Nucleic Acids Conference 2019

Structures, Mechanisms and Interactions with Proteins

28 – 30 June 2019 University of Dundee, UK Dalhousie Building

 

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Welcome Celebrating 40 years of the Lilley laboratory in Dundee The background for this conference is an approaching 40th anniversary of the laboratory of David Lilley in the University of Dundee. It also marks the passage of his 70th birthday in 2018. All the invited speakers have some connection with the Lilley laboratory, being present or former members, collaborators or long-standing scientific friends. Find out more about the history of the Lilley lab from page 8.

 

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Thanks to our sponsors

•   The Agouron Institute •   ATDBio Ltd. •   Glen Research •   New England Biolabs •   The RNA Society •   Biosearch Techologies •   ChemGenes •   PCCP for sponsoring the lectureship by Dr Joseph Piccirill •   The Gait Lectureship of the RSC Nucleic Acids Group, to be awarded to Dr Wei

Yang

 

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Scientific Programme

All scientific sessions will be held in SG11, lecture theatre 4 on the ground floor of the

Dalhousie Building. Breaks and lunch will be in the foyer.

FRIDAY 28 June

Session 1: Chair David Lilley FRS

14:00 – 14:10 Introduction

14:10 - 14:50 Yamuna Krishnan University of Chicago, USA

DNA reporters for discovery biology

14:50 - 15:20 Ben Luisi University of Cambridge

The dynamic machinery of bacterial riboregulation

15:20 - 15:50 Dan Lafontaine Sherbrooke University, Canada

Time for a break: importance of pausing in riboswitch activity

Break

16:20 - 17:00 Taekjip Ha Johns Hopkins University, USA

CRISPR and DNA repair

17:00 - 17:30 Yiliang Ding 丁一倞 John Innes Centre, Norwich

RNA structure-dependent activation of endonuclease RISC promotes miRNA cleavage

in vivo

17:30 - 18:20 Wei Yang 杨薇 (Gait Lecture) National Institutes of Health, USA

Structure, assembly and reaction chemistry of the DNA replisome

18:30 Reception in the Street, School of Life Sciences Complex SATURDAY 29 June

Session 2: Chair Steve Halford FRS

09:00 - 09:30 David Rueda Imperial College London

How CRISPR/Cas9 finds off-targets

09:30 - 10:10 Steve West FRS Francis Crick Institute

A life on Holliday

 

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10:10 - 10:30 Tim Wilson University of Dundee

Alternative catalytic strategies employed by the nucleolytic ribozymes

Break

11:00 - 11:20 Carlos Penedo University of St. Andrews

The lysine riboswitch: tuning function at physiological conditions

11:20 - 12:00 Yi Zhang 张翼 ABLife Inc., Wuhan, Hubei, China

The dynamics of FTO binding and demethylation from the m6A motifs

12:00 - 12:30 Sangchul Hohng Seoul National University, Seoul, South Korea

Secrets about the birth of RNAs revealed by single-molecule fluorescence

measurements

Lunch

Session 3: Chair Simon Phillips

14:00 – 14:40 Malcolm White University of St. Andrews

Ring War: virus-host conflict mediated by cyclic oligoadenylate signalling

14:40 – 15:10 Darrin York Rutgers University, USA Bridging the gap between theory and experiment: how computational enzymology can shed light on ribozyme mechanisms

15:10 – 15:30 Lin Huang 黄林 University of Dundee

Ligand binding and specificity in riboswitches

Break

16:10 – 16:50 Joe Piccirilli (The PCCP Lecture) University of Chicago, USA

Progress in the use of antibodies as RNA crystallization chaperones

16:50 – 17:10 Christian Hammann Jacobs University, Bremen, Germany

The elongator complex of D. discoideum

17:10 – 18:00 David Lilley FRS University of Dundee

Branching out into nucleic acids : retrospective

18:30 Reception in 172 The Caird for lab and invited guests

 

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SUNDAY 30 June

Session 4: Chair Mike Gait

09:00 – 09:40 Eric Westhof Université de Strasbourg, France

The multiple flavours of GU pairs.

