David M J Lilley

Summary

Affiliation: University of Dundee
Country: UK

Publications

  1. pmc Ion-induced folding of a kink turn that departs from the conventional sequence
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Nucleic Acids Res 37:7281-9. 2009
  2. pmc RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Structure 19:1233-40. 2011
  3. pmc The functional exchangeability of pk- and k-turns in RNA structure
    Peter Daldrop
    Cancer Research UK Nucleic Acid Structure Research Group MSI WTB Complex The University of Dundee Dundee, UK
    RNA Biol 10:445-52. 2013
  4. doi request reprint The structure and folding of kink turns in RNA
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
    Wiley Interdiscip Rev RNA 3:797-805. 2012
  5. pmc The chemical origins of life and its early evolution: an introduction
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Philos Trans R Soc Lond B Biol Sci 366:2853-6. 2011
  6. pmc Mechanisms of RNA catalysis
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, MSI WTB complex, Dow Street, Dundee DD1 5EH, UK
    Philos Trans R Soc Lond B Biol Sci 366:2910-7. 2011
  7. ncbi request reprint Structure, folding and mechanisms of ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
    Curr Opin Struct Biol 15:313-23. 2005
  8. doi request reprint Analysis of branched nucleic acid structure using comparative gel electrophoresis
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee, UK
    Q Rev Biophys 41:1-39. 2008
  9. ncbi request reprint A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
    Biol Chem 388:699-704. 2007
  10. doi request reprint The interaction of four-way DNA junctions with resolving enzymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Biochem Soc Trans 38:399-403. 2010

Collaborators

  • Nan Sheng Li
  • John Rouse
  • Taekjip Ha
  • Shinya Harusawa
  • Anton Gartner
  • Jia Wang
  • Jun Lu
  • Joseph A Piccirilli
  • Benoit Masquida
  • Luis Sanchez-Pulido
  • Kay Hofmann
  • Chris P Ponting
  • Lihua Wang
  • Roland Kanaar
  • Stephen C West
  • Thomas Helleday
  • KLAUS J SCHULTEN
  • Xulong Zhang
  • Timothy J Wilson
  • Anne Cécile Déclais
  • Kersten T Schroeder
  • David G Norman
  • Alasdair D J Freeman
  • Jonathan Ouellet
  • Jia Liu
  • Peter Daldrop
  • Asif Iqbal
  • Daniel A Lafontaine
  • Sean A McKinney
  • Sungchul Hohng
  • Jonathan M Hadden
  • Ben Turner
  • Scott A McPhee
  • Zheng yun Zhao
  • Michelle K Nahas
  • Terry A Goody
  • Sonya E Melcher
  • Lisa Araki
  • Lin Huang
  • Tomás Fessl
  • Dennis Castor
  • Burak Okumus
  • Aileen C McLeod
  • Stephanie Kath-Schorr
  • J Carlos Penedo
  • Linas Urnavicius
  • Thomas J MacArtney
  • Simon E V Phillips
  • Rachel Toth
  • Craig MacKay
  • Aymeric P Bailly
  • Elliot Tan
  • Ivan M Munoz
  • Jean François Lemay
  • Takushi Kurihara
  • Chirlmin Joo
  • Robert M Clegg
  • Jonathan M Fogg
  • Christian Hammann
  • Mamuka Kvaratskhelia
  • Christophe Lachaud
  • Nidhi Nair
  • J Simon C Arthur
  • Stephanie Schorr
  • Hassane El Mkami
  • Richard Ward
  • Alasdair Freeman
  • Andrew J Deans
  • Shawn Ahmed
  • Ana Agostinho
  • Cecilia Lundin
  • Julie Hall
  • John K Frederiksen
  • Sonya Melcher
  • Arno Alpi
  • Yiliang Ding
  • Karolina Hain
  • Johannes M Heuckmann
  • Mary Gardiner
  • Geraldine W Toh
  • Berina Eppink
  • Max Byrne
  • Thomas MacArtney
  • Gerard Giraud
  • Sinan Arslan
  • Katherine C Thompson
  • Ruobo Zhou
  • Stephen B Carr
  • Michelle Nahas
  • Jin Yu

Detail Information

Publications75

  1. pmc Ion-induced folding of a kink turn that departs from the conventional sequence
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Nucleic Acids Res 37:7281-9. 2009
    ....
