D T Dryden

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. ncbi request reprint The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications
    D T Dryden
    Institute of Cell and Molecular Biology, University of Edinburgh, U K
    Biochemistry 36:1065-76. 1997
  2. doi request reprint The Orf18 gene product from conjugative transposon Tn916 is an ArdA antirestriction protein that inhibits type I DNA restriction-modification systems
    Dimitra Serfiotis-Mitsa
    School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    J Mol Biol 383:970-81. 2008
  3. pmc Strong physical constraints on sequence-specific target location by proteins on DNA molecules
    Henrik Flyvbjerg
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 34:2550-7. 2006
  4. pmc DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping
    Tsueu Ju Su
    School of Chemistry The King s Buildings The University of Edinburgh Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 33:3235-44. 2005
  5. pmc StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI
    S A Keatch
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 33:6540-6. 2005
  6. pmc The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
    Christopher K Kennaway
    Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK
    Nucleic Acids Res 37:762-70. 2009
  7. pmc Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
    Stephen A McMahon
    Centre for Biomolecular Science, The University, St Andrews KY16 9ST, UK
    Nucleic Acids Res 37:4887-97. 2009
  8. pmc Single-molecule imaging of Bacteroides fragilis AddAB reveals the highly processive translocation of a single motor helicase
    Marcel Reuter
    EastChem School of Chemistry and COSMIC, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JR, UK
    Nucleic Acids Res 38:3721-31. 2010
  9. pmc Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity
    Gareth A Roberts
    EaStCHEM School of Chemistry, University of Edinburgh, UK
    FEBS J 280:4903-14. 2013
  10. pmc Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations
    Gareth A Roberts
    EaStCHEM School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK and Division of Clinical Sciences, St George s, University of London, Cranmer Terrace, London, SW17 0RE, UK
    Nucleic Acids Res 41:7472-84. 2013

