 383:1459-62. 2002
    ..The application of this procedure is demonstrated for the analysis of the Escherichia coli MutHLS system...
  22. ncbi request reprint Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP
    U Pieper
    Institut für Biochemie FB 15, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, Giessen, D 35392, Germany
    J Mol Biol 272:190-9. 1997
    ..v) Substitution of N339 and N376 with alanine allowed us to identify NTAD (339 to 342) rather than NKKA (376 to 379) as the equivalent of the third consensus sequence motif characteristic for guanine nucleotide binding proteins, NKXD...
  23. pmc Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats
    Lilia Gabsalilow
    Institute for Biochemistry, Justus Liebig University Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 41:e83. 2013
    ..TALE-MutH is a programmable nickase...
  24. ncbi request reprint A mutational analysis of the PD...D/EXK motif suggests that McrC harbors the catalytic center for DNA cleavage by the GTP-dependent restriction enzyme McrBC from Escherichia coli
    Uwe Pieper
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biochemistry 41:5236-44. 2002
    ..Thus, whereas McrC variants defective in DNA cleavage can stimulate the GTPase activity of McrB, the DNase activity of McrC is not supported by McrB variants defective in GTP hydrolysis...
  25. ncbi request reprint Engineering site-specific endonucleases
    Peter Friedhoff
    Institut fur Biochemie, Justus Liebig Universitat, Giessen, Germany
    Methods Mol Biol 352:111-23. 2007
    ....
  26. doi request reprint Identification of ICAD-derived peptides capable of inhibiting caspase-activated DNase
    Daniel Kutscher
    Institute of Biochemistry, Justus Liebig University Giessen, Germany
    FEBS J 279:2917-28. 2012
    ..In these assays, two ICAD-derived peptides were identified that are capable of efficiently and specifically inhibiting CAD activity in solution...
  27. doi request reprint On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Mol Biol 393:140-60. 2009
    ..Our conclusions are supported by molecular dynamics simulations and are consistent with the structural observations of both one and two Me(2+) binding to these enzymes...
  28. ncbi request reprint Defining the location and function of domains of McrB by deletion mutagenesis
    U Pieper
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Germany
    Biol Chem 380:1225-30. 1999
    ..Thus, DNA and GTP binding are spatially separated on the McrB molecule, and the respective domains function quite independently...
  29. ncbi request reprint A fluorimetric assay for on-line detection of DNA cleavage by restriction endonucleases
    Kristin Eisenschmidt
    Justus Liebig Universitat, Institut für Biochemie FB08, 35392 Giessen, Germany
    J Biotechnol 96:185-91. 2002
    ..This assay can be carried out in a microplate format, which allows for the analysis of many restriction endonuclease variants in parallel...
  30. ncbi request reprint Evolutionary relationship between different subgroups of restriction endonucleases
    Vera Pingoud
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Biol Chem 277:14306-14. 2002
    ..This may explain why similarities may be more pronounced between members of different subtypes of restriction enzymes than among the members of a given subtype...
  31. ncbi request reprint Application of the C4'-alkylated deoxyribose primer system (CAPS) in allele-specific real-time PCR for increased selectivity in discrimination of single nucleotide sequence variants
    Björn Tews
    Institut fur Biochemie, FB 08, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Biol Chem 384:1533-41. 2003
    ..Targeting of SNPs assures a universal exertion of this method, since these markers are gender-independent, highly abundant and ubiquitous...
  32. pmc The effect of ICAD-S on the formation and intracellular distribution of a nucleolytically active caspase-activated DNase
    Sebastian Richard Scholz
    Institut für Biochemie FB 08, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 30:3045-51. 2002
    ....
  33. ncbi request reprint Validation of an algorithm for automatic quantification of nucleic acid copy numbers by real-time polymerase chain reaction
    Jochen Wilhelm
    Institut fur Biochemie, FB 08, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Anal Biochem 317:218-25. 2003
    ..The melting curve data are corrected for signal changes not due to the melting process and are smoothed by fitting cubic splines. Therefore, sensitivity, resolution, and accuracy of melting curve analyses are improved...
  34. ncbi request reprint The recognition of methylated DNA by the GTP-dependent restriction endonuclease McrBC resides in the N-terminal domain of McrB
    F U Gast
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Germany
    Biol Chem 378:975-82. 1997
    ..vi) Mutations in McrB which lead to a reduction in GTP binding and/or hydrolysis can affect DNA binding, suggesting that the two activities are coupled in the full-length protein...
  35. pmc Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases
    Ines Fonfara
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392, Giessen, Germany
    Nucleic Acids Res 40:847-60. 2012
    ....
  36. pmc A novel zinc-finger nuclease platform with a sequence-specific cleavage module
    Benno Schierling
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 40:2623-38. 2012
    ..These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs...