  2. pmc RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Structure 19:1233-40. 2011
    ..This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure...
  3. pmc The functional exchangeability of pk- and k-turns in RNA structure
    Peter Daldrop
    Cancer Research UK Nucleic Acid Structure Research Group MSI WTB Complex The University of Dundee Dundee, UK
    RNA Biol 10:445-52. 2013
    ..Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. ..
  4. doi request reprint The structure and folding of kink turns in RNA
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
    Wiley Interdiscip Rev RNA 3:797-805. 2012
    ..We can identify two classes of k-turns, that differ in the manner of the hydrogen bonding at the adenine of the bulge-distal G•A pair...
  5. pmc The chemical origins of life and its early evolution: an introduction
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Philos Trans R Soc Lond B Biol Sci 366:2853-6. 2011
    ..Ultimately, the RNA world would probably have given way to protein-based life quite quickly, and the origins of peptidyl transferase activity are discussed below...
  6. pmc Mechanisms of RNA catalysis
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, MSI WTB complex, Dow Street, Dundee DD1 5EH, UK
    Philos Trans R Soc Lond B Biol Sci 366:2910-7. 2011
    ..Guanine nucleobases appear to be a common choice of general base, but the general acid is more variable. By contrast, the larger ribozymes such as the self-splicing introns and RNase P act as metalloenzymes...
  7. ncbi request reprint Structure, folding and mechanisms of ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee DD1 5EH, UK
    Curr Opin Struct Biol 15:313-23. 2005
    ..Lastly, important new folding-enhancing elements have been discovered...
  8. doi request reprint Analysis of branched nucleic acid structure using comparative gel electrophoresis
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, University of Dundee, Dundee, UK
    Q Rev Biophys 41:1-39. 2008
    ..Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes...
  9. ncbi request reprint A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
    Biol Chem 388:699-704. 2007
    ..The dependence of the hairpin ribozyme reaction rates on pH has been studied. Both cleavage and ligation reactions display a bell-shaped pH dependence, consistent with general acid-base catalysis involving the nucleotide at position 8...
  10. doi request reprint The interaction of four-way DNA junctions with resolving enzymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Biochem Soc Trans 38:399-403. 2010
    ..Recent success in obtaining X-ray crystal structures of resolving enzymes bound to DNA junctions has revealed how the structural selectivity of these enzymes is achieved...
  11. doi request reprint Catalysis by the nucleolytic ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Biochem Soc Trans 39:641-6. 2011
    ..The hairpin ribozyme is probably closely similar, while the remaining nucleolytic ribozymes provide some interesting contrasts...
  12. pmc The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA
    Jia Liu
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, UK
    RNA 13:200-10. 2007
    ..These interactions are generally more polymorphic, and hydrogen bonds probably form where possible, as permitted by the global structure...
  13. ncbi request reprint Folding and catalysis by the VS ribozyme
    Daniel A Lafontaine
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, UK
    Biochimie 84:889-96. 2002
    ..The A730 loop is the probable active site of the ribozyme, and A756 within it is a strong candidate to play a direct role in the transesterification chemistry, possibly by general acid-base catalysis...
  14. doi request reprint The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA
    Ben Turner
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    J Mol Biol 381:431-42. 2008
    ..However, in all such cases the affinity is lowered, and the results underline the importance of both G.A pairs to the stability of the K-turn...
  15. pmc A guanine nucleobase important for catalysis by the VS ribozyme
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, UK
    EMBO J 26:2489-500. 2007
    ..This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution...
  16. pmc Nucleobase catalysis in the hairpin ribozyme
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee
    RNA 12:980-7. 2006
    ..7 +/- 0.1 and 7.7 +/- 0.1 for cleavage and 6.1 +/- 0.3 and 6.9 +/- 0.3 for ligation. The data provide good evidence for general acid-base catalysis by the nucleobases...
