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. & Rueda, D. S., 7 Oct 2022, In: Nature Communications. 13, 13 p., 5921.

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

  Open Access

  File

  • Cruciform DNA 100%
  • Facilitated Diffusion 97%
  • enzymes 68%
  • deoxyribonucleic acid 58%
  • DNA 36%
  5 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., Liao, X., Li, M., Wang, J., Peng, X., Wilson, T. J. & Lilley, D. M. J., 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

  • Ions 100%
  • RNA 83%
  • X Ray Crystallography 82%
  • Fluorescence Resonance Energy Transfer 80%
  • Nucleic Acids 59%
  2 Citations (Scopus)

  32 Downloads (Pure)

• The potential versatility of RNA catalysis

  Wilson, T. J. & Lilley, D., 1 Sept 2021, In: Wiley Interdisciplinary Reviews: RNA. 12, 5, 12 p., e1651.

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

  Open Access

  File

  • RNA Structure 100%
  • Catalysis 88%
  • RNA 51%
  • Chemistry 43%
  • Phosphoryl 41%
  11 Citations (Scopus)

  72 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., 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

  • DNA 100%
  • Chromatids 90%
  • Chromosome Segregation 44%
  • Caenorhabditis elegans 39%
  • Enzymes 39%
  7 Citations (Scopus)

  47 Downloads (Pure)

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

  Huang, L., Wang, J. & Lilley, D. M. J., 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

  • Riboswitch 100%
  • NAD 66%
  • Adenosine Diphosphate 64%
  • Ligands 45%
  • Base Pairing 44%
  15 Citations (Scopus)

  46 Downloads (Pure)
• 2019

  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., 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

  • Catalytic RNA 100%
  • hammerhead ribozyme 82%
  • Nucleophile 22%
  • Conformations 18%
  • Acid 18%
  33 Citations (Scopus)

  138 Downloads (Pure)

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

  Ashraf, S., Huang, L. & Lilley, D., 2019, In: RNA Biology. 16, 10, p. 1377-1385 9 p.

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

  Open Access

  File

  • Adenine 100%
  • Base Pairing 86%
  • Protein Binding 84%
  • Methylation 76%
  • RNA Folding 65%
  6 Citations (Scopus)

  112 Downloads (Pure)

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

  Zhou, R., Yang, O., Declais, A-C., Jin, H., Gwon, G. H., Freeman, A., Cho, Y., Lilley, D. & Ha, T., 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

  • Cruciform DNA 100%
  • Enzymes 35%
  • Genetic Recombination 20%
  • Bacteriophage T7 15%
  • Fluorescence Resonance Energy Transfer 14%
  15 Citations (Scopus)

  111 Downloads (Pure)

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

  Huang, L., Wang, J., Wilson, T. & Lilley, D., 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

  • Riboswitch 100%
  • Guanidine 62%
  • Ligands 45%
  • diguanidine 36%
  • X-Rays 12%
  7 Citations (Scopus)

  151 Downloads (Pure)

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

  Huang, L., Ashraf, S. & Lilley, D. M. J., 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

  • Archaea 100%
  • Archaeoglobus fulgidus 72%
  • RNA 56%
  • Untranslated Regions 55%
  • Nucleic Acid Conformation 30%
  8 Citations (Scopus)

  170 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., 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

  • Ions 100%
  • DNA 67%
  • Substrate Specificity 67%
  • Enzymes 66%
  • Catalytic Domain 54%
  5 Citations (Scopus)

  119 Downloads (Pure)

• Structure and ligand binding of the SAM-V riboswitch

  Huang, L. & Lilley, D. M. J., 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

  • Riboswitch 100%
  • Ligands 45%
  • Binding Sites 33%
  • Hydrogen Bonding 26%
  • Adenine 25%
  24 Citations (Scopus)

  136 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., 1 Sept 2017, In: EMBO Reports. 18, 9, p. 1473-1671 15 p.