  37. ncbi request reprint Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops
    P Friedhoff
    , , D-35392 Giessen, Germany
    J Biol Chem 276:23581-8. 2001
    ..We suggest that the dimeric form of Sau3AI supplies two DNA-binding sites, one that is associated with the catalytic center and one that serves as an effector site...
  38. ncbi request reprint SoFAR: software for fully automatic evaluation of real-time PCR data
    Jochen Wilhelm
    Justus Liebig Universitat Giessen, Giessen, Germany
    Biotechniques 34:324-32. 2003
    ..The SoFAR software minimizes the time required for evaluation and increases the accuracy and reliability of the results. The software is available upon request...
  39. ncbi request reprint High-throughput purification of polyHis-tagged recombinant fusion proteins
    Thomas Lanio
    Justus Liebig Universitat, Institut fur Biochemie, Giessen, Germany
    Methods Mol Biol 205:199-203. 2003
  40. ncbi request reprint Haemophilus influenzae and Vibrio cholerae genes for mutH are able to fully complement a mutH defect in Escherichia coli
    Peter Friedhoff
    Institut für Biochemie FB 08, Justus Liebig Universitat, D 35392, Giessen, Germany
    FEMS Microbiol Lett 208:123-8. 2002
    ..coli MutL protein. These results allow to narrow down regions that are important for the interaction of MutH with MutL...
  41. pmc Real-time PCR-based method for the estimation of genome sizes
    Jochen Wilhelm
    Institut fur Biochemie, FB 08, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Nucleic Acids Res 31:e56. 2003
    ..The method was evaluated on three different eukaryotic species, Saccharomyces cerevisiae (12.1 Mb), Xiphophorus maculatus (550 Mb) and Homo sapiens sapiens (2.9 Gb), and found to be fast, highly accurate and reliable...
  42. pmc Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae
    Marika Midon
    Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
    Nucleic Acids Res 39:623-34. 2011
    ..Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays...
  43. ncbi request reprint Real-time polymerase chain reaction
    Jochen Wilhelm
    Institut fur Pathologie, Klinikum der Justus Liebig Universität Giessen, Langhansstrasse 10, 35392 Giessen, Germany
    Chembiochem 4:1120-8. 2003
    ..Finally, examples of applications of this extremely versatile technique are given that demonstrate the enormous impact of real-time PCR on life sciences and molecular medicine...
  44. ncbi request reprint Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction--amplified short tandem repeats during denaturing capillary electrophoresis
    M Hahn
    Department of Biochemistry, Justus Liebig University Giessen, Germany
    Electrophoresis 22:2691-700. 2001
    ..Therefore, in denaturing CE the coseparation of a defined allele ladder labelled with the same dye as the unknown sample fragments remains the method of choice for accurate genotyping...
  45. ncbi request reprint Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence
    V Pingoud
    Institut fur Biochemie, Fachbereich Biologie, Justus Liebig Universitat, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    J Biol Chem 274:10235-43. 1999
    ..This result further supports the finding that at least one His residue is in close contact to the DNA. Based on these and published results, conclusions are drawn regarding the DNA binding site of PI-SceI...
  46. ncbi request reprint Structural and functional analysis of the homing endonuclease PI-sceI by limited proteolytic cleavage and molecular cloning of partial digestion products
    V Pingoud
    Institut fur Biochemie, Fachbereich Biologie, Justus Liebig Universitat, Giessen, Germany
    Biochemistry 37:8233-43. 1998
    ..These results are discussed in light of the recently solved crystal structure of PI-SceI and used to refine a model for the mechanism of DNA binding and cleavage by PI-SceI...
  47. ncbi request reprint Biochemical characterization of Anabaena sp. strain PCC 7120 non-specific nuclease NucA and its inhibitor NuiA
    G Meiss
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Germany
    Eur J Biochem 251:924-34. 1998
    ..The interaction of NucA with NuiA was also investigated by CD spectroscopy and revealed no major conformational changes upon complex formation of the two proteins...
  48. ncbi request reprint Engineering novel restriction endonucleases: principles and applications
    A Jeltsch
    Institut fur Biochemie, Fachbereich Biologie, Justus Liebig Universitat, Giessen, Germany
    Trends Biotechnol 14:235-8. 1996
    ....
  49. ncbi request reprint The GTP-binding domain of McrB: more than just a variation on a common theme?
    U Pieper
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, Giessen, D 35392, Germany
    J Mol Biol 292:547-56. 1999
    ....
  50. ncbi request reprint HER-2/neu gene copy number quantified by real-time PCR: comparison of gene amplification, heterozygosity, and immunohistochemical status in breast cancer tissue
    Melanie Konigshoff
    Institut fur Biochemie, FB 08, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Clin Chem 49:219-29. 2003
    ....
  51. ncbi request reprint Immobilization of sugar-non-specific nucleases by utilizing the streptavidin--biotin interaction
    F U Gast
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35292 Giessen, Germany
    J Biotechnol 87:131-41. 2001
    ..These methods should be of general use for similar enzyme systems...
