Nucleic Acid Structure

  • United Kingdom

Research Output 1995 2019

2019
5 Citations (Scopus)

A Gadolinium Spin Label with Both a Narrow Central Transition and Short Tether for Use in Double Electron Electron Resonance Distance Measurements

Shah, A., Roux, A., Starck, M., Mosely, J. A., Stevens, M., Norman, D. G., Hunter, R. I., El Mkami, H., Smith, G. M., Parker, D. & Lovett, J. E., 4 Mar 2019, In : Inorganic Chemistry. 58, 5, p. 3015-3025 11 p.

Research output: Contribution to journalArticle

Electron resonance
Spin Labels
Distance measurement
Gadolinium
gadolinium
12 Citations (Scopus)
65 Downloads (Pure)

Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Clifton-Brown, J., Harfouche, A., Casler, M. D., Dylan Jones, H., Macalpine, W. J., Murphy-Bokern, D., Smart, L. B., Adler, A., Ashman, C., Awty-Carroll, D., Bastien, C., Bopper, S., Botnari, V., Brancourt-Hulmel, M., Chen, Z., Clark, L. V., Cosentino, S., Dalton, S., Davey, C., Dolstra, O. & 39 others, Donnison, I., Flavell, R., Greef, J., Hanley, S., Hastings, A., Hertzberg, M., Hsu, T. W., Huang, L. S., Iurato, A., Jensen, E., Jin, X., Jørgensen, U., Kiesel, A., Kim, D. S., Liu, J., McCalmont, J. P., McMahon, B. G., Mos, M., Robson, P., Sacks, E. J., Sandu, A., Scalici, G., Schwarz, K., Scordia, D., Shafiei, R., Shield, I., Slavov, G., Stanton, B. J., Swaminathan, K., Taylor, G., Torres, A. F., Trindade, L. M., Tschaplinski, T., Tuskan, G. A., Yamada, T., Yeon Yu, C., Zalesny, R. S., Zong, J. & Lewandowski, I., Jan 2019, In : Global Change Biology: Bioenergy. 11, 1, p. 118-151 34 p.

Research output: Contribution to journalArticle

Open Access
File
Miscanthus
Panicum virgatum
energy crops
Crops
Biomass
5 Downloads (Pure)

Breeding strategies to improve Miscanthus as a sustainable source of biomass for bioenergy and biorenewable products

Clifton-Brown, J., Schwarz, K. U., Awty-Carroll, D., Iurato, A., Meyer, H., Greef, J., Gwyn, J., Mos, M., Ashman, C., Hayes, C., Huang, L., Norris, J., Rodgers, C., Scordia, D., Shafiei, R., Squance, M., Swaller, T., Youell, S., Cosentino, S., Flavell, R. & 2 others, Donnison, I. & Robson, P., 24 Oct 2019, In : Agronomy. 9, 11, p. 1-17 17 p., 673.

Research output: Contribution to journalArticle

Open Access
File
Miscanthus
bioenergy
biomass
breeding
East Asia
19 Downloads (Pure)

Classification of the nucleolytic ribozymes based upon catalytic mechanism

Lilley, D. M. J., 19 Aug 2019, In : F1000Research. 8, p. 1-10 10 p., 1462.

Research output: Contribution to journalReview article

Open Access
File
Catalytic RNA
Catalysis
RNA Cleavage
Acids
Hydroxyl Radical
2 Citations (Scopus)
39 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., 2019, In : Journal of the American Chemical Society. 141, 19, p. 7865-7875 11 p.

Research output: Contribution to journalArticle

Open Access
File
Catalytic RNA
Conformations
Nucleophiles
Acids
Metal ions
28 Downloads (Pure)

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

Ashraf, S., Huang, L. & Lilley, D., 24 Jun 2019, In : RNA Biology. 16, 10, p. 1377-1385 9 p.

Research output: Contribution to journalArticle

Open Access
File
Adenine
Protein Binding
Base Pairing
Methylation
RNA Folding
1 Citation (Scopus)
39 Downloads (Pure)

Exploration of the TRIM fold of MuRF1 using EPR reveals a canonical antiparallel structure and extended COS-box

Stevens, M., Franke, B., Skorupka, K. A., Cafiso, D. S., Pornillos, O., Mayans, O. & Norman, D., 12 Jul 2019, In : Journal of Molecular Biology. 431, 15, p. 2900-2909 10 p.