Collaborators

Detail Information

Publications39

  1. ncbi request reprint The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications
    D T Dryden
    Institute of Cell and Molecular Biology, University of Edinburgh, U K
    Biochemistry 36:1065-76. 1997
    ....
  2. doi request reprint The Orf18 gene product from conjugative transposon Tn916 is an ArdA antirestriction protein that inhibits type I DNA restriction-modification systems
    Dimitra Serfiotis-Mitsa
    School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    J Mol Biol 383:970-81. 2008
    ..Our results suggest that ArdA can overcome the restriction barrier following conjugation and so helps increase the spread of antibiotic resistance genes by horizontal gene transfer...
  3. pmc Strong physical constraints on sequence-specific target location by proteins on DNA molecules
    Henrik Flyvbjerg
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 34:2550-7. 2006
    ..This effectively rules out any significant role in target location for mechanisms invoking one-dimensional, linear diffusion along DNA...
  4. pmc DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping
    Tsueu Ju Su
    School of Chemistry The King s Buildings The University of Edinburgh Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 33:3235-44. 2005
    ..This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine the methylation status of two adenine bases separated by a considerable distance in double-stranded DNA and select the required enzymatic response...
  5. pmc StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI
    S A Keatch
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 33:6540-6. 2005
    ..This supports a role for nucleoid-associated proteins in restriction alleviation during times of cell stress...
  6. pmc The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
    Christopher K Kennaway
    Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK
    Nucleic Acids Res 37:762-70. 2009
    ..EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years...
  7. pmc Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
    Stephen A McMahon
    Centre for Biomolecular Science, The University, St Andrews KY16 9ST, UK
    Nucleic Acids Res 37:4887-97. 2009
    ....
  8. pmc Single-molecule imaging of Bacteroides fragilis AddAB reveals the highly processive translocation of a single motor helicase
    Marcel Reuter
    EastChem School of Chemistry and COSMIC, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JR, UK
    Nucleic Acids Res 38:3721-31. 2010
    ..These results demonstrate the importance of processivity for facilitating encounters with recognition sequences that modify enzyme function during homologous recombination...
  9. pmc Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity
    Gareth A Roberts
    EaStCHEM School of Chemistry, University of Edinburgh, UK
    FEBS J 280:4903-14. 2013
    ....
  10. pmc Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations
    Gareth A Roberts
    EaStCHEM School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK and Division of Clinical Sciences, St George s, University of London, Cranmer Terrace, London, SW17 0RE, UK
    Nucleic Acids Res 41:7472-84. 2013
    ..We show that a lack of specific target sites enables plasmids to evade the Type I RM system thereby contributing to the evolution of increasingly resistant community and hospital MRSA. ..
  11. pmc Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats
    Long Ma
    EaStCHEM School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 41:4999-5009. 2013
    ....
  12. pmc Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA restriction and modification system produces a new type of system and links the different families of Type I systems
    Gareth A Roberts
    EaStCHEM School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 40:10916-24. 2012
    ..The fusion protein forms an evolutionary intermediate form lying between the Type IA family of RM enzymes and the Type IB family of RM enzymes which have the frameshift located at a different part of the gene sequence...
  13. pmc Exploring the DNA mimicry of the Ocr protein of phage T7
    Gareth A Roberts
    EaStCHEM School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JZ, UK
    Nucleic Acids Res 40:8129-43. 2012
    ....
  14. pmc An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme
    Gareth A Roberts
    University of Edinburgh, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 39:7667-76. 2011
    ..Lastly, we discuss whether turnover is an evolutionary requirement for restriction, show that the ATP hydrolysis is not deleterious to the host cell and discuss how foreign DNA occasionally becomes fully methylated by these systems...
  15. pmc Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification
    Augoustinos S Stephanou
    EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
    J Mol Biol 391:565-76. 2009
    ..Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to approximately 800-fold...
  16. pmc Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes
    Kai Chen
    School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JJ, UK
    Biochem Biophys Res Commun 398:254-9. 2010
    ..EcoKI enzyme. Distances determined from the energy transfer experiments corroborate the structural model of M.EcoKI...
  17. pmc How much of protein sequence space has been explored by life on Earth?
    David T F Dryden
    School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    J R Soc Interface 5:953-6. 2008
    ....
  18. ncbi request reprint DNA mimicry by proteins and the control of enzymatic activity on DNA
    David T F Dryden
    School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    Trends Biotechnol 24:378-82. 2006
    ..This review highlights the roles of DNA mimics in the control of DNA-binding proteins, suggests other possible candidate proteins using DNA mimicry, and puts forward a range of potential uses of DNA mimics...
  19. pmc DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements
    David T F Dryden
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 39:4525-31. 2011
    ..We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes...
  20. ncbi request reprint DNA mimicry by proteins
    D T F Dryden
    School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    Biochem Soc Trans 34:317-9. 2006
    ..The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins...