  17. ncbi request reprint Structural recognition between a four-way DNA junction and a resolving enzyme
    Anne Cécile Déclais
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee
    J Mol Biol 359:1261-76. 2006
    ..Our data show that the form of the complex between endonuclease I and a DNA junction depends on the core of the junction and on interactions with the first six base-pairs of the arms containing the 5' ends of the continuous strands...
  18. ncbi request reprint Functional group requirements in the probable active site of the VS ribozyme
    Daniel A Lafontaine
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, University of Dundee, Dundee, DD1 5EH, UK
    J Mol Biol 323:23-34. 2002
    ..However, no restoration was obtained with exogenous adenine base either, indicating that the cavity that might result from ablation of the base was closed...
  19. pmc The structure of sulfoindocarbocyanine 3 terminally attached to dsDNA via a long, flexible tether
    Linas Urnavicius
    Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
    Biophys J 102:561-8. 2012
    ..This result is in close agreement with our FRET data, supporting the contention that FRET data can be used to provide orientational information...
  20. pmc Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
    Timothy J Wilson
    Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
    Proc Natl Acad Sci U S A 107:11751-6. 2010
    ..We conclude that cleavage of the substrate by the VS ribozyme is catalyzed by deprotonation of the 2'-O nucleophile by G638 and protonation of the 5'-O leaving group by A756...
  21. pmc Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids
    Asif Iqbal
    Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    Proc Natl Acad Sci U S A 105:11176-81. 2008
    ..Our data unequivocally establish that Förster transfer obeys the orientation dependence as expected for a dipole-dipole interaction...
  22. pmc The complex between a four-way DNA junction and T7 endonuclease I
    Anne Cécile Déclais
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    EMBO J 22:1398-409. 2003
    ..This shows how the enzyme is selective for the structure of a four-way junction, such that both continuous strands can be accommodated into the two active sites so that a productive resolution event is possible...
  23. ncbi request reprint Metal ion binding in the active site of the junction-resolving enzyme T7 endonuclease I in the presence and in the absence of DNA
    Alasdair D J Freeman
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    J Mol Biol 333:59-73. 2003
    ..Calorimetry points to particularly critical role of Asp55, as mutation completely abolishes all binding of both manganese and calcium ions...
  24. ncbi request reprint Folding and activity of the hammerhead ribozyme
    Christian Hammann
    Department of Biochemistry, MSI WTB complex, Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, Scotland UK
    Chembiochem 3:690-700. 2002
    ..The 10(5)-fold rate enhancement is probably brought about by a combination of metal-ion participation and stereochemical factors in the environment of the folded RNA structure...
  25. pmc Cooperative control of holliday junction resolution and DNA repair by the SLX1 and MUS81-EME1 nucleases
    Dennis Castor
    MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
    Mol Cell 52:221-33. 2013
    ..These findings shed light on HJ resolution in mammals and on maintenance of genome stability. ..
  26. pmc Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers
    Jonathan Ouellet
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
    Biophys J 101:1148-54. 2011
    ..This is consistent with the transition moments becoming approximately aligned with the long axis of the terminal basepair for the long-linker species...
  27. doi request reprint The importance of the N-terminus of T7 endonuclease I in the interaction with DNA junctions
    Alasdair D J Freeman
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    J Mol Biol 425:395-410. 2013
    ..In the absence of this, we find that a cruciform junction is no longer subject to bilateral cleavage, but instead, just one strand is cleaved. Thus, the N-terminus is required for a productive resolution of the junction...
  28. ncbi request reprint Stereospecific effects determine the structure of a four-way DNA junction
    Jia Liu
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    Chem Biol 12:217-28. 2005
    ..It is likely that the stereochemical environment of the methyl group affects the interaction with metal ions in the center of the junction...
  29. pmc Structure and folding of a rare, natural kink turn in RNA with an A*A pair at the 2b*2n position
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    RNA 18:1257-66. 2012
    ..The 2b and 2n adenine nucleobases are not directly hydrogen bonded, but each makes hydrogen bonds to their opposing strands...
  30. ncbi request reprint RNA folding and the origins of catalytic activity in the hairpin ribozyme
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Blood Cells Mol Dis 38:8-14. 2007
    ..We observe significant rates of cleavage and ligation, and a bell-shaped pH dependence for both...