Research output: Contribution to journalArticle

Open Access
File
Dimerization
Proteins
Ubiquitin-Protein Ligases
Conserved Sequence
Electron Spin Resonance Spectroscopy
1 Citation (Scopus)
29 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 journalArticle

Open Access
File
Cruciform DNA
Enzymes
Genetic Recombination
Bacteriophage T7
Chromosome Segregation
65 Downloads (Pure)

Structure and ligand binding of the glutamine-II riboswitch

Huang, L., Wang, J., Watkins, A. M., Das, R. & Lilley, D. M. J., 22 Aug 2019, In : Nucleic Acids Research. 47, 14, p. 7666-7675 10 p.

Research output: Contribution to journalArticle

Open Access
File
Riboswitch
Glutamine
RNA
Ligands
Binding Sites
64 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 journalArticle

Open Access
File
Riboswitch
Guanidine
Ligands
Binding Sites
X-Rays
3 Citations (Scopus)
83 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 journalArticle

Open Access
File
Archaea
Archaeoglobus fulgidus
RNA
Untranslated Regions
Proteins
2018
1 Citation (Scopus)
46 Downloads (Pure)
Open Access
File
Ions
DNA
Enzymes
Substrate Specificity
Catalytic Domain
1 Citation (Scopus)

Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes

Liu, Y., Freeman, A., Déclais, A-C., Gartner, A. & Lilley, D. M. J., 2018, Mechanisms of DNA Recombination and Genome Rearrangements: Methods to Study Homologous Recombination. Spies, M. & Malkova, A. (eds.). Academic Press, Vol. 600. p. 543-568 26 p. (Methods in Enzymology; vol. 600).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Cruciform DNA
Structural properties
Enzymes
Chaetomium
DNA
2 Citations (Scopus)
49 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 journalArticle

Open Access
File
Riboswitch
Ligands
Binding Sites
Adenine
Hydrogen Bonding
13 Citations (Scopus)
75 Downloads (Pure)

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

Sundaramoorthy, R., Hughes, A., El-Mkami, H., Norman, D. & Owen-Hughes, T., 6 Aug 2018, In : eLife. 2018, 7, p. 1-28 28 p., e35720.

Research output: Contribution to journalArticle

Open Access
File
Chromatin Assembly and Disassembly
Nucleosomes
Chromatin
Histones
DNA
4 Citations (Scopus)

The kink-turn in the structural biology of RNA

Huang, L. & Lilley, D. M. J., 2018, In : Quarterly Reviews of Biophysics. 51, p. 1-32 32 p., e5.

Research output: Contribution to journalReview article

RNA
Metals
Ions
Base Pairing
Carrier Proteins
2017
13 Citations (Scopus)
78 Downloads (Pure)

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

Huang, L., Ashraf, S., Wang, J. & Lilley, D. M. J., 1 Sep 2017, In : EMBO Reports. 18, 9, p. 1473-1671 15 p.

Research output: Contribution to journalArticle

Open Access
File
Small Nucleolar Ribonucleoproteins
Methylation
Adenine
RNA
Sugars
4 Citations (Scopus)
104 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 journalArticle

Open Access
File
Double-Stranded RNA
RNA
Fluorescence Resonance Energy Transfer
X Ray Crystallography
Base Pairing
7 Citations (Scopus)
101 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 journalArticle

Open Access
File
Cytosine
RNA
Fluorescence
Fluorescence Polarization
DNA
2 Citations (Scopus)
131 Downloads (Pure)

Holliday junction-resolving enzymes - structures and mechanisms

Lilley, D. M. J., Apr 2017, In : FEBS Letters. 591, 8, p. 1073-1082 10 p.

Research output: Contribution to journalReview article

Open Access
File
Cruciform DNA
Fungal Structures
Eukaryotic Cells
Enzymes
Crystal lattices
13 Citations (Scopus)
592 Downloads (Pure)

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

Lilley, D. M. J., 15 Jun 2017, In : Biochemical Society Transactions. 45, 3, p. 683-691 9 p.

Research output: Contribution to journalReview article

Open Access
File
Catalytic RNA
RNA
14 Citations (Scopus)
179 Downloads (Pure)

Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

Llères, D., Bailly, A. P., Perrin, A., Norman, D. G., Xirodimas, D. P. & Feil, R., 14 Feb 2017, In : Cell Reports. 18, 7, p. 1791-1803 13 p.