09:40 - 10:00 Steffi Kath-Schorr Universität Bonn, Germany

RNA functionalization via an expanded genetic alphabet

10:00 – 10:30 Mark Dillingham Bristol University

Bacterial machines for repairing broken DNA and how phage shut them down

Break

11:10 - 11:50 David Sherratt FRS Oxford University

Organising and unlinking the E. coli chromosome

11:50 - 12:20 Alastair Murchie Fudan University, Shanghai, China

The identification of novel regulatory RNAs

Lunch

Session 5: Chair Malcolm Buckle

14:00 - 14:20 Jonathan Fogg Baylor College of Medicine, Houston, USA

Interplay between supercoiling-induced localized denaturation and DNA dynamics

14:20 – 14:50 Jan Lipfert Ludwig-Maximilian-Universität, München, Germany

From SAXSy RNA to nucleic acids at a stretch

14:50 – 15:10 Marie-Josèphe Giraud-Panis IRCAN, Nice, France

The telomeric TRF2 protein: a story with a twist at the end

15:10 – 15:40 Marco Bianchi San Raffaele Università, Milano

TBA

15:40 – 16:10 Anton Gartner University of Dundee

The longest of all molecules : Massive next generation sequencing to work out basic

mechanisms of mutagenesis using the C. elegans model and cancer genomes

Depart

 

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A  scientific  history  of  the  Lilley  lab  1981  –  present    The key discovery that set the future path of the lab was published in 1980, a year before the Dundee lab opened. This was the finding that inverted repeat sequences could extrude cruciform structures in negatively supercoiled DNA 1. As well as the first demonstration of topological stabilization of perturbed local structure, the cruciform was an example of a four-way junction in DNA, and this pretty much set the agenda for the foreseeable future. We showed these structures were substrates for T4 endonuclease VII 2, and two decades later the supercoil-stabilized cruciform structures became powerful tools in the mechanistic investigation of junction resolution. Another aspect of DNA supercoiling drew the attention of the lab in those early days. We picked up the mystery of the activation of the leu-500 promoter in Salmonella that was suppressed by the supX mutation that turned out to be topA, the structural gene for topoisomerase I. Our first postdoc Mark Richardson generated a series of topA and gyr mutants in S. typhimurium, but we were puzzled because the activation of leu-500 seemed to correlate with topA, not the level of supercoiling per se 3. This remained a mystery for ten years, whereupon Chen Dong Rong and Richard Bowater picked up the problem, and were able to explain it 4. It turned out that negative supercoiling arising from transcription of a divergent promoter activated the mutant leu-500 promoter. In a topA cell this is not relaxed by topoisomerase I. Thus promoters can be topologically coupled. In between those two sets of experiments some extremely key experiments were done on the structure of the four-way DNA junction. Gerald Gough built pseudocruciform structures using single-strand DNA phages of opposite polarity, and showed that the junction kinked the DNA so that it

migrated slowly in polyacrylamide gels 5. Derek Duckett subsequently elaborated this experiment using synthetic DNA junctions in electrophoretic experiments designed to compare the six inter-helical angles 6. From this we proposed the stacked X-structure for the Holliday junction. That emerged from the discussion in one of the most exciting lab meetings we ever had! Over a decade later that was confirmed by X-ray crystallography.

