Nucleic Acid Structure

  • United Kingdom

Research Output 1995 2019

574 Citations (Scopus)

3-Phosphoinositide-dependent protein kinase-1 (PDK1): structural and functional homology with the Drosophila DSTPK61 kinase

Alessi, D. R., Deak, M., Casamayor, A., Caudwell, F. B., Morrice, N., Norman, D. G., Gaffney, P., Reese, C. B., MacDougall, C. N., Harbison, D., Ashworth, A. & Bownes, M., 1997, In : Current Biology. 7, 10, p. 776-789 14 p.

Research output: Contribution to journalArticle

3-Phosphoinositide-Dependent Protein Kinases
protein kinases
Drosophila
phosphotransferases (kinases)
Phosphotransferases
11 Citations (Scopus)

A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes

Lilley, D. M. J., Jul 2007, In : Biological Chemistry. 388, 7, p. 699-704 6 p.

Research output: Contribution to journalArticle

Catalytic RNA
Ligation
Catalysis
Acids
Nucleosides
12 Citations (Scopus)
172 Downloads (Pure)
Open Access
File
Base Pairing
Riboswitch
RNA
Hydrogen Bonding
Ribosomes
23 Citations (Scopus)
83 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
6 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
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

66 Citations (Scopus)

A guanine nucleobase important for catalysis by the VS ribozyme

Wilson, T. J., McLeod, A. C. & Lilley, D. M. J., 16 May 2007, In : EMBO Journal. 26, 10, p. 2489-2500 12 p.

Research output: Contribution to journalArticle

Catalytic RNA
Guanine
Catalysis
Substrates
Acids
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
1 Citation (Scopus)
49 Downloads (Pure)
Open Access
File
Ions
DNA
Enzymes
Substrate Specificity
Catalytic Domain
20 Citations (Scopus)

Analysis of branched nucleic acid structure using comparative gel electrophoresis

Lilley, D. M. J., Feb 2008, In : Quarterly Reviews of Biophysics. 41, 1, p. 139 39 p.

Research output: Contribution to journalReview article

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

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

86 Downloads (Pure)
Open Access
File
Deoxyribonuclease I
Peptides
DNA
Enzymes
Proteins
5 Citations (Scopus)

Analyzing reverse gyrase activity.

Duguet, M., Jaxel, C., Déclais, A-C., Confalonieri, F., Marsault, J., Bouthier, C. D. L. T., Nadal, M. & Portemer, C., 2001, DNA Topoisomerase Protocols. Osheroff, N. & Bjornsti, M. A. (eds.). Humana Press, Vol. 95. p. 35-49 (Methods in Molecular Biology; vol. 95).

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)
122 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
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

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
26 Citations (Scopus)

Biochemistry: The evolution of ribozyme chemistry

Wilson, T. J. & Lilley, D. M. J., 13 Mar 2009, In : Science. 323, 5920, p. 1436-1438 3 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)
79 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
15 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
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

551 Citations (Scopus)
126 Downloads (Pure)

CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations

Scott, J. W., Hawley, S. A., Green, K. A., Anis, M., Stewart, G., Scullion, G. A., Norman, D. G. & Hardie, D. G., 2004, In : Journal of Clinical Investigation. 113, 2, p. 274-284 11 p.

Research output: Contribution to journalArticle

Open Access
File
AMP-Activated Protein Kinases
IMP Dehydrogenase
Cystathionine
Adenosine
Inborn Genetic Diseases

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
113 Citations (Scopus)

Characterisation of the interaction between PCNA and Gadd45

Hall, P. A., Kearsey, J. M., Coates, P. J., Norman, D. G., Warbrick, E. & Cox, L. S., 1995, In : Oncogene. 10, 12, p. 2427-2433 7 p.

Research output: Contribution to journalArticle

Proliferating Cell Nuclear Antigen
DNA Repair
Amino Acids
Two-Hybrid System Techniques
Proteins
2 Citations (Scopus)
86 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
30 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
4 Citations (Scopus)

Comparative gel electrophoresis analysis of helical junctions in RNA

Lilley, D. M. J., 2009, Biophysical, chemical, and functional probes of RNA structure, interactions and folding : Part B. Herschlag, D. (ed.). San Diego: Academic Press, p. 143-157 15 p. (Methods in Enzymology; vol. 469).

Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

3 Citations (Scopus)
50 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
16 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
15 Citations (Scopus)
84 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
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
227 Citations (Scopus)

Coordination of Structure-Specific Nucleases by Human SLX4/BTBD12 Is Required for DNA Repair

Munoz, I. M., Hain, K., Declais, A-C., Gardiner, M., Toh, G. W., Sanchez-Pulido, L., Heuckmann, J. M., Toth, R., Macartney, T., Eppink, B., Kanaar, R., Ponting, C. P., Lilley, D. M. J. & Rouse, J., 10 Jul 2009, In : Molecular Cell. 35, 1, p. 116-127 12 p.

Research output: Contribution to journalArticle

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
18 Citations (Scopus)
79 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
76 Citations (Scopus)

Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I.

Hadden, JM., Convery, MA., Déclais, AC., Lilley, DM. & Phillips, S. E. V., Jan 2001, In : Nature Structural and Molecular Biology. 8, 1, p. 62-67

Research output: Contribution to journalArticle

Cruciform DNA
Deoxyribonuclease I
Enzymes
Catalytic Domain
DNA Restriction Enzymes
44 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
4 Citations (Scopus)
114 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
61 Citations (Scopus)
dissection
folding
nuclear magnetic resonance
ions
websites
30 Citations (Scopus)

Distance determination in heterogeneous DNA model systems by pulsed EPR

Ward, R., Keeble, D. J., El-Mkami, H. & Norman, D. G., Nov 2007, In : ChemBioChem. 8, 16, p. 1957-1964 8 p.

Research output: Contribution to journalArticle

Paramagnetic resonance
Spin Labels
DNA
Electron Spin Resonance Spectroscopy
Deconvolution

DNA revisited

Lilley, D. M. J., Dec 2008, In : Nature Chemical Biology. 4, 12, p. 725-726 2 p.

Research output: Contribution to journalComment/debate

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

36 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
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

15 Citations (Scopus)
Organophosphonates
Static Electricity
Phosphates
DNA
Ions
22 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
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

1 Citation (Scopus)
54 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
43 Citations (Scopus)
2-Aminopurine
Base Pairing
Fluorescence
Potassium Permanganate
Thymine