Research output: Contribution to journalArticle

Open Access
File
Optical Imaging
Energy Transfer
Energy transfer
Chromatin
Microscopy
3 Citations (Scopus)
86 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 journalArticle

Open Access
File
Small Nucleolar Ribonucleoproteins
Riboswitch
Metals
RNA
Ions
26 Citations (Scopus)
90 Downloads (Pure)

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Bottcher, B., Norman, D. G. & Owen-Hughes, T., 13 Apr 2017, In : eLife. 6, 28 p., e22510.

Research output: Contribution to journalArticle

Open Access
File
Chromatin Assembly and Disassembly
Nucleosomes
Chromatin
DNA
Enzymes
1 Citation (Scopus)

The Guanidine Riboswitch-A Poor Orphan No Longer

Lilley, D. M. J., 16 Feb 2017, In : Cell Chemical Biology. 24, 2, p. 130-131 2 p.

Research output: Contribution to journalReview article

Riboswitch
Guanidine
Gene expression
Ions
Ligands
19 Citations (Scopus)
138 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 journalArticle

Open Access
File
Catalytic RNA
Metals
Ions
Phosphates
RNA
8 Citations (Scopus)
96 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 journalArticle

Open Access
File
Riboswitch
Guanidine
Cations
Methylguanidine
Agmatine
11 Citations (Scopus)
96 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 journalArticle

Open Access
File
Riboswitch
Guanidine
Guanine
Methylguanidine
Agmatine
2016
12 Citations (Scopus)
156 Downloads (Pure)
Open Access
File
Base Pairing
Riboswitch
RNA
Hydrogen Bonding
Ribosomes
77 Downloads (Pure)
Open Access
File
Deoxyribonuclease I
Peptides
DNA
Enzymes
Proteins
6 Citations (Scopus)
113 Downloads (Pure)

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

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

Research output: Contribution to journalArticle

Open Access
File
RNA
Crystal lattices
Complementary RNA
Molecules
X ray crystallography
1 Citation (Scopus)

Editorial overview: Nucleic acids and their protein complexes

Lilley, D. M. J. & Pyle, A. M., 2016, In : Current Opinion in Structural Biology. 36, p. vii-viii 2 p.

Research output: Contribution to journalEditorial

34 Citations (Scopus)
102 Downloads (Pure)

Phase II randomized preoperative window-of-opportunity study of the PI3K inhibitor pictilisib plus anastrozole compared with anastrozole alone in patients with estrogen receptor-positive breast cancer

Schmid, P., Pinder, S. E., Wheatley, D., Macaskill, J., Zammit, C., Hu, J., Price, R., Bundred, N., Hadad, S., Shia, A., Sarker, S. J., Lim, L., Gazinska, P., Woodman, N., Korbie, D., Trau, M., Mainwaring, P., Gendreau, S., Lackner, M. R., Derynck, M. & 6 others, Wilson, T. R., Butler, H., Earl, G., Parker, P., Purushotham, A. & Thompson, A., 10 Jun 2016, In : Journal of Clinical Oncology. 34, 17, p. 1987-1994 8 p.

Research output: Contribution to journalArticle

Open Access
File
Phosphatidylinositol 3-Kinases
Estrogen Receptors
Breast Neoplasms
Neoplasms
Therapeutics
1 Citation (Scopus)

Preface

Huang, Z. & Lilley, D. M. J., Jun 2016, In : Frontiers of Chemical Science and Engineering. 10, 2, p. 177 1 p.

Research output: Contribution to journalEditorial

Open Access
19 Citations (Scopus)

Ribozymes and the mechanisms that underlie RNA catalysis

Wilson, T. J., Liu, Y. & Lilley, D. M. J., Jun 2016, In : Frontiers of Chemical Science and Engineering. 10, 2, p. 178-185 8 p.

Research output: Contribution to journalArticle

Catalytic RNA
RNA
Catalysis
Coenzymes
Acids
13 Citations (Scopus)
189 Downloads (Pure)

The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3–H4 tetramers and Asf1–H3–H4 complexes

Hammond, C. M., Sundaramoorthy, R., Larance, M., Lamond, A., Stevens, M. A., El-Mkami, H., Norman, D. & Owen-Hughes, T., 27 Jul 2016, In : Nucleic Acids Research. 44, 13, p. 6157-6172 16 p.