  31. pmc Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein
    Jia Wang
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
    Biophys J 103:2541-8. 2012
    ..The data support a passive conformational selection model by which the protein selects a fraction of RNA that is already in the kinked conformation, thereby drawing the equilibrium into this form...
  32. pmc Induced fit of RNA on binding the L7Ae protein to the kink-turn motif
    Ben Turner
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    RNA 11:1192-200. 2005
    ..Thus this RNA may act as a relatively flexible hinge during RNA folding, until fixed into its ultimate kinked structure by the binding of L7 or related protein...
  33. doi request reprint Analysis of conformational changes in the DNA junction-resolving enzyme T7 endonuclease I on binding a four-way junction using EPR
    Alasdair D J Freeman
    Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Biochemistry 50:9963-72. 2011
    ..These studies reveal that structural changes in both DNA and protein occur in the action of this junction-resolving enzyme...
  34. pmc The Varkud satellite ribozyme
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK
    RNA 10:151-8. 2004
    ..NAIM experiments indicate that a protonated base is required at this position for the ligation reaction. A756 is thus a strong candidate for nucleobase participation in the catalytic chemistry...
  35. pmc Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD15EH, United Kingdom
    RNA 17:213-21. 2011
    ..It appears that the two ribozymes are mechanistically equivalent...
  36. ncbi request reprint Nucleobase participation in ribozyme catalysis
    Zheng yun Zhao
    CR UK Nucleic Acid Structure Research Group, MSI WTB complex, University of Dundee, Dundee DD1 5EH, UK
    J Am Chem Soc 127:5026-7. 2005
    ..The novel ribozyme is active in both cleavage and ligation reactions. The reaction is efficient, although relatively slow. The results are consistent with a role for nucleobase catalysis in the catalytic mechanism of this ribozyme...
  37. pmc Metal ion binding and the folding of the hairpin ribozyme
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee
    RNA 8:587-600. 2002
    ..This transition occurs in response to the noncooperative, site-specific binding of magnesium ions. We observe a good correlation between the extent of ion-induced folding and cleavage activity...
  38. pmc General acid-base catalysis mediated by nucleobases in the hairpin ribozyme
    Stephanie Kath-Schorr
    Cancer Research UK, Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    J Am Chem Soc 134:16717-24. 2012
    ....
  39. pmc The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment
    Peter Daldrop
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    RNA 19:357-64. 2013
    ..While it has the N1 structure in the ribosome, on engineering it into the SAM-I riboswitch, it changes to the N3 structure, resulting in a significant alteration in the trajectory of the helical arms...
  40. pmc Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes
    Jonathan Ouellet
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
    RNA 15:1822-6. 2009
    ..This regaining of cleavage activity by complementation indicates that helix I of one VS RNA can interact with another VS RNA molecule to generate a functional active site in trans...
  41. ncbi request reprint Efficient, pH-dependent RNA ligation by the VS ribozyme in trans
    Aileen C McLeod
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, UK
    Biochemistry 43:1118-25. 2004
    ..05 min(-1)) and the cleavage reaction in its protonated state (rate 0.18 min(-1)). A756 is a candidate for the nucleobase undergoing protonation/deprotonation...
  42. pmc Structure of the three-way helical junction of the hepatitis C virus IRES element
    Jonathan Ouellet
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    RNA 16:1597-609. 2010
    ..Moreover, analysis of single-molecule FRET data at an 8-msec resolution failed to reveal evidence for structural transitions. It seems probable that this junction adopts a single conformation as a unique and stable fold...
  43. pmc The kink-turn motif in RNA is dimorphic, and metal ion-dependent
    Terry A Goody
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK
    RNA 10:254-64. 2004
    ..The K-turn is therefore unlikely to be of itself a primary organizing feature in RNA...
  44. ncbi request reprint The origins of RNA catalysis in ribozymes
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, MSI WTB complex, The University of Dundee, Dundee, UK, DD1 5EH
    Trends Biochem Sci 28:495-501. 2003
    ..The main players are the RNA nucleobases and bound metal ions. Although most ribozymes carry out phosphoryl transfer, the same considerations appear to apply to peptidyl transfer in the ribosome...
