Nucleic Acid Structure Research Group

 

 

D. Chen, S. Bachellier and D.M.J. Lilley Activation of the leu-500 promoter by a reversed-polarity tetA gene: response to global plasmid supercoiling. J. Biol. Chem. 273, 653-659 (1998).

 

R.J. Grainger A.I.H. Murchie and D.M.J. Lilley (1998) Exchange between stacking conformers in a four-way DNA junction Biochemistry 37, 23-32.

 

J.R.G. Pöhler, D.G. Norman, J. Bramham, M.E. Bianchi and D.M.J. Lilley HMG-box proteins bind to four-way DNA junctions in their open conformation. EMBO J. 17, 817-826 (1998).

 

M.-J.E. Giraud-Panis and D.M.J. Lilley Structural recognition and distortion by the DNA junction-resolving enzyme RusA. J. Molec. Biol. 278, 117-133 (1998).

 

M. Fojta, R.P. Bowater, D.M.J. Lilley and E. Palecek Two superhelix-dependent DNA transitions detected by changes in DNA adsorption/desorption behaviour. Biochemistry 37, 4853-4862 (1998).

 

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

 

F. Walter, A.I.H. Murchie, D.R. Duckett and D.M.J. Lilley Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer. RNA 4, 719-728 (1998).

 

M.J. Schofield, D. M.J. Lilley and M.F. White Dissection of the sequence specificity of the Holliday junction endonuclease CCE1. Biochemistry 37, 7733-7740 (1998).

 

F. Walter, A.I.H. Murchie, J.B. Thomson and D.M.J. Lilley Structure and activity of the hairpin ribozyme in its natural junction conformation; effect of metal ions Biochemistry 37, 14195-14203 (1988).

 

A. I.H. Murchie, F. Walter and D.M.J. Lilley The folding of the four-way RNA junction of the hairpin ribozyme Biochemistry 37, 17629-17636 (1998).

 

J.B. Thomson and D.M.J. Lilley The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form. RNA 5, 180-187 (1999).

 

M.F. White and D.M.J. Lilley Interaction of the resolving enzyme YDC2 with the four-way DNA junction Nucleic Acids Res. 26, 5609-5616 (1998).

 

D. Chen and D.M.J. Lilley Transcription-induced hypersupercoiling of plasmid DNA J. Molec. Biol. 285, 443-448 (1999).

 

M.J. Parkinson, J.R.G. Pöhler and D.M.J. Lilley Catalytic and binding mutants of the junction-resolving enzyme endonuclease I of bacteriophage T7: role of acidic residues Nucleic Acids Res. 27, 682-689 (1999).

 

G.S. Bassi, N.E. Møllegaard, A.I.H.Murchie and D.M.J. Lilley RNA folding and misfolding of the hammerhead ribozyme Biochemistry 38, 3345-3354 (1999).

 

R.J. Grainger D.G. Norman and D.M.J. Lilley Binding of U1A protein to the 3’ untranslated region of its pre-mRNA J. Molec. Biol. 288, 585-594 (1999).

 

J.M. Fogg, M.J. Schofield, M.F. White and D.M.J. Lilley Sequence and functional-group specificity for cleavage of DNA junctions by RuvC of Escherichia coli Biochemistry 38, 11349-11358 (1999).

 

E.L. Zechiedrich, A.B. Khodursky, S. Bachellier, R. Schneider, D. Chen, D.M.J. Lilley and N.R. Cozzarelli Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J. Biol. Chem. 275, 8103-8113 (2000).

 

A.-C. Déclais and D.M.J. Lilley Extensive central disruption of a four-way junction on binding CCE1 resolving enzyme J. Molec. Biol. 296, 421-433 (2000).

 

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

 

D.G. Norman, R.J. Grainger, D. Uhrin and D.M.J. Lilley The location of Cyanine-3 on double-stranded DNA; importance for fluorescence resonance energy transfer studies Biochemistry 39, 6317-6324 (2000).

 

Z. Zhao, T.J. Wilson, K. Maxwell and D.M.J. Lilley The folding of the hairpin ribozyme : Dependence on the loops and the junction. RNA 6, 1833-1846 (2000).

 

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

 

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

 

C. Hammann, A. Cooper and D.M.J. Lilley Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme : An isothermal titration calorimetric study Biochemistry 40, 1423-1429 (2001).

 

K. Havas, A. Flaus, M. Phelan, R. Kingston, P.A. Wade, D.M.J. Lilley and T. Owen-Hughes Generation of superhelical torsion by ATP-dependent chromatin remodelling activities. Cell 103, 1133-1142 (2000).

 

T.J. Wilson, Z.-Y. Zhao, K. Maxwell, L. Kontogiannis and D.M.J. Lilley Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme Biochemistry 40, 2291-2302 (2001).

 

D.A. Lafontaine, D.G. Norman and D.M.J. Lilley Structure, folding and activity of the VS ribozyme : Importance of the 2-3-6 helical junction EMBO J. 20 1415-1424 (2001).