The stacked X-structure of the Holliday junction

The work on the structure of the junction almost immediately opened a new vista in the lab. Alastair Murchie and I were looking at models of the junction generated by Eberhard von Kiting and Stephan Diekmann 7, and were thinking of how we might test them in a completely different way. We hit on the idea of using FRET between pairs of fluorophores attached to the ends of arms in a pairwise manner. When Alastair first arrived in the lab he set up the chemical synthesis of nucleic acids, and this has been invaluable to our approaches ever since, allowing us to introduce modified nucleotides, phosphorothioates and fluorophores. Scott McPhee and Saira Ashraf have continued to develop our synthetic methods. We initiated a long collaboration with Bob Clegg (then at the MPI in Göttingen) who worked out the powerful acceptor normalization method. These spectroscopic experiments confirmed and extended our understanding of the structure 8. They were really the first of the modern generation of FRET

 

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studies of nucleic acids, and this lab has used the method continuously to the present day, both for DNA and RNA. Subsequently this placed us in a good position to exploit FRET to study the dynamics of single molecules. One Saturday afternoon I was talking with Bob Clegg in the physics department of the University of Illinois in Urbana-Champaign (Bob had moved there a few years before) when Taekjip Ha wandered in, sat down and joined in the discussion. He had just been appointed at UIUC, and after a while he proposed we should collaborate. The resulting experiments demonstrated conformer exchange in DNA junctions 9, that would have been impossible in bulk measurements. The collaboration continued for several years in both DNA and RNA studies. More recently we have been interested in fluorophore positioning, using the k2 orientation parameter in FRET to provide angular information, experiments that were performed by Asif Iqbal  10. Around the mid-1990s we briefly became interested in guanine tetraplex structures. Alastair Murchie initiated studies of a parallel-stranded G4 structure, that was then solved by NMR in solution by Fareed Aboul-ela 11 and in the crystal in collaboration with Ben Luisi 12. These structures are unlikely to be of biological importance, but that was less apparent at that time. From the mid-1990s we also began a long study of the Holliday junction-resolving enzymes, particularly from phage, bacteria and yeast mitochondria. This really began when Derek Duckett and Marie-Jo Giraud-Panis cloned and expressed T7 endonuclease I 13 and T4 endonuclease VII 14. A little later Malcolm White came into the lab, identified the gene for yeast CCE1, cloned and expressed it 15. They, Richard Pöhler, Jonathan Fogg Anne-Cécile Déclais and Alasdair Freeman worked out all the key properties required by a junction-resolving enzyme 16. The enzyme should bind with high affinity and

great selectivity to the four-way junction, and introduce coordinated bilateral cleavages. The latter aspect was shown by careful kinetic analysis (thanks to Anne-Cécile Déclais) of the cleavage of a supercoil-stabilized cruciform. Jonathan Fogg showed that second strand cleavage was significantly accelerated in these enzymes, so ensuring a productive resolution 17-18. At the same time we collaborated with Simon Phillips and Jon Hadden in Leeds to obtain the crystal structure of T7 endonuclease I first as free protein 19, and subsequently as a complex with a DNA junction 20. By a happy coincidence the latter was solved at the same moment that Yang Wei (NIH) solved the complex of T4 endonuclease VII bound to a junction. The structures were quite different, and were published back-to-back. Much more recently our attention turned to eukaryotic junction-resolving enzymes. One of these is GEN1 identified in Steve West’s lab. The human enzyme is highly prone to aggregation and our colleague Toni Gartner suggested working with the enzyme from a thermophilic fungus. Alasdair Freeman expressed this and studied the biochemistry, finding it to have properties closely similar to the enzymes of lower organisms that we studied for so long 21. As so often, the basic principles of function are elucidated by studying enzymes from viruses or lower organisms. In parallel with the biochemistry, Liu Yijin solved the X-ray crystal structure bound to its product of resolution 22. From associations in the lattice it was also possible to deduce the likely structure of the intact complex of a dimer of GEN1 bound to a four-way DNA junction. Liu Yijin and Subbu Sundaramoorthy are currently extending this work using cryo-EM.