  52. pmc Identification of functionally relevant histidine residues in the apoptotic nuclease CAD
    G Meiss
    , , Heinrich-Buff-Ring 58, 35392 Giessen, Germany
    Nucleic Acids Res 29:3901-9. 2001
    ..On the basis of these results, possible roles for His127, His263, His304, His308 and His313 in DNA binding and cleavage are discussed for murine CAD...
  53. pmc TALE-PvuII fusion proteins--novel tools for gene targeting
    Mert Yanik
    Institute for Biochemistry, Justus Liebig University Giessen, Giessen, Germany
    PLoS ONE 8:e82539. 2013
    ..In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity. ..
  54. pmc The rotation-coupled sliding of EcoRV
    Jasmina Dikic
    Laboratoire Kastler Brossel, ENS, UPMC Paris6, CNRS UMR 8552, 24 rue Lhomond, 75005 Paris, France
    Nucleic Acids Res 40:4064-70. 2012
    ..The similarity of EcoRV to other type II REs and DNA binding proteins suggests that this type of motion could be widely preserved in other biological contexts...
  55. pmc Involvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD
    Christian Korn
    Institut fur Biochemie, Justus Liebig Universitat, Heinrich Buff Ring 58, 35392 Giessen, Germany
    Nucleic Acids Res 30:1325-32. 2002
    ..They did not show any significant deviation from the wild-type enzyme. Based on these and published data possible roles of the amino acid residues under investigation are discussed...
  56. ncbi request reprint Nucleic acid quantification by delta pH measurement
    F U Gast
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Heinrich Buff Ring 58, D 35392, Giessen, Germany
    J Biotechnol 88:107-17. 2001
    ....
  57. doi request reprint Controlling the DNA cleavage activity of light-inducible chimeric endonucleases by bidirectional photoactivation
    Benno Schierling
    Institute of Biochemistry, Justus Liebig University, Heinrich Buff Ring 58, D 35392 Giessen, Germany
    Bioconjug Chem 23:1105-9. 2012
    ..e., increased DNA cleavage activity was observed either in the dark state, with a compact folded LOV domain, or in the blue light photoexcitation state, when the LOV domain is partially unfolded. ..
  58. ncbi request reprint Detection and quantification of insertion/deletion variations by allele-specific real-time PCR: application for genotyping and chimerism analysis
    Jochen Wilhelm
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Germany
    Biol Chem 383:1423-33. 2002
    ..Our protocol is particularly useful for rapid, reliable and inexpensive genotyping and quantitative chimerism analysis without requiring expensive fluorophor dye labelled probes...
  59. ncbi request reprint Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII
    Aspasia Spyridaki
    Department of Biology, IMBB FORTH, University of Crete, PO Box 1527, Heraklion, GR 71110, Crete, Greece
    J Mol Biol 331:395-406. 2003
    ..These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases...
  60. pmc Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
    Isabelle Bonnet
    Laboratoire Kastler Brossel, ENS, UPMC Paris 6, CNRS UMR 8552, France
    Nucleic Acids Res 36:4118-27. 2008
    ..Our results substantiate that sliding alternates with hopping/jumping during the facilitated diffusion of EcoRV and, furthermore, set up a framework for the investigation of target site location by other DNA-binding proteins...
  61. ncbi request reprint A sliding restriction enzyme pauses
    Alfred Pingoud
    Structure 15:391-3. 2007
  62. ncbi request reprint The nuclease A inhibitor represents a new variation of the rare PR-1 fold
    Thomas W Kirby
    National Institute of Environmental Health Sciences, P O Box 12233, MD MR 01, Research Triangle Park, NC 27709, USA
    J Mol Biol 320:771-82. 2002
    ..This hypothesis is supported by data that show that when NuiA is bound to NucA significant changes in chemical shift occur in the extended loop between helices III and IV...
  63. pmc High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI
    Erik Werner
    Crystallography Group, Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, 13092 Berlin, Germany
    Nucleic Acids Res 30:3962-71. 2002
    ....
  64. ncbi request reprint Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena
    Mahua Ghosh
    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 280:27990-7. 2005
    ....
  65. pmc A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    Richard J Roberts
    New England Biolabs, Beverly, MA 01915, USA
    Nucleic Acids Res 31:1805-12. 2003
    ..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes...
  66. ncbi request reprint Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group
    Philipp Rathert
    Biochemistry Laboratory International University Bremen, School of Engineering and Science, Campus Ring 1, 28759 Bremen, Germany
    Chembiochem 8:202-7. 2007
    ..Irradiation of the inactivated enzyme with near-ultraviolet light (320-400 nm) restored 60 % of the catalytic activity. This indicates that caging by DMNBB can be used for the reversible inactivation of M.SssI...