  45. ncbi request reprint Mechanistic aspects of the DNA junction-resolving enzyme T7 endonuclease I
    Jia Liu
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Biochemistry 45:3934-42. 2006
    ..A mechanism of hydrolysis consistent with all of these data is proposed...
  46. pmc Structure of a rare non-standard sequence k-turn bound by L7Ae protein
    Lin Huang
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Nucleic Acids Res 42:4734-40. 2014
    ..This potentially can affect any tertiary interactions in which the RNA participates. ..
  47. pmc Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2
    Craig MacKay
    MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
    Cell 142:65-76. 2010
    ..Depletion of FAN1 from human cells causes hypersensitivity to ICLs, defects in ICL repair, and genome instability. These data at least partly explain how ubiquitination of FANCD2 promotes DNA repair...
  48. pmc Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
    J Carlos Penedo
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
    RNA 10:880-8. 2004
    ..The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions...
  49. ncbi request reprint The chirality of a four-way helical junction in RNA
    Terry A Goody
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    J Am Chem Soc 126:4126-7. 2004
    ....
  50. ncbi request reprint Electrostatic interactions and the folding of the four-way DNA junction: analysis by selective methyl phosphonate substitution
    Jia Liu
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    J Mol Biol 343:851-64. 2004
    ....
  51. pmc The dynamic nature of the four-way junction of the hepatitis C virus IRES
    Sonya E Melcher
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    RNA 9:809-20. 2003
    ..These dynamic properties may be important in mediating interactions between the IRES and the ribosome and initiation factors...
  52. pmc A structural database for k-turn motifs in RNA
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee DD1 5EH, United Kingdom
    RNA 16:1463-8. 2010
    ..This site provides (1) a database of sequence and structure, as a resource for the RNA community, and (2) a tool to enable the manipulation and comparison of 3D structures where known...
  53. pmc Measurement of the change in twist at a helical junction in RNA using the orientation dependence of FRET
    Tomás Fessl
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, University of Dundee, Dundee, UK
    Biophys J 105:2175-81. 2013
    ..The data reveal a 29.5° overwinding and a small axial extension. This shows the power of this approach for measuring orientational information in biologically important RNA junctions. ..
  54. doi request reprint Comparative gel electrophoresis analysis of helical junctions in RNA
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, United Kingdom
    Methods Enzymol 469:143-57. 2009
    ..It has had a number of significant successes in RNA, DNA and DNA-protein complexes, and in all cases to date the results have stood the test of time and eventual comparison with crystallographic analysis...
  55. doi request reprint The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies
    Asif Iqbal
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, UK
    Biochemistry 47:7857-62. 2008
    ....
  56. ncbi request reprint Analysis of global conformational transitions in ribozymes
    David M J Lilley
    Department of Biochemistry, MIS WTB Complex, The University of Dundee, UK
    Methods Mol Biol 252:77-108. 2004
    ..The FRET approach can also be extended into the time domain to analyze conformational equilibria, and increasingly to the single-molecule level...
  57. doi request reprint A mechanistic comparison of the Varkud satellite and hairpin ribozymes
    Timothy J Wilson
    Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
    Prog Mol Biol Transl Sci 120:93-121. 2013
    ..As a class, the nucleolytic ribozymes all appear to use general acid-base catalysis; guanine nucleobases in particular are very common participants. ..
  58. pmc The k-junction motif in RNA structure
    Jia Wang
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
    Nucleic Acids Res 42:5322-31. 2014
    ..Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn. ..
  59. pmc The global structure of the VS ribozyme
    Daniel A Lafontaine
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI WTB complex, The University of Dundee, DD1 5EH, UK
    EMBO J 21:2461-71. 2002
    ..This is consistent with the dependence of activity on the length of helix III. The scissile phosphate is well placed to interact with the probable active site of the ribozyme, the loop containing A730...
