Nucleic Acid Structure

  • United Kingdom

Research Output 1995 2019

2014
63 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)
121 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
11 Citations (Scopus)
128 Downloads (Pure)
Open Access
File
Fungi
Enzymes
Chaetomium
Cruciform DNA
DNA
3 Citations (Scopus)
127 Downloads (Pure)
Open Access
File
Distance measurement
Hordeolum
Histone Chaperones
Electrons
Structural Models
2 Citations (Scopus)

Structure-based virtual screening for the identification of RNA-binding ligands

Daldrop, P. & Brenk, R., 2014, Therapeutic applications of ribozymes and riboswitches: methods and protocols. Lafontaine, D. & Dubé, A. (eds.). Humana Press, p. 127-139 13 p. (Methods in Molecular Biology; vol. 1103).

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

RNA
Ligands
Software
Proteins
8 Citations (Scopus)
137 Downloads (Pure)

Structure of a rare non-standard sequence k-turn bound by L7Ae protein

Huang, L. & Lilley, D. M. J., Apr 2014, In : Nucleic Acids Research. 42, 7, p. 4734-4740 7 p.

Research output: Contribution to journalArticle

Open Access
File
RNA
Thelohania
Riboswitch
Small Nucleolar RNA
Proteins
23 Citations (Scopus)
157 Downloads (Pure)

The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution

Bowman, A., Hammond, C. M., Stirling, A., Ward, R., Shang, W., El-Mkami, H., Robinson, D. A., Svergun, D. I., Norman, D. G. & Owen-Hughes, T., 2014, In : Nucleic Acids Research. 42, 9, p. 6038-6051 13 p.

Research output: Contribution to journalArticle

Open Access
File
Histone Chaperones
Histones
Electrons
Saccharomycetales
Nucleosomes
12 Citations (Scopus)
256 Downloads (Pure)

The k-junction motif in RNA structure

Wang, J., Daldrop, P., Huang, L. & Lilley, D. M. J., Apr 2014, In : Nucleic Acids Research. 42, 8, p. 5322-5331 10 p.

Research output: Contribution to journalArticle

Open Access
File
Riboswitch
Nucleotide Motifs
Arabidopsis
Electrophoresis
Hydrogen
18 Citations (Scopus)
107 Downloads (Pure)

The K-turn motif in riboswitches and other RNA species

Lilley, D. M. J., Oct 2014, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1839, 10, p. 995-1004 10 p.

Research output: Contribution to journalArticle

Open Access
File
Riboswitch
RNA
Protein Binding
Binding Sites
Ligands
8 Citations (Scopus)
114 Downloads (Pure)

The spatial effect of protein deuteration on nitroxide spin-label relaxation: implications for EPR distance measurement

El Mkami, H., Ward, R., Bowman, A., Owen-Hughes, T. & Norman, D. G., Nov 2014, In : Journal of Magnetic Resonance . 248, p. 36-41 6 p.

Research output: Contribution to journalArticle

Open Access
File
Spin Labels
Distance measurement
Paramagnetic resonance
Electrons
proteins
2013
2 Citations (Scopus)

A mechanistic comparison of the varkud satellite and hairpin ribozymes

Wilson, T. J. & Lilley, D. M. J., 2013, Catalytic RNA. Soukup, G. A. (ed.). London: Academic Press, p. 93-121 29 p. (Progress in molecular biology and translational science; vol. 120).

Research output: Chapter in Book/Report/Conference proceedingChapter

Catalytic RNA
Transesterification
Guanine
Catalysis
Acids

Analysis of RNA conformation using comparative gel electrophoresis

Lilley, D. M. J., Sep 2013, RNA Structure and Folding: Biophysical Techniques and Prediction Methods. Walter de Gruyter GmbH, p. 101-124 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)
85 Downloads (Pure)

Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone

Dow, J. M., Grahl, S., Ward, R., Evans, R., Byron, O., Norman, D. G., Palmer, T. & Sargent, F., 9 Dec 2013, In : FEBS Journal. 281, 1, p. 246-260 15 p.

Research output: Contribution to journalArticle

Open Access
File
Nitrate Reductase
Protein Sorting Signals
Arginine
Proteins
Ultracentrifugation
93 Citations (Scopus)

Cooperative Control of Holliday Junction Resolution and DNA Repair by the SLX1 and MUS81-EME1 Nucleases

Castor, D., Nair, N., Déclais, A-C., Lachaud, C., Toth, R., Macartney, T. J., Lilley, D. M. J., Arthur, J. S. C. & Rouse, J., 24 Oct 2013, In : Molecular Cell. 52, 2, p. 221-233 13 p.

Research output: Contribution to journalArticle

Cruciform DNA
DNA Repair
Chromosome Segregation
Genetic Structures
Genomic Instability
7 Citations (Scopus)

Measurement of the Change in Twist at a Helical Junction in RNA Using the Orientation Dependence of FRET

Fessl, T. & Lilley, D. M. J., 5 Nov 2013, In : Biophysical Journal. 105, 9, p. 2175-2181 7 p.

Research output: Contribution to journalArticle

RNA
Fluorescence Resonance Energy Transfer
Hepacivirus
Nucleic Acids
Internal Ribosome Entry Sites
37 Citations (Scopus)

Structural plasticity of histones H3–H4 facilitates their allosteric exchange between RbAp48 and ASF1

Zhang, W., Yyl, M., Ward, R., Sobott, F., Maman, J., Murthy, A., Watson, A., Fedorov, O., Bowman, A., Owen-Hughes, T., El Mkami, H., Murzina, N., Norman, D. G. & Laue, E., Jan 2013, In : Nature Structural & Molecular Biology. 20, 1, p. 29-35 7 p.

Research output: Contribution to journalArticle

Histones
Histone Chaperones
Proteins
Nucleosomes
DNA Replication
8 Citations (Scopus)

The architecture of EssB, an integral membrane component of the type VII secretion system

Zoltner, M., Norman, D. G., Fyfe, P. K., El Mkami, H., Palmer, T. & Hunter, W. N., 2 Apr 2013, In : Structure. 21, 4, p. 595-603 9 p.

Research output: Contribution to journalArticle

Bacterial Secretion Systems
Geobacillus
Cell Membrane
Membranes
Peptidoglycan
5 Citations (Scopus)

The functional exchangeability of pk- and k-turns in RNA structure

Daldrop, P., Masquida, B. & Lilley, D. M. J., Mar 2013, In : RNA Biology. 10, 3, p. 445-452 8 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)
28 Citations (Scopus)
66 Downloads (Pure)

The molecular recognition of kink-turn structure by the L7Ae class of proteins

Huang, L. & Lilley, D. M. J., Dec 2013, In : RNA. 19, 12, p. 1703-1710 8 p.

Research output: Contribution to journalArticle

Open Access
File
Proteins
Haloarcula marismortui
Archaeoglobus fulgidus
Consensus Sequence
Guanine
23 Citations (Scopus)
2012
48 Citations (Scopus)
58 Downloads (Pure)

General Acid–Base Catalysis Mediated by Nucleobases in the Hairpin Ribozyme

Kath-Schorr, S., Wilson, T. J., Li, N. S., Lu, J., Piccirilli, J. A. & Lilley, D. M. J., 10 Oct 2012, In : Journal of the American Chemical Society. 134, 40, p. 16717-16724 8 p.

Research output: Contribution to journalArticle

Open Access
File
Catalysis
Catalytic RNA
Acids
Substitution reactions
Guanine
23 Citations (Scopus)
53 Downloads (Pure)

Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein

Wang, J., Fessl, T., Schroeder, K. T., Ouellet, J., Liu, Y., Freeman, A. D. J. & Lilley, D. M. J., 19 Dec 2012, In : Biophysical Journal. 103, 12, p. 2541-2548 8 p.

Research output: Contribution to journalArticle

Open Access
File
Carrier Proteins
Observation
RNA
Immobilized Proteins
Proteins
13 Citations (Scopus)

Structure and folding of a rare, natural kink turn in RNA with an A•A pair at the 2•d2n position

Schroeder, K. T., Daldrop, P., McPhee, S. A. & Lilley, D. M. J., Jun 2012, In : RNA: a Publication of the RNA Society. 18, 6, p. 1257-1266 10 p.

Research output: Contribution to journalArticle

Hydrogen
Adenine
RNA
Thelohania
Riboswitch
14 Citations (Scopus)

Synthesis of novel tetrazole C5-linked C0- and C2-ribonucleoside phosphoramidites using MePOM and POM groups for probing RNA catalysis

Harusawa, S., Yoneyama, H., Fujisue, D., Nishiura, M., Fujitake, M., Usami, Y., Zhao, Z., Mcphee, S. A., Wilson, T. J. & Lilley, D. M. J., 2012, In : Tetrahedron Letters. 53, 44, p. 5891-5894 4 p.

Research output: Contribution to journalArticle

Ribonucleosides
Catalysis
Catalytic RNA
RNA
Acids

The structure and folding of helical junctions in RNA

Lilley, D. M. J., 2012, Innovations in Biomolecular Modeling and Simulations. Schlick, T. (ed.). Cambridge: Royal Society of Chemistry, (RSC Biomolecular Sciences).

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

23 Citations (Scopus)

The structure and folding of kink turns in RNA

Lilley, D. M. J., 2012, In : Wiley Interdisciplinary Reviews: RNA. 3, 6, p. 797-805 9 p.

Research output: Contribution to journalArticle

Adenine
Hydrogen bonds
RNA
Double-Stranded RNA
Hydrogen Bonding
18 Citations (Scopus)

The Structure of Sulfoindocarbocyanine 3 Terminally Attached to dsDNA via a Long, Flexible Tether

Urnavicius, L., McPhee, S. A., Lilley, D. M. J. & Norman, D. G., 8 Feb 2012, In : Biophysical Journal. 102, 3, p. 561-568 8 p.

Research output: Contribution to journalArticle

2011
10 Citations (Scopus)

A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage

Li, N-S., Frederiksen, J. K., Koo, S. C., Lu, J., Wilson, T. J., Lilley, D. M. J. & Piccirilli, J. A., Mar 2011, In : Nucleic Acids Research. 39, 5, p. - 16 p., e31.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Analysis of Conformational Changes in the DNA Junction-Resolving Enzyme T7 Endonuclease I on Binding a Four-Way Junction Using EPR

Freeman, A. D. J., Ward, R., El Mkami, H., Lilley, D. M. J. & Norman, D. G., 22 Nov 2011, In : Biochemistry. 50, 46, p. 9963-9972 10 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Catalysis by the nucleolytic ribozymes

Lilley, D. M. J., Apr 2011, In : Biochemical Society Transactions. 39, p. 641-646 6 p.

Research output: Contribution to journalArticle

Cell migration modulating compounds

Schor, A. M., Schor, S. L., Marquez, R. & Norman, D. G., 19 Oct 2011, Patent No. EP1917012

Research output: Patent

Fibronectins
Cell Movement
Wound Healing
Peptides
Fibroblasts
32 Citations (Scopus)

Mechanisms of RNA catalysis

Lilley, D. M. J., 27 Oct 2011, In : Philosophical Transactions of the Royal Society B - Biological Sciences. 366, 1580, p. 2910-2917 8 p.

Research output: Contribution to journalReview article

57 Citations (Scopus)

Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

Daldrop, P., Reyes, F. E., Robinson, D. A., Hammond, C. M., Lilley, D. M., Batey, R. T. & Brenk, R., 25 Mar 2011, In : Chemistry & Biology. 18, 3, p. 324-335 12 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Orientation of Cyanine Fluorophores Terminally Attached to DNA via Long, Flexible Tethers

Ouellet, J., Schorr, S., Iqbal, A., Wilson, T. J. & Lilley, D. M. J., 7 Sep 2011, In : Biophysical Journal. 101, 5, p. 1148-1154 7 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Protein Phosphatase 2A (PP2A)-specific Ubiquitin Ligase MID1 Is a Sequence-dependent Regulator of Translation Efficiency Controlling 3-Phosphoinositide-dependent Protein Kinase-1 (PDPK-1)

Aranda-Orgilles, B., Rutschow, D., Zeller, R., Karagiannidis, A. I., Köhler, A., Chen, C., Wilson, T., Krause, S., Roepcke, S., Lilley, D., Schneider, R. & Schweiger, S., 18 Nov 2011, In : Journal of Biological Chemistry. 286, 46, p. 39945-39957 13 p.

Research output: Contribution to journalArticle

39 Citations (Scopus)

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

Schroeder, K. T., Daldrop, P. & Lilley, D. M. J., 7 Sep 2011, In : Structure. 19, 9, p. 1233-1240 8 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Synthesis of Imidazole C1- and C3-Ribonucleoside Phosphoramidites for Probing Catalytic Mechanism in Ribozyme

Harusawa, S., Fujii, K., Nishiura, M., Araki, L., Usami, Y., Zhao, Z. & Lilley, D. M. J., 1 Sep 2011, In : Heterocycles. 83, 9, p. 2041-2055 15 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

The chemical origins of life and its early evolution: an introduction

Lilley, D. M. J. & Sutherland, J., 27 Oct 2011, In : Philosophical Transactions of the Royal Society B - Biological Sciences. 366, 1580, p. 2853-2856 4 p.

Research output: Contribution to journalEditorial

55 Citations (Scopus)
139 Downloads (Pure)

The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation

Bowman, A., Ward, R., Wiechens, N., Singh, V., El-Mkami, H., Norman, D. G. & Owen-Hughes, T., 18 Feb 2011, In : Molecular Cell. 41, 4, p. 398-408 11 p.

Research output: Contribution to journalArticle

File
2010
71 Citations (Scopus)

A structural database for k-turn motifs in RNA

Schroeder, K. T., McPhee, S. A., Ouellet, J. & Lilley, D. M. J., Aug 2010, In : RNA: a Publication of the RNA Society. 16, 8, p. 1463-1468 6 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Efficient Synthesis of 2’-O-Cyanoethylated Imidazole C-Ribonucleoside Phosphoramidite: A Practical Building Block for Probing the Catalytic Mechanism of Ribozymes

Araki, L., Zhao, Z., Lilley, D. M. J. & Harusawa, S., 1 Aug 2010, In : Heterocycles. 81, 8, p. 1861-1869 9 p.

Research output: Contribution to journalArticle

92 Citations (Scopus)

EPR distance measurements in deuterated proteins

Ward, R., Bowman, A., Sozudogru, E., El-Mkami, H., Owen-Hughes, T. & Norman, D. G., Nov 2010, In : Journal of Magnetic Resonance Imaging. 207, 1, p. 164-167 4 p.

Research output: Contribution to journalArticle

197 Citations (Scopus)

Identification of KIAA1018/FAN1, a DNA Repair Nuclease Recruited to DNA Damage by Monoubiquitinated FANCD2

MacKay, C., Declais, A-C., Lundin, C., Agostinho, A., Deans, A. J., MacArtney, T. J., Hofmann, K., Gartner, A., West, S. C., Helleday, T., Lilley, D. M. J. & Rouse, J., 9 Jul 2010, In : Cell. 142, 1, p. 65-76 12 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Multi-factorial modulation of IGD motogenic potential in MSF (Migration Stimulating Factor)

Ellis, I. R., Jones, S. J., Staunton, D., Vakonakis, I., Norman, D. G., Potts, J. R., Milner, C. M., Meenan, N. A. G., Raibaud, S., Ohea, G., Schor, A. M. & Schor, S. L., 10 Sep 2010, In : Experimental Cell Research. 316, 15, p. 2465-2476 12 p.

Research output: Contribution to journalArticle

55 Citations (Scopus)

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

Wilson, T. J., Li, N-S., Lu, J., Frederiksen, J. K., Piccirilli, J. A. & Lilley, D. M. J., 29 Jun 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 26, p. 11751-11756 6 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)
93 Downloads (Pure)

Probing the (H3-H4)(2) histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling

Bowman, A., Ward, R., El-Mkami, H., Owen-Hughes, T. & Norman, D. G., Jan 2010, In : Nucleic Acids Research. 38, 2, p. 695-707 13 p.

Research output: Contribution to journalArticle

Open Access
File
25 Citations (Scopus)

Structure of the three-way helical junction of the hepatitis C virus IRES element

Ouellet, J., Melcher, S., Iqbal, A., Ding, Y. & Lilley, D. M. J., Aug 2010, In : RNA: a Publication of the RNA Society. 16, 8, p. 1597-1609 13 p.

Research output: Contribution to journalArticle

61 Citations (Scopus)

The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair

Bailly, A. P., Freeman, A., Hall, J., Declais, A-C., Alpi, A., Lilley, D. M. J., Ahmed, S. & Gartner, A., Jul 2010, In : PLoS Genetics. 6, 7, p. - 16 p., e1001025.

Research output: Contribution to journalArticle