 

A.-C. Déclais, J. Hadden, S.E.V. Phillips and D.M.J. Lilley The active site of the junction-resolving enzyme T7 endonuclease I. J. Molec. Biol. 307, 1145-1158 (2001).

 

C. Hammann, D.G. Norman and D.M.J. Lilley Dissection of the ion-induced folding of the hammerhead ribozyme using ¹⁹F NMR Proc. Natl. Acad. Sci. USA 98, 5503-5508 (2001).

 

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

 

J.M. Fogg, M. Kvaratskhelia, M.F. White and D.M.J. Lilley Distortion of DNA junctions imposed by the binding of resolving enzymes ; A fluorescence study. J. Molec. Biol. 313, 751-764 (2001).

 

M. Kvaratskhelia , B.N. Wardleworth, C.S. Bond, J.M. Fogg, D.M.J. Lilley and M.F. White Holliday junction resolution is modulated by archaeal chromatin components in vitro. J. Biol. Chem. 277, 2992-2996 (2002).

 

T.J. Wilson and D.M.J. Lilley Metal ion binding and the folding of the hairpin ribozyme RNA 8, 587-600 (2002).

 

D.A. Lafontaine, D.G. Norman and D. M.J. Lilley The global structure of the VS ribozyme. EMBO J. 21, 2461-2471 (2002).

 

J.M. Hadden, A.-C. Déclais, S.E. V. Phillips and D.M. J. Lilley Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I EMBO J. 21, 3505-3515 (2002).

 

D.A. Lafontaine, T.J. Wilson, Z.-Y. Zhao and D.M.J. Lilley Functional group requirements in the probable active site of the VS ribozyme J. Molec. Biol. 323, 23-34 (2002).

 

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

 

A.-C. Déclais, J.M. Fogg, A. Freeman, F. Coste, J. Hadden, S.E.V. Phillips and D.M.J. Lilley The complex between a four-way DNA junction and T7 endonuclease I EMBO J. 22, 1398-1409 (2003).

 

S. E. Melcher, T. J. Wilson and D. M. J. Lilley The dynamic nature of the four-way junction of the hepatitis C virus IRES RNA 9, 809-820 (2003).

 

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

 

A. Freeman, A.-C. Déclais and D.M.J. Lilley Metal ion binding in the active site of the junction-resolving enzyme T7 endonuclease I in the presence and absence of DNA. J.Molec. Biol. 333, 59-73 (2003).

 

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

 

A.C. McLeod and D.M.J. Lilley Efficient, pH-dependent RNA ligation by the VS ribozyme in trans Biochemistry 43, 1118 – 1125 (2004).

 

S. Hohng, T.J. Wilson, E. Tan, R. M. Clegg, D.M.J. Lilley and T. Ha Conformational flexibility of four-way junctions in RNA J. Molec. Biol. 336, 69-79 (2004).

 

L. Araki, S. Harusawa, M. Yamaguchi, S. Yonezawa, N. Taniguchi, D. M. J. Lilley, Z. Zhao, and T. Kurihara Synthesis of C4-linked imidazole ribonucleoside phosphoramidite with pivaloyloxymethyl (POM) group Tetrahedron Lett. 45, 2657-2661 (2004).

 

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

 

T. A. Goody, D. M. J. Lilley and D. G. Norman The chirality of a four-way helical junction in RNA J. Amer. Chem. Soc. 126, 4126-4127 (2004).

 

C. Joo, S.A. McKinney, D.M.J. Lilley and T. Ha Exploring rare conformational species and ionic effects from single Holliday junctions J. Molec. Biol. 341, 635-882 (2004).

 

B. Okumus, T. J. Wilson, D.M.J. Lilley and T. Ha. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic Biophys. J. 87, 2798-2806 (2004).

 

J. Liu, A.-C. Déclais and D.M.J. Lilley Electrostatic interactions and the folding of the four-way DNA junction: analysis by selective methyl phosphonate substitution J. Molec. Biol. 343, 851–864 (2004).

 

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

 

J. Liu, A.-C. Déclais, S. McKinney, T. Ha, D.G. Norman and D.M.J. Lilley Stereospecific effects determine the structure of a four-way DNA junction Chem. & Biol. 12, 217-228 (2005).

 

Z. Zhao, A. McLeod, S. Harusawa, L. Araki, M. Yamaguchi, T. Kurihara and D. M. J. Lilley Nucleobase participation in ribozyme catalysis J. Amer. Chem. Soc. 127, 5026-5027 (2005).

 

S. A. McKinney, A. D. Freeman, D. M. J. Lilley and T. Ha Observing spontaneous branch migration of Holliday junctions one step at a time Proc. Natl. Acad. Sci. USA 102, 5715-5720 (2005).

 

B. Turner, S. E. Melcher, T. J. Wilson, D. G. Norman and D. M. J. Lilley Induced fit of RNA on binding the L7Ae protein to the kink-turn motif RNA 11, 1192-1200 (2005).

