Dynamics of Eukaryotic Junction-Resolving Enzyme GEN1 - DNA Junction Interactions

Research output

Research output per year 2016 2016 2017 2019 2022

• 24 Article
• 5 Review article
• 1 Editorial

Research output per year

Research output per year

Search results

• 2022

  Search and processing of Holliday junctions within long DNA by junction-resolving enzymes

  Kaczmarczyk, A. P., Déclais, A.-C., Newton, M. D., Boulton, S. J., Lilley, D. M. J. (Lead / Corresponding author) & Rueda, D. S. (Lead / Corresponding author), 7 Oct 2022, In: Nature Communications. 13, 13 p., 5921.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Holliday Junction 100%
  • Endonuclease 66%
  • Single-stranded DNA (ssDNA) 66%
  • Facilitated Diffusion 66%
  • Diffusion 66%
  12 Citations (Scopus)

  68 Downloads (Pure)
• 2021

  Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules

  Huang, L. (Lead / Corresponding author), Liao, X., Li, M., Wang, J., Peng, X., Wilson, T. J. & Lilley, D. M. J. (Lead / Corresponding author), 4 Jun 2021, In: Nucleic Acids Research. 49, 10, p. 5916-5924 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Structural Prediction 100%
  • Kink-turn 100%
  • RNA Species 100%
  • Structured RNA 100%
  • Prediction Rule 100%
  5 Citations (Scopus)

  83 Downloads (Pure)

• The potential versatility of RNA catalysis

  Wilson, T. J. & Lilley, D. (Lead / Corresponding author), 1 Sept 2021, In: Wiley Interdisciplinary Reviews: RNA. 12, 5, 12 p., e1651.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Riboswitch 100%
  • RNA Catalysis 100%
  • RNA 100%
  • RNA-based 66%
  • RNA Structure 66%
  26 Citations (Scopus)

  232 Downloads (Pure)
• 2020

  Human ANKLE1 is a nuclease specific for branched DNA

  Song, J., Freeman, A. D. J., Knebel, A., Gartner, A. & Lilley, D. M. J. (Lead / Corresponding author), 2 Oct 2020, In: Journal of Molecular Biology. 432, 21, p. 5825-5834 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nuclease 100%
  • Branched DNA 100%
  • ANKLE1 100%
  • Enzyme 66%
  • Branch Point 50%
  15 Citations (Scopus)

  118 Downloads (Pure)

• Structure and ligand binding of the ADP-binding domain of the NAD⁺ riboswitch

  Huang, L., Wang, J. & Lilley, D. M. J. (Lead / Corresponding author), Jul 2020, In: RNA: a Publication of the RNA Society. 26, 7, p. 878-887 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Ligand-binding Domain 100%
  • Ligand Binding 100%
  • Nicotinamide Adenine Dinucleotide (NAD+) 100%
  • Riboswitch 100%
  • Adenosine Diphosphate 100%
  25 Citations (Scopus)

  102 Downloads (Pure)
• 2019

  Classification of the nucleolytic ribozymes based upon catalytic mechanism

  Lilley, D. M. J. (Lead / Corresponding author), 19 Aug 2019, In: F1000Research. 8, 10 p., 1462.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Catalytic Mechanism 100%
  • Ribozyme 100%
  • Nucleolytic Ribozymes 100%
  • Nucleobase 100%
  • Hydroxyl Group 100%
  34 Citations (Scopus)

  170 Downloads (Pure)

• Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

  Wilson, T. J., Liu, Y., Li, N.-S., Dai, Q., Piccirilli, J. A. & Lilley, D. M. J. (Lead / Corresponding author), 15 May 2019, In: Journal of the American Chemical Society. 141, 19, p. 7865-7875 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Hammerhead Ribozyme 100%
  • Pistol Ribozyme 100%
  • Similarities 100%
  • Dimensional Structure 100%
  • Active Site 100%
  46 Citations (Scopus)

  195 Downloads (Pure)

• Effect of methylation of adenine N6 on kink turn structure depends on location

  Ashraf, S., Huang, L. & Lilley, D. (Lead / Corresponding author), 2019, In: RNA Biology. 16, 10, p. 1377-1385 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Protein Binding 100%
  • Methylation 100%
  • Kink-turn 100%
  • Turn Structure 100%
  • Adenine 100%
  8 Citations (Scopus)

  156 Downloads (Pure)

• Junction resolving enzymes use multivalency to keep the Holliday junction dynamic

  Zhou, R. (Lead / Corresponding author), Yang, O., Declais, A.-C., Jin, H., Gwon, G. H., Freeman, A., Cho, Y., Lilley, D. & Ha, T. (Lead / Corresponding author), 1 Mar 2019, In: Nature Chemical Biology. 15, 3, p. 269-275 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Holliday Junction 100%
  • Multivalency 100%
  • Junction Dynamics 100%
  • Enzyme 100%
  • Conformational Isomer 100%
  23 Citations (Scopus)