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

  Open Access

  File

  • Small Nucleolar Ribonucleoproteins 100%
  • Adenine 67%
  • Methylation 52%
  • RNA 39%
  • Sugars 27%
  31 Citations (Scopus)

  197 Downloads (Pure)

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

  Liu, Y. & Lilley, D. M. J., 5 Dec 2017, In: Biophysical Journal. 113, 11, p. 2236-2343 8 p.

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

  Open Access

  File

  • cyanine dye 5 100%
  • Double-Stranded RNA 77%
  • RNA 29%
  • X Ray Crystallography 29%
  • Fluorescence Resonance Energy Transfer 28%
  7 Citations (Scopus)

  190 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., 24 May 2017, In: Scientific Reports. 7, p. 1-8 8 p., 2393.

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

  Open Access

  File

  • Cytosine 100%
  • RNA 58%
  • Fluorescence 30%
  • Fluorescence Polarization 12%
  • Circular Dichroism 11%
  16 Citations (Scopus)

  181 Downloads (Pure)

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

  Ashraf, S., Huang, L. & Lilley, D. M. J., 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

  • Small Nucleolar Ribonucleoproteins 100%
  • Riboswitch 88%
  • Metals 74%
  • Ions 71%
  • RNA 59%
  7 Citations (Scopus)

  155 Downloads (Pure)

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

  Liu, Y., Wilson, T. & Lilley, D., May 2017, In: Nature Chemical Biology. 13, 5, p. 508-513 7 p.

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

  Open Access

  File

  • Catalytic RNA 100%
  • Metals 65%
  • Ions 62%
  • Phosphates 26%
  • RNA 20%
  39 Citations (Scopus)

  286 Downloads (Pure)

• The structure of the Guanidine-III Riboswitch

  Huang, L., Wang, J., Wilson, T. J. & Lilley, D. M. J., 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 83%
  • Guanidinium 78%
  • Nucleobase 70%
  • Methylguanidine 55%
  31 Citations (Scopus)

  176 Downloads (Pure)

• The Structure of the Guanidine-II Riboswitch

  Huang, L., Wang, J. & Lilley, D. M. J., 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 83%
  • Guanine 63%
  • Methylguanidine 55%
  • Agmatine 50%
  40 Citations (Scopus)

  167 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., 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

  • Base Pairing 100%
  • U4 small nuclear RNA 86%
  • Riboswitch 75%
  • RNA 67%
  • Hydrogen Bonding 58%
  15 Citations (Scopus)

  298 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., 2 Aug 2016, In: Biochemistry. 55, 30, p. 4166-4172 7 p.

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

  Open Access

  File

  • Deoxyribonuclease I 100%
  • Peptides 53%
  • Peptide 48%
  • DNA 46%
  • Enzymes 45%
  3 Citations (Scopus)

  158 Downloads (Pure)

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

  Huang, L. & Lilley, D. M. J., 7 Sept 2016, In: Nanoscale. 8, 33, p. 15189-15195 7 p.

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

  Open Access

  File

  • RNA 100%
  • Crystal lattices 84%
  • Cyclohexane 64%
  • Complementary RNA 59%
  • X Ray Crystallography 56%
  11 Citations (Scopus)

  176 Downloads (Pure)

• The Novel Chemical Mechanism of the Twister Ribozyme

  Wilson, T. J., Liu, Y., Domnick, C., Kath-Schorr, S. & Lilley, D. M. J., 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

  • Catalytic RNA 100%
  • Phosphates 60%
  • Catalysis 46%
  • Substitution reactions 34%
  • Phosphate 34%
  55 Citations (Scopus)

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

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

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

  Open Access

  File

  • Amino Acid Motifs 100%
  • Interferometry 68%
  • RNA 54%
  • X-Rays 36%
  • RNA Probes 22%
  29 Citations (Scopus)

  155 Downloads (Pure)