  21. pmc Nucleoside triphosphate-dependent restriction enzymes
    D T Dryden
    Department of Chemistry, University of Edinburgh, Joseph Black Building, The King s Buildings, Mayfield Road, Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 29:3728-41. 2001
    ..The only well-documented GTP-dependent restriction enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond cleavage...
  22. pmc Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7
    C Atanasiu
    Institute of Cell and Molecular Biology, The King's Buildings, University of Edinburgh, Edinburgh EH9 3JR, UK
    Nucleic Acids Res 29:3059-68. 2001
    ..This charge distribution may be complementary to the charge distribution within the DNA binding site of type I DNA restriction and modification enzymes...
  23. ncbi request reprint Shape of Ocr, the gene 0.3 protein of bacteriophage T7: modeling based on light scattering experiments
    J J Blackstock
    Department of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ, UK
    Biochemistry 40:9944-9. 2001
    ..4 nm by 2.6 nm. The size and shape predicted by this model are consistent with ocr acting as a mimic of the DNA structure bound by type Iota restriction enzymes...
  24. pmc Central modules of the vaccinia virus complement control protein are not in extensive contact
    M D Kirkitadze
    Edinburgh Centre for Protein Technology, Department of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, U K
    Biochem J 344:167-75. 1999
    ....
  25. ncbi request reprint DNA recognition by the methyl-CpG binding domain of MeCP2
    A Free
    Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
    J Biol Chem 276:3353-60. 2001
    ..The majority of missense mutations within the MBD found in the human genetic disorder Rett syndrome were shown or predicted to affect folding of the domain rather than the DNA recognition event directly...
  26. pmc Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence
    A Chen
    Institute of Cell and Molecular Biology, University of Edinburgh, UK
    Nucleic Acids Res 23:1177-83. 1995
    ..This suggests that tyrosine 27 may make a similar DNA contact in these other enzymes...
  27. ncbi request reprint Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7
    S S Sturrock
    Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland
    Acta Crystallogr D Biol Crystallogr 57:1652-4. 2001
    ..8 A. The presence of caesium was found to be required for good crystal growth. Anomalous X-ray data was used to identify possible positions for Se and Cs atoms in the unit cell...
  28. doi request reprint A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7
    Augoustinos S Stephanou
    EaStCHEM School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh EH9 3JJ, UK
    Biochem Biophys Res Commun 378:129-32. 2009
    ..Contrary to expectations, all of the single and double site mutations of ocr constructed were active as anti-R/M proteins in vivo and in vitro indicating that the mimicry of DNA by ocr is very resistant to change...
  29. pmc Alleviation of restriction by DNA condensation and non-specific DNA binding ligands
    Steven A Keatch
    School of Chemistry, The University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 32:5841-50. 2004
    ....
  30. pmc The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro
    Dimitra Serfiotis-Mitsa
    EaStCHEM School of Chemistry, University of Edinburgh, The King s Buildings, Edinburgh, EH9 3JJ, UK
    Nucleic Acids Res 38:1723-37. 2010
    ..We also present the structure determined by NMR spectroscopy of the pBP136 KlcA protein. The structure shows a novel protein fold and it is clearly not a DNA structural mimic...
  31. ncbi request reprint Assembly of EcoKI DNA methyltransferase requires the C-terminal region of the HsdM modification subunit
    Lynn M Powell
    Institute of Cell and Molecular Biology, The King s Buildings, University of Edinburgh, Edinburgh, Scotland EH9 3JR, UK
    Biophys Chem 103:129-37. 2003
    ..We conclude that the C-terminal region of the modification subunit of EcoKI is essential for the assembly of the EcoKI methyltransferase...
  32. pmc Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
    Robert K Neely
    School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
    Nucleic Acids Res 33:6953-60. 2005
    ..Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures...
  33. ncbi request reprint The biology of restriction and anti-restriction
    Mark R Tock
    School of Chemistry, The King s Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
    Curr Opin Microbiol 8:466-72. 2005
    ..Recently, there have been several studies that have shed light on the still developing field of restriction-modification and on the newly re-emerging field of anti-restriction...
  34. ncbi request reprint Reeling in the bases
    David T F Dryden
    Nat Struct Mol Biol 11:804-6. 2004
  35. ncbi request reprint Continuous assays for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases
    Sarah E McClelland
    DNA Protein Interactions Group, Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
    J Mol Biol 348:895-915. 2005
    ..Furthermore, we demonstrated that enzymes deficient in DNA cleavage but with maximal ATPase activity showed initiation and translocation rates identical to wild-type, confirming that DNA strand breaks are not a pre-requisite of motion...
  36. pmc Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies
    Ben Youngblood
    Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106 9510, USA
    Nucleic Acids Res 36:2917-25. 2008
    ..These results provide a plausible explanation of the way in which destabilization of reaction intermediates can lead to changes in substrate specificity...
  37. pmc DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes
    Neal Crampton
    Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, UK
    EMBO J 26:3815-25. 2007
    ..On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes...
  38. pmc Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping
    Neal Crampton
    Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
    Proc Natl Acad Sci U S A 104:12755-60. 2007
    ..On the basis of our results, we conclude that EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive DNA loop formation and ATPase-driven translocation of the intervening DNA contour...
  39. 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...