 

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The GEN1-DNA complex in the crystal

In the 1990s we turned to the study of RNA for the first time. This began with studies of base bulges by Anamitra Bhattacharyya 23 and helical junctions by Derek Duckett 24. In 2004 we began a study of the kink-turn (k-turn) in RNA, an extremely widespread motif that introduces a very sharp turn into the axis of duplex RNA. These studies were begun by Terry Goody and Liu Jia 25-26, and continued more recently by Kersten Schroeder, Peter Daldrop, Huang Lin, Scott McPhee and Wang Jia. This work has defined all the structural and folding properties of the k-turn, to the point where it is arguably the best-understood motif in RNA architecture (see a recent review written by Huang Lin and DMJL 27). The L7Ae family of proteins bind k-turns in the ribosome, spliceosome, snoRNPs and even RNaseP. Ben Turner showed these bind with pM affinity 28, Huang Lin solved the crystal structure of a complex of L7Ae bound to Kt-7 at the highest resolution yet obtained 29, and Wang Jia obtained single-molecule data consistent with conformer selection 30. Huang Lin has used k-turns as a building block in nano-scale assembly 31. Huang Lin and Saira Ashraf have shown that k-turn folding can be disrupted by inclusion of N6-methyladenine 32, the most common covalent modification of RNA, and that this forms the basis of a probable regulatory mechanism for box C/D snoRNP assembly in humans. A long interest in the structure, folding and catalytic mechanism of ribozymes began in 1995

when Gurminder Bassi and Alastair Murchie studied the two-step folding of the hammerhead ribozyme 33-34. Somewhat later it was shown that a key tertiary contact had been omitted from the forms that everyone studied. Carlos Penedo used steady-state FRET to show that folding was much more efficient if this element was included 35. Similarly in 1998 Alastair Murchie and Frank Walter found that a four-way helical junction was critical to the function of the hairpin ribozyme 36. Somewhat later in collaboration with Taekjip Ha, Tim Wilson obtained single-molecule data that showed the importance of the junction to folding 37, and Michelle Nahas and Tim Wilson demonstrated cycles of cleavage and ligation in single hairpin ribozyme molecules 38. In the early 2000’s we began studies of the Varkud Satellite (VS) ribozyme, the largest of the nucleolytic ribozymes. Daniel Lafontaine carried out gel electrophoretic and steady-state FRET experiments to define the conformation of the three-way helical junctions, and then we assembled the whole structure based on small-angle X-ray scattering experiments performed by Jonathan Ouellet and Jan Lipfert 39. Dan Lafontaine had identified A576 as a key nucleobase 40, and later Tim Wilson found G638 as the second nucleobase 41. From the pH dependence coupled with atomic mutagenesis we knew that these two nucleobases were acting in concerted general acid-base catalysis, but could not say which was which. This was finally nailed down by Tim Wilson using phosphorothiolates synthesized in Joe Piccirilli’s lab in Chicago 42. This pretty much defined the catalytic mechanism of the VS ribozyme, and by the time that the crystal structure of the VS ribozyme was finally obtained by Joe everything was pretty much where we expected it to be 43. Analogous phosphorothiolate experiments allowed Stephanie Schorr and Tim Wilson to work out the mechanism of the hairpin ribozyme 44.

 

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The catalytic center of the twister ribozyme.

In the last five years most of the ribozyme work has moved on to the new nucleolytic ribozymes discovered in the Breaker lab. Liu Yijin has solved crystal structures for the twister 45, TS 46 and pistol ribozymes 47, and Tim Wilson has analysed their catalytic mechanisms. Twister uses guanine and adenine nucleobases as general base and acid, but unusually the proton is donated by the highly acidic N3 of adenine, not the usual N1  48. This is probably now the best-understood of the nucleolytic ribozymes. TS uses a hydrated metal ion as general base 46, while pistol uses a metal ion as general acid, together with a guanine

nucleobase as general base {Wilson, 2019 #5383. With nine nucleolytic ribozymes to compare we are now able to perceive mechanistic groupings within this class of ribozyme. In the last three years we have also become interested in another class of RNA molecules, the riboswitches. Huang Lin has solved crystal structures of the guanidine-II 47, guanidine-III 49, SAM-V 50 and glutamine-II 51 riboswitches. These

demonstrate that RNA is a remarkable ligand for small molecules, binding with great selectivity.

Guanidine bound to the guanidine-III riboswitch This brings us up to date, and work is continuing in many of these areas, as well as new ones that have opened up. In this short overview I can only present a flavour of the work that has gone on, and I could only directly acknowledge the work of some of the (mainly longer-serving) members of the lab. Sadly two of the people whose work is discussed above are no longer with us. Gurminder Bassi passed away at far too young an age in Paris. He was extremely smart, and was the first to set up FRET experiments in this laboratory. Bob Clegg passed away in 2012. He knew more about fluorescence than anyone I know, and indeed his knowledge of physics was encyclopaedic. He and I would often sit in a bar somewhere in Göttingen or Urbana talking science into the small hours of the night. Both Gummi and Bob are sadly missed, a great loss to science.

1. Lilley, D. M. J., The inverted repeat as a recognisable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA 1980, 77, 6468-6472.

2. Lilley, D. M. J.; Kemper, B., Cruciform-resolvase interactions in supercoiled DNA. Cell 1984, 36, 413 - 422.

3. Richardson, S. M. H.; Higgins, C. F.; Lilley, D. M. J., The genetic control of DNA supercoiling in Salmonella typhimurium. EMBO J. 1984, 3, 1745-1752.

4. Chen, D.; Bowater, R.; Dorman, C.; Lilley, D. M. J., Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an

adjacent gene. Proc. Natl. Acad. Sci. USA 1992, 89, 8784-8788.

5. Gough, G. W.; Lilley, D. M. J., DNA bending induced by cruciform formation. Nature 1985, 313, 154 - 156.

6. Duckett, D. R.; Murchie, A. I. H.; Diekmann, S.; von Kitzing, E.; Kemper, B.; Lilley, D. M. J., The structure of the Holliday junction and its resolution. Cell 1988, 55, 79-89.

7. von Kitzing, E.; Lilley, D. M. J.; Diekmann, S., The stereochemistry of a four-way DNA junction: a theoretical study. Nucleic Acids Res. 1990, 18 (9), 2671-2683.

8. Murchie, A. I. H.; Clegg, R. M.; von Kitzing, E.; Duckett, D. R.; Diekmann, S.; Lilley, D. M. J.,

 

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Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 1989, 341, 763-766.

9. McKinney, S. A.; Déclais, A.-C.; Lilley, D. M. J.; Ha, T., Structural dynamics of individual Holliday junctions. Nature Struct. Biol. 2003, 10 (2), 93-97.

10. Iqbal, A.; Arslan, S.; Okumus, B.; Wilson, T. J.; Giraud, G.; Norman, D. G.; Ha, T.; Lilley, D. M. J., Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally-attached to double-stranded nucleic acids. Proc. Natl. Acad. Sci. USA 2008, 105 (32), 11176-11181.

11. Aboul-ela, F.; Murchie, A. I. H.; Lilley, D. M. J., NMR study of parallel-stranded tetraplex formation by dTG4T. Nature 1992, 360, 280-282.

12. Laughlan, G.; Murchie, A. I. H.; Norman, D. G.; Moore, M. H.; Moody, P. C. E.; Lilley, D. M. J.; Luisi, B., The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science 1994, 265, 520-524.

13. Duckett, D. R.; Giraud-Panis, M.-E.; Lilley, D. M. J., Binding of the junction-resolving enzyme bacteriophage T7 endonuclease I to DNA: separation of binding and catalysis by mutation. J. Molec. Biol. 1995, 246, 95-107.

14. Giraud-Panis, M.-J. E.; Duckett, D. R.; Lilley, D. M. J., The modular character of a DNA junction resolving enzyme: a zinc binding motif in T4 endonuclease VII. J. Molec. Biol. 1995, 252, 596-610.

15. White, M. F.; Lilley, D. M. J., The structure-selectivity and sequence-preference of the junction-resolving enzyme CCE1 of Saccharomyces cerevisiae. J. Molec. Biol. 1996, 257, 330-341.