Research output: Contribution to journalArticle

Open Access
File
Histone Chaperones
Histones
Electrons
Structural Models
X Ray Crystallography
24 Citations (Scopus)
47 Downloads (Pure)

The Kink Turn, a Key Architectural Element in RNA Structure

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

Research output: Contribution to journalReview article

Open Access
File
Hydrogen
RNA
Adenine
Nucleotides
Metals
31 Citations (Scopus)

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 journalArticle

Catalytic RNA
Phosphates
Catalysis
Substitution reactions
Acids
19 Citations (Scopus)
72 Downloads (Pure)

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 journalArticle

Open Access
File
Amino Acid Motifs
Interferometry
RNA
X-Rays
RNA Probes
8 Citations (Scopus)
75 Downloads (Pure)

The use of the Rx spin label in orientation measurement on proteins, by EPR

Stevens, M. A., McKay, J. E., Robinson, J. L. S., El Mkami, H., Smith, G. M. & Norman, D. G., 2016, In : Physical Chemistry Chemical Physics. 18, 8, p. 5799-5806 8 p.

Research output: Contribution to journalArticle

Open Access
File
Spin Labels
Paramagnetic resonance
proteins
attachment
Proteins
2015
18 Citations (Scopus)
73 Downloads (Pure)

Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

Liu, Y., Freeman, A. D. J., Déclais, A. C., Wilson, T. J., Gartner, A. & Lilley, D. M. J., 22 Dec 2015, In : Cell Reports. 13, 11, p. 2565-2575 11 p.

Research output: Contribution to journalArticle

Open Access
File
Crystal structure
DNA
Enzymes
2-Aminopurine
Crystal lattices
43 Citations (Scopus)

Crystal structure of the Varkud satellite ribozyme

Suslov, N. B., Dasgupta, S., Huang, H., Fuller, J. R., Lilley, D. M. J., Rice, P. A. & Piccirilli, J. A., Nov 2015, In : Nature Chemical Biology. 11, p. 840-846 7 p.

Research output: Contribution to journalArticle

Catalytic Domain
RNA
Neurospora
Protein Subunits
Catalytic RNA
21 Citations (Scopus)

EPR distance measurements in deuterated proteins

El Mkami, H. & Norman, D. G., 2015, Electron paramagnetic resonance investigations of biological systems by using spin labels, spin probes, and intrinsic metal ions, Part B. Qin, P. Z. & Warncke, K. (eds.). Academic Press, p. 125-152 28 p. (Methods in enzymology; vol. 564).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Electrons
Proteins
Electron Spin Resonance Spectroscopy
Artifacts

Ribozymes: ancient and modern

Lilley, D. M. J., Apr 2015, In : Biochemist. 37, 2, p. 4-8 5 p.

Research output: Contribution to journalArticle

Catalytic RNA
RNA
Planets
Proteins
Molecules
7 Citations (Scopus)

RNA catalysis-is that it?

Wilson, T. J. & Lilley, D. M. J., Apr 2015, In : RNA: a Publication of the RNA Society. 21, 4, p. 534-537 4 p.

Research output: Contribution to journalArticle

2014
23 Citations (Scopus)
76 Downloads (Pure)

A critical base pair in k-turns that confers folding characteristics and correlates with biological function

McPhee, S. A., Huang, L. & Lilley, D. M. J., 29 Oct 2014, In : Nature Communications. 5, 6 p., 5127.

Research output: Contribution to journalArticle

Open Access
File
Riboswitch
Base Pairing
folding
Metal ions
Ions
15 Citations (Scopus)

Conserved structure and domain organization among bacterial Slc26 transporters

Compton, E. L. R., Page, K., Findlay, H. E., Haertlein, M., Moulin, M., Zachariae, U., Norman, D. G., Gabel, F. & Javelle, A., 15 Oct 2014, In : Biochemical Journal. 463, 2, p. 297-307 11 p.

Research output: Contribution to journalArticle

Small Angle Scattering
Neutrons
Sigma Factor
Neutron scattering
Sulfates
62 Citations (Scopus)

Crystal structure and mechanistic investigation of the twister ribozyme

Liu, Y., Wilson, T. J., McPhee, S. A. & Lilley, D. M. J., Sep 2014, In : Nature Chemical Biology. 10, 9, p. 739-744 6 p.

Research output: Contribution to journalArticle

Catalytic RNA
Guanine
Phosphates
Acids
Adenine
9 Citations (Scopus)
112 Downloads (Pure)

FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain

Pennell, S., Déclais, A-C., Li, J., Haire, L. F., Berg, W., Saldanha, J. W., Taylor, I. A., Rouse, J., Lilley, D. M. J. & Smerdon, S. J., 10 Jul 2014, In : Cell Reports. 8, 1, p. 84-93 10 p.

Research output: Contribution to journalArticle

Open Access
File
Dimerization
Virus Replication
Viruses
DNA Repair
Holliday Junction Resolvases