Search Results - "Lilley, David M.J"

Classification of the nucleolytic ribozymes based upon catalytic mechanism [version 1; peer review: 3 approved] by Lilley, David M.J

“…The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2′-oxygen atom on the adjacent phosphorus with an…”
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Cooperative control of holliday junction resolution and DNA repair by the SLX1 and MUS81-EME1 nucleases by Castor, Dennis, Nair, Nidhi, Déclais, Anne-Cécile, Lachaud, Christophe, Toth, Rachel, Macartney, Thomas J, Lilley, David M J, Arthur, J Simon C, Rouse, John

“…Holliday junctions (HJs) are X-shaped DNA structures that arise during homologous recombination, which must be removed to enable chromosome segregation. The…”
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Orientation of Cyanine Fluorophores Terminally Attached to DNA via Long, Flexible Tethers by Ouellet, Jonathan, Schorr, Stephanie, Iqbal, Asif, Wilson, Timothy J., Lilley, David M.J.

“…Cyanine fluorophores are commonly used in single-molecule FRET experiments with nucleic acids. We have previously shown that indocarbocyanine fluorophores…”
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Measurement of the Change in Twist at a Helical Junction in RNA Using the Orientation Dependence of FRET by Fessl, Tomáš, Lilley, David M.J.

“…Indocarbocyanine fluorophores attached via the 5′ terminus of double-stranded nucleic acids have a strong propensity to stack onto the terminal basepair. We…”
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Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA by Liu, Yijin, Freeman, Alasdair D.J., Déclais, Anne-Cécile, Wilson, Timothy J., Gartner, Anton, Lilley, David M.J.

“…We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have…”
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Structural dynamics of individual Holliday junctions by Ha, Taekjip, McKinney, Sean A, Déclais, Anne-Cécile, Lilley, David M.J

“…The four-way DNA (Holliday) junction is the central intermediate of genetic recombination, but the dynamic aspects of this important structure are presently…”
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Single-Molecule Observation of the Induction of k-Turn RNA Structure on Binding L7Ae Protein by Wang, Jia, Fessl, Tomáš, Schroeder, Kersten T., Ouellet, Jonathan, Liu, Yijin, Freeman, Alasdair D.J., Lilley, David M.J.

“…The k-turn is a commonly occurring structural motif that introduces a tight kink into duplex RNA. In free solution, it can exist in an extended form, or by…”
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The Structure of Sulfoindocarbocyanine 3 Terminally Attached to dsDNA via a Long, Flexible Tether by Urnavicius, Linas, McPhee, Scott A., Lilley, David M.J., Norman, David G.

“…Fluorescence resonance energy transfer (FRET) is an important source of long-range distance information in macromolecules. However, extracting maximum…”
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FAN1 Activity on Asymmetric Repair Intermediates Is Mediated by an Atypical Monomeric Virus-type Replication-Repair Nuclease Domain by Pennell, Simon, Déclais, Anne-Cécile, Li, Jiejin, Haire, Lesley F., Berg, Wioletta, Saldanha, José W., Taylor, Ian A., Rouse, John, Lilley, David M.J., Smerdon, Stephen J.

“…FAN1 is a structure-selective DNA repair nuclease with 5′ flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. It is the only…”
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How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes by Lilley, David M J

“…Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. The discovery of several new…”
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The global structure of the VS ribozyme by Lafontaine, Daniel A., Norman, David G., Lilley, David M.J.

“…The VS ribozyme comprises five helical segments (II–VI) in a formal H shape, organized by two three‐way junctions. It interacts with its stem–loop substrate…”
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Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes by Wilson, Timothy J, Liu, Yijin, Li, Nan-Sheng, Dai, Qing, Piccirilli, Joseph A, Lilley, David M. J

“…Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have…”
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The Kink Turn, a Key Architectural Element in RNA Structure by Huang, Lin, Lilley, David M.J.

“…Kink turns (k-turns) are widespread structural elements that introduce an axial bend into duplex RNA with an included angle of 50°. These mediate key tertiary…”
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The K-turn motif in riboswitches and other RNA species by Lilley, David M.J.

“…The kink turn is a widespread structure motif that introduces a tight bend into the axis of duplex RNA. This generally functions to mediate tertiary…”
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Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids by Iqbal, Asif, Arslan, Sinan, Okumus, Burak, Wilson, Timothy J, Giraud, Gerard, Norman, David G, Ha, Taekjip, Lilley, David M.J

“…We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is…”
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Identification of KIAA1018/FAN1, a DNA Repair Nuclease Recruited to DNA Damage by Monoubiquitinated FANCD2 by MacKay, Craig, Déclais, Anne-Cécile, Lundin, Cecilia, Agostinho, Ana, Deans, Andrew J., MacArtney, Thomas J., Hofmann, Kay, Gartner, Anton, West, Stephen C., Helleday, Thomas, Lilley, David M.J., Rouse, John

“…DNA interstrand crosslinks (ICLs) are highly toxic because they block the progression of replisomes. The Fanconi Anemia (FA) proteins, encoded by genes that…”
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The molecular recognition of kink-turn structure by the L7Ae class of proteins by Huang, Lin, Lilley, David M J

“…L7Ae is a member of a protein family that binds kink-turns (k-turns) in many functional RNA species. We have solved the X-ray crystal structure of the…”
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Coordination of Structure-Specific Nucleases by Human SLX4/BTBD12 Is Required for DNA Repair by Muñoz, Ivan M., Hain, Karolina, Déclais, Anne-Cécile, Gardiner, Mary, Toh, Geraldine W., Sanchez-Pulido, Luis, Heuckmann, Johannes M., Toth, Rachel, Macartney, Thomas, Eppink, Berina, Kanaar, Roland, Ponting, Chris P., Lilley, David M.J., Rouse, John

“…Budding yeast Slx4 interacts with the structure-specific endonuclease Slx1 to ensure completion of ribosomal DNA replication. Slx4 also interacts with the…”
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Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction by Lafontaine, Daniel A., Norman, David G., Lilley, David M.J.

“…The VS nucleolytic ribozyme has a core comprising five helices organized by two three‐way junctions. The ribozyme can act in trans on a hairpin‐loop substrate,…”
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Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA by Liu, Yijin, Lilley, David M.J.

“…The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially…”
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