  185 Downloads (Pure)

• Structure-guided design of a high affinity ligand for a riboswitch

  Huang, L., Wang, J., Wilson, T. & Lilley, D. (Lead / Corresponding author), Apr 2019, In: RNA: a Publication of the RNA Society. 25, 4, p. 423-430 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Structure-based Design 100%
  • Riboswitch 100%
  • High-affinity Ligands 100%
  • Guanidine 60%
  • Binding Pocket 40%
  10 Citations (Scopus)

  221 Downloads (Pure)

• The role of RNA structure in translational regulation by L7Ae protein in archaea

  Huang, L., Ashraf, S. & Lilley, D. M. J. (Lead / Corresponding author), Jan 2019, In: RNA: a Publication of the RNA Society. 25, 1, p. 60-69 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • RNA 100%
  • Translational Regulation 100%
  • RNA Structure 100%
  • Archaeon 100%
  • L7Ae 100%
  10 Citations (Scopus)

  205 Downloads (Pure)
• 2018

  A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1

  Liu, Y., Freeman, A. D. J., Déclais, A.-C. & Lilley, D. M. J. (Lead / Corresponding author), 16 Nov 2018, In: Nucleic Acids Research. 46, 20, p. 11089-11098 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Substrate Specificity 100%
  • Na + 100%
  • Active Sites 100%
  • Cs + 100%
  • DNA Binding 100%
  7 Citations (Scopus)

  188 Downloads (Pure)

• Structure and ligand binding of the SAM-V riboswitch

  Huang, L. & Lilley, D. M. J. (Lead / Corresponding author), 27 Jul 2018, In: Nucleic Acids Research. 46, 13, p. 6869-6879 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Ligand Binding 100%
  • Riboswitch 100%
  • Triple Helix 66%
  • Binding Site 66%
  • Helix 33%
  35 Citations (Scopus)

  190 Downloads (Pure)
• 2017

  Control of box C/D snoRNP assembly by N⁶-methylation of adenine

  Huang, L., Ashraf, S., Wang, J. & Lilley, D. M. J. (Lead / Corresponding author), 1 Sept 2017, In: EMBO Reports. 18, 9, p. 1473-1671 15 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Methylation 100%
  • SnoRNP 100%
  • Adenine 100%
  • RNA 75%
  • 3-methyladenine (3-MA) 50%
  40 Citations (Scopus)

  241 Downloads (Pure)

• Crystal structures of cyanine fluorophores stacked onto the end of double-stranded RNA

  Liu, Y. & Lilley, D. M. J. (Lead / Corresponding author), 5 Dec 2017, In: Biophysical Journal. 113, 11, p. 2236-2343 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Double-stranded RNA 100%
  • Fluorophore 100%
  • Cyanine Fluorophores 100%
  • Nuclear Magnetic Resonance Spectroscopy 100%
  • Nuclear Magnetic Resonance 100%
  8 Citations (Scopus)

  235 Downloads (Pure)

• Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations

  Füchtbauer, A. F., Preus, S., Börjesson, K., McPhee, S. A., Lilley, D. M. J. & Wilhelmsson, L. M. (Lead / Corresponding author), 24 May 2017, In: Scientific Reports. 7, p. 1-8 8 p., 2393.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • RNA Duplex 100%
  • Cytosine Analogs 100%
  • Detailed Dynamics 100%
  • Detailed Structure 100%
  • Structure Investigation 100%
  20 Citations (Scopus)

  214 Downloads (Pure)

• Holliday junction-resolving enzymes - structures and mechanisms

  Lilley, D. M. J. (Lead / Corresponding author), Apr 2017, In: FEBS Letters. 591, 8, p. 1073-1082 10 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Enzyme Mechanism 100%
  • Holliday Junction 100%
  • Enzyme Structure 100%
  • Enzyme 100%
  • Crystal Structure 100%
  23 Citations (Scopus)

  341 Downloads (Pure)

• How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes

  Lilley, D. M. J. (Lead / Corresponding author), 15 Jun 2017, In: Biochemical Society Transactions. 45, 3, p. 683-691 9 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • Nuclease 100%
  • Nucleolytic Ribozymes 100%
  • RNA 100%
  • Ribozyme 100%
  • Mechanistic Study 100%
  31 Citations (Scopus)

  1015 Downloads (Pure)

• Sequence determinants of the folding properties of box C/D kink-turns in RNA

  Ashraf, S., Huang, L. & Lilley, D. M. J. (Lead / Corresponding author), Dec 2017, In: RNA: a Publication of the RNA Society. 23, 12, p. 1927-1935 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Metal Ions 100%
  • Kink-turn 100%
  • RNA 100%
  • Conformation 100%
  • Biological Functions 100%
  7 Citations (Scopus)

  184 Downloads (Pure)

• The Guanidine Riboswitch-A Poor Orphan No Longer

  Lilley, D. M. J. (Lead / Corresponding author), 16 Feb 2017, In: Cell Chemical Biology. 24, 2, p. 130-131 2 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Riboswitch 100%
  • Guanidine 100%
  • Gene Expression 50%
  • Small Molecules 50%
  • Small Ions 50%
  2 Citations (Scopus)

• The structure of a nucleolytic ribozyme that employs a catalytic metal ion

  Liu, Y., Wilson, T. & Lilley, D. (Lead / Corresponding author), May 2017, In: Nature Chemical Biology. 13, 5, p. 508-513 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Ribozyme 100%
  • Nucleolytic Ribozymes 100%
  • Catalytic Metal Ions 100%
  • Divalent Metal Ions 75%
  • Phosphate 50%
  48 Citations (Scopus)

  367 Downloads (Pure)

• The structure of the Guanidine-III Riboswitch

  Huang, L., Wang, J., Wilson, T. J. & Lilley, D. M. J. (Lead / Corresponding author), 16 Nov 2017, In: Cell Chemical Biology. 24, 11, p. 1407-1415.e2 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Riboswitch 100%
  • Guanidine 100%
  • Nucleobases 50%
  • Nucleobase 50%
  • Nucleic Acid Base 40%
  40 Citations (Scopus)

  235 Downloads (Pure)

• The Structure of the Guanidine-II Riboswitch

  Huang, L., Wang, J. & Lilley, D. M. J. (Lead / Corresponding author), 22 Jun 2017, In: Cell Chemical Biology. 24, 6, p. 695-702.e2 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Riboswitch 100%
  • Guanidine 100%
  • Stem-loop 75%
  • Stem-Loop 75%
  • Guanine 50%
  56 Citations (Scopus)

  227 Downloads (Pure)
• 2016

  A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function

  Huang, L., Wang, J. & Lilley, D. M. J. (Lead / Corresponding author), 20 Jun 2016, In: Nucleic Acids Research. 44, 11, p. 5390-5398 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Biological Function 100%
  • Critical Base 100%
  • Conformation 100%
  • Biological Functions 100%
  • RNA 66%
  17 Citations (Scopus)

  367 Downloads (Pure)

• Analysis of the Intrinsically Disordered N-Terminus of the DNA Junction-Resolving Enzyme T7 Endonuclease I: Identification of Structure Formed upon DNA Binding

  Freeman, A. D. J., Stevens, M., Declais, A. C., Leahy, A., Mackay, K., El Mkami, H., Lilley, D. M. J. & Norman, D. G. (Lead / Corresponding author), 2 Aug 2016, In: Biochemistry. 55, 30, p. 4166-4172 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • N-terminus 100%
  • DNA Binding 100%
  • T7 Exonuclease 100%
  • DNA Junctions 100%
  • Intrinsically Disordered 100%
  3 Citations (Scopus)

  210 Downloads (Pure)

• A quasi-cyclic RNA nano-scale molecular object constructed using kink turns

  Huang, L. & Lilley, D. M. J. (Lead / Corresponding author), 7 Sept 2016, In: Nanoscale. 8, 33, p. 15189-15195 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Tertiary Interaction 100%
  • Kink-turn 100%
  • Crystal Lattice 100%
  • Cyclic RNA 100%
  • Quasi-cyclic 100%
  14 Citations (Scopus)

  206 Downloads (Pure)

• Editorial overview: Nucleic acids and their protein complexes

  Lilley, D. M. J. (Lead / Corresponding author) & Pyle, A. M. (Lead / Corresponding author), 2016, In: Current Opinion in Structural Biology. 36, p. vii-viii 2 p.

  Research output: Contribution to journal › Editorial › peer-review
  1 Citation (Scopus)

• The Kink Turn, a Key Architectural Element in RNA Structure

  Huang, L. & Lilley, D. M. J. (Lead / Corresponding author), 27 Feb 2016, In: Journal of Molecular Biology. 428, 5, p. 790-801 12 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  File

  • RNA Structure 100%
  • Kink-turn 100%
  • Architectural Elements 100%
  • RNA 100%
  • Hydrogen Bond 100%
  42 Citations (Scopus)

  153 Downloads (Pure)

• The Novel Chemical Mechanism of the Twister Ribozyme

  Wilson, T. J., Liu, Y., Domnick, C., Kath-Schorr, S. & Lilley, D. M. J. (Lead / Corresponding author), 18 May 2016, In: Journal of the American Chemical Society. 138, 19, p. 6151-6162 12 p.

  Research output: Contribution to journal › Article › peer-review

  • Phosphate 100%
  • Novel Chemicals 100%
  • Chemical Mechanism 100%
  • Twister Ribozyme 100%
  • Nitrogen Atom 100%
  62 Citations (Scopus)

• The solution structural ensembles of RNA kink-turn motifs and their protein complexes

  Shi, X. (Lead / Corresponding author), Huang, L., Lilley, D. M. J., Harbury, P. B. (Lead / Corresponding author) & Herschlag, D. (Lead / Corresponding author), Mar 2016, In: Nature Chemical Biology. 12, 3, p. 146-152 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Protein Complex 100%
  • Kink-turn 100%
  • Structural Ensembles 100%
  • Solution and Solubility 100%
  • RNA 100%
  33 Citations (Scopus)

  216 Downloads (Pure)