 

J. Liu, A.-C. Déclais and D.M.J. Lilley Mechanistic aspects of the DNA junction-resolving enzyme T7 endonuclease I Biochemistry 45, 3934-3942 (2006).

 

T. J. Wilson, J. Ouellet, Z. Zhao, S. Harusawa, L. Araki, T. Kurihara and D. M. J. Lilley Nucleobase catalysis in the hairpin ribozyme. RNA 12, 980-987 (2006).

 

A.-C. Déclais, J. Liu, A. D. J. Freeman and D. M. J. Lilley Structural recognition between a four-way DNA junction and a resolving enzyme J. Molec.Biol. 359, 1261-1276 (2006).

 

J.-F. Lemay, J. C. Penedo, R. Tremblay, D. M. J. Lilley and D. A. Lafontaine Folding of the adenine riboswitch Chem. & Biol. 13, 857-868 (2006).

 

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

 

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

 

J. M. Hadden, A.–C. Déclais, S. B. Carr, D. M. J. Lilley and S. E. V. Phillips The structural basis of Holliday junction resolution by T7 endonuclease I. Nature 449, 621-624 (2007).

 

S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley and T. Ha Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction Science 318, 279-283 (2007).

 

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

 

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

 

A. Iqbal, L. Wang, K. C. Thompson, D. M. J. Lilley and D. G. Norman The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies. Biochemistry 30, 7857-7862 (2008).

 

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

 

A. Poulet, R. Buisson, C. Faivre-Moskalenko, M. Koelblen, S. Amiard, F. Montel, S. Cuesta-Lopez, O. Bornet, F. Guerlesquin, T. Godet, J. Moukhtar, F. Argoul, A.-C. Déclais, D. M. J Lilley, S. C. Y. Ip, S. C. West, E. Gilson and M.-J. Giraud-Panis, TRF2 promotes, remodels and protects telomeric Holliday junctions EMBO J. 28, 641-651 (2009).

 

L. Araki, K. Morita, M. Yamaguchi, Z. Zhao, T. J. Wilson, D. M. J. Lilley and S. Harusawa Synthesis of novel C4-linked C2-imidazole ribonucleoside phosphoramidite, and its application to probing the catalytic mechanism of a ribozyme. J. Org. Chem. 74, 2350–2356 (2009).

 

I. M. Muñoz, K. Hain, A.-C. Déclais, M. Gardiner, G. W.Toh, L. Sanchez-Pulido, J. Heuckmann, R. Toth, T. Macartney, B. Eppink, R. Kanaar, C. P. Ponying, D. M. J. Lilley and J. W. Rouse Coordination of structure–specific nucleases by human SLX4/BTBD12 is essential for DNA repair Molec. Cell 35, 116-127 (2009).

 

J. Ouellet, M. Byrne and D. M. J. Lilley Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes RNA 15, 1822-1826 (2009).

 

K. T. Schroeder and D. M. J. Lilley Ion-induced folding of a kink turn that departs from the conventional sequence Nucleic Acids Res. 37, 7281-7289 (2009).

 

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

 

C. MacKay, A.-C. Déclais, C. Lundin, A. Agostinho, A. J. Deans, T. J. MacArtney, K. Hofmann, A. Gartner, S. C. West, T. Helleday, D. M. J. Lilley and J. Rouse Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2 Cell. 142, 65-76 (2010).

A. P. Bailly, A. D. J. Freeman, J. Hall, A.-C. Déclais, A. Alpi, D. M. J. Lilley,  S. Ahmed and A. Gartner  The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair. PLoS Genetics  6(7): e1001025.

 

L. Araki, Z.-y. Zhao, D. M. J. Lilley, and S. Harusawa   Efficient synthesis of 2’-O-cyanoethylated imidazole C-ribonucleoside phosphoramidite: a practical building block for probing the catalytic mechanism of ribozymes Heterocycles  81, 1861-1869 (2010).

 

T. J. Wilson and D. M. J. Lilley Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis ? A critical assessment of available experimental data. RNA 17, 213-221 (2011).

 

N.-S. Li, J. K. Frederiksen, S. Koo, J. Lu, T. J. Wilson, D. M. J. Lilley, J. A. Piccirilli   A general and efficient Approach for the construction of RNA oligonucleotides containing a 5´-phosphorothiolate linkage Nucleic Acids Res. 39, e31 (2011).

 

P. Daldrop, F. E. Reyes, D. A. Robinson, C. M. Hammond, D. M. J. Lilley, R.T. Batey, R. Brenk   Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Chem. Biol. 18, 324-335 (2010).

 

S. Harusawa, K. Fujii,  M. Nishiura,  L. Araki, Y. Usami, Z.-y. Zhao and D. M. J. Lilley Syntheses of novel imidazole C1 and C3-ribonucleoside phosphoramidites for probing catalytic mechanism in ribozyme Heterocycles 83, 2041-2055 (2011).

 

K. T. Schroeder, P. Daldrop and D. M. J. Lilley RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Structure 19, 1