16. Declais, A. C.; Lilley, D. M., New insight into the recognition of branched DNA structure by junction-resolving enzymes. Current opinion in structural biology 2008, 18 (1), 86-95.

17. Fogg, J. M.; Schofield, M. J.; Déclais, A.-C.; Lilley, D. M. J., The yeast resolving enzyme CCE1 makes sequential cleavages in DNA junctions within the lifetime of the complex. Biochemistry 2000, 39, 4082-4089.

18. Fogg, J. M.; Lilley, D. M. J., Ensuring productive resolution by the junction-resolving enzyme RuvC: large enhancement of the second-strand cleavage rate. Biochemistry 2000, 39 (51), 16125-16134.

19. Hadden, J. M.; Convery, M. A.; Déclais, A.-C.; Lilley, D. M. J.; Phillips, S. E. V., Crystal structure of the Holliday junction-resolving enzyme T7 endonuclease I at 2.1 Å resolution. Nature Struct. Biol. 2001, 8, 62-67.

20. Hadden, J. M.; Declais, A. C.; Carr, S. B.; Lilley, D. M.; Phillips, S. E., The structural basis of Holliday junction resolution by T7 endonuclease I. Nature 2007, 449 (7162), 621-4.

21. Freeman, A. D. J.; Liu, Y.; Déclais, A.-C.; Gartner, A.; Lilley, D. M. J., GEN1 from a thermophilic

fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes J. Molec. Biol. 2014, 426, 3946-3959.

22. Liu, Y.; Freeman, A. D. J.; Déclais, A.-C.; Wilson, T. J.; Gartner , A.; Lilley, D. M. J., Crystal structure of a eukaryotic GEN1 resolving enzyme bound to DNA. Cell Reports 2015, 13, 2565-2575.

23. Bhattacharyya, A.; Murchie, A. I. H.; Lilley, D. M. J., RNA bulges and the helical periodicity of double-stranded RNA. Nature 1990, 343, 484-487.

24. Duckett, D. R.; Murchie, A. I. H.; Lilley, D. M. J., The global folding of four-way helical junctions in RNA, including that in U1 snRNA. Cell 1995, 83, 1027-1036.

25. Goody, T. A.; Melcher, S. E.; Norman, D. G.; Lilley, D. M. J., The kink-turn motif in RNA is dimorphic, and metal ion dependent. RNA 2004, 10, 254–264.

26. Liu, J.; Lilley, D. M. J., The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA. RNA 2007, 13 (2), 200-210.

27. Huang, L.; Lilley, D. M. J., The kink-turn in the structural biology of RNA. Quart. Rev. Biophys. 2018, 51, 1-32.

28. Turner, B.; Lilley, D. M. J., The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA. J. Molec. Biol. 2008, 381 (2), 431-442.

29. Huang, L.; Lilley, D. M. J., The molecular recognition of kink-turn structure by the L7Ae class of proteins. RNA 2013, 19 (12), 1703-1710.

30. Wang, J.; Fessl, T.; Schroeder, K. T.; Ouellet, J.; Liu, Y.; Freeman, A. D.; Lilley, D. M. J., Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein. Biophys. J. 2012, 103 (12), 2541-2548.

31. Huang, L.; Lilley, D. M. J., A quasi-cyclic RNA nano-scale molecular object constructed using kink turns. Nanoscale 2016, 8, 15189-15195

32. Huang, L.; Ashraf, S.; Wang, J.; Lilley, D. M., Control of box C/D snoRNP assembly by N6-methylation of adenine. EMBO rep. 2017, 18, 1631–1645.

33. Bassi, G.; Møllegaard, N. E.; Murchie, A. I. H.; von Kitzing, E.; Lilley, D. M. J., Ionic interactions and the global conformations of the hammerhead ribozyme. Nature Struct. Biol. 1995, 2 (1), 45-55.

34. Bassi, G. S.; Murchie, A. I. H.; Walter, F.; Clegg, R. M.; Lilley, D. M. J., Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study. EMBO J. 1997, 16 (24), 7481-7489.

35. Penedo, J. C.; Wilson, T. J.; Jayasena, S. D.; Khvorova, A.; Lilley, D. M. J., Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 2004, 10, 880-888.

 

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36. Murchie, A. I. H.; Thomson, J. B.; Walter, F.; Lilley, D. M. J., Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Molec. Cell 1998, 1, 873-881.

37. Tan, E.; Wilson, T. J.; Nahas, M. K.; Clegg, R. M.; Lilley, D. M. J.; Ha, T., A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA 2003, 100, 9308-9313.

38. Nahas, M. K.; Wilson, T. J.; Hohng, S.; Jarvie, K.; Lilley, D. M. J.; Ha, T., Observation of internal cleavage and ligation reactions of a ribozyme. Nature Struct. Molec. Biol. 2004, 11 (11), 1107-1113.

39. Lipfert, J.; Ouellet, J.; Norman, D. G.; Doniach, S.; Lilley, D. M. J., The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure 2008, 16, 1357-1367.

40. Lafontaine, D. A.; Wilson, T. J.; Norman, D. G.; Lilley, D. M. J., The A730 loop is an important component of the active site of the VS ribozyme. J. Molec. Biol. 2001, 312 (4), 663-674.

41. Wilson, T. J.; McLeod, A. C.; Lilley, D. M. J., A guanine nucleobase important for catalysis by the VS ribozyme EMBO J. 2007, 26 (10), 2489-2500.

42. Wilson, T. J.; Li, N.-S.; Lu, J.; Frederiksen, J. K.; Piccirilli, J. A.; Lilley, D. M. J., Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc. Natl. Acad. Sci. USA 2010, 107, 11751-11756.

43. Suslov, N. B.; DasGupta, S.; Huang, H.; Fuller, J. R.; Lilley, D. M.; Rice, P. A.; Piccirilli, J. A., Crystal structure of the Varkud satellite ribozyme. Nature Chem. Biol. 2015, 11 (11), 840-846.

44. Kath-Schorr, S.; Wilson, T. J.; Li, N. S.; Lu, J.; Piccirilli, J. A.; Lilley, D. M., General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J. Amer. Chem. Soc. 2012, 134 (40), 16717-24.

45. Liu, Y.; Wilson, T. J.; McPhee, S. A.; Lilley, D. M., Crystal structure and mechanistic investigation of the twister ribozyme. Nature Chem. Biol. 2014, 10 (9), 739-744.

46. Liu, Y.; Wilson, T. J.; Lilley, D. M. J., The structure of a nucleolytic ribozyme that employs a catalytic metal ion. Nature Chem. Biol. 2017, 13, 508-513.

47. Wilson, T. J.; Liu, Y.; Li, N. S.; Dai, Q.; Piccirilli, J. A.; Lilley, D. M. J., Comparison of the structures and mechanisms of the pistol and hammerhead ribozymes. J. Amer. Chem. Soc. 2019, in the press.

48. Wilson, T. J.; Liu, Y.; Domnick, C.; Kath-Schorr, S.; Lilley, D. M., The novel chemical mechanism of the twister ribozyme. J. Amer. Chem. Soc. 2016, 138 (19), 6151-6162.

49. Huang, L.; J., W.; Lilley, D. M. J., The structure of the guanidine-II riboswitch. Cell Chem. Biol. 2017, 24, 695-702.

50. Huang, L.; Wang, J.; Wilson, T. J.; Lilley, D. M. J., Structure of the Guanidine III Riboswitch. Cell Chem Biol 2017, 24 (11), 1407-1415 e2.

51. Huang, L.; Wang, J.; Watkins, A. M.; Das, R.; Lilley, D. M. J., Structure and ligand binding of the glutamine-II riboswitch. Nucleic Acids res. 2019, In the press.

 

 

Lilley Laboratory Timeline

       

       

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University of Dundee Nethergate, Dundee DD1 4HN t: +44 (0)1382 383000 e: dundee.ac.uk