  60. doi request reprint Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair
    Ivan M Munoz
    MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
    Mol Cell 35:116-27. 2009
    ..Depletion of SLX4 causes a decrease in DSB-induced homologous recombination. These data show that SLX4 is a regulator of structure-specific nucleases and that SLX4 and SLX1 are important regulators of genome stability in human cells...
  61. doi request reprint The structure and folding of branched RNA analyzed by fluorescence resonance energy transfer
    David M J Lilley
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee, United Kingdom
    Methods Enzymol 469:159-87. 2009
    ..In addition to the provision of distance information, recent studies have emphasized the orientation dependence of energy transfer...
  62. pmc The Caenorhabditis elegans homolog of Gen1/Yen1 resolvases links DNA damage signaling to DNA double-strand break repair
    Aymeric P Bailly
    Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    PLoS Genet 6:e1001025. 2010
    ..Our study suggests that GEN-1 might act as a dual function Holliday junction resolvase that may coordinate DNA damage signaling with a late step in DNA double-strand break repair...
  63. ncbi request reprint Ribozymes--a snip too far?
    David M J Lilley
    Nat Struct Biol 10:672-3. 2003
  64. ncbi request reprint Conformational flexibility of four-way junctions in RNA
    Sungchul Hohng
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 336:69-79. 2004
    ....
  65. ncbi request reprint Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy
    Chirlmin Joo
    Physics Department, University of Illinois, Urbana Champaign, Urbana, IL 61801, USA
    J Mol Biol 341:739-51. 2004
    ..This further supports the notion that electrostatic stabilization of the stacked structures dictates the interconversion rates between different structural forms...
  66. pmc Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic
    Burak Okumus
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois USA
    Biophys J 87:2798-806. 2004
    ..This strongly indicates that the observed heterogeneity in dynamic properties does not arise as an artifact of surface attachment, but is intrinsic to the nature of the molecules...
  67. ncbi request reprint Observation of internal cleavage and ligation reactions of a ribozyme
    Michelle K Nahas
    Physics Department, University of Illinois, Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Struct Mol Biol 11:1107-13. 2004
    ....
  68. pmc A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
    Elliot Tan
    Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 100:9308-13. 2003
    ..Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules...
  69. ncbi request reprint Folding of the adenine riboswitch
    Jean François Lemay
    Departement de Biologie, Faculte des Sciences, Universite de Sherbrooke, Quebec J1K 2R1, Canada
    Chem Biol 13:857-68. 2006
    ..Thus, riboswitch function should depend on the relative rates of ligand binding and the transcriptional process...
  70. ncbi request reprint Structural dynamics of individual Holliday junctions
    Sean A McKinney
    Physics Department, University of Illinois, Urbana Champaign, 61801, USA
    Nat Struct Biol 10:93-7. 2003
    ..This provides a mechanism whereby the sequence-dependent conformational bias could determine the extent of genetic exchange upon junction resolution...
  71. pmc Observing spontaneous branch migration of Holliday junctions one step at a time
    Sean A McKinney
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 102:5715-20. 2005
    ....
  72. ncbi request reprint Holliday junction resolution is modulated by archaeal chromatin components in vitro
    Mamuka Kvaratskhelia
    Centre for Biomolecular Science, University of Saint Andrews, North Haugh, Saint Andrews, KY16 9ST, United Kingdom
    J Biol Chem 277:2992-6. 2002
    ..Analysis of crystal packing interactions in the crystal structure of Hjc suggests a molecular basis for this autoinhibition. The wider implications of these findings for the quantitative study of DNA-protein interactions is discussed...
  73. ncbi request reprint The structural basis of Holliday junction resolution by T7 endonuclease I
    Jonathan M Hadden
    Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
    Nature 449:621-4. 2007
    ..These interactions effectively measure the relative orientations and positions of the arms of the junction, thereby ensuring that binding is selective for branched DNA that can achieve this geometry...
  74. pmc Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction
    Sungchul Hohng
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 318:279-83. 2007
    ..This method of mapping two-dimensional reaction landscapes at low forces is readily applicable to other nucleic acid systems and their interactions with proteins and enzymes...
  75. pmc Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I
    Jonathan M Hadden
    Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
    EMBO J 21:3505-15. 2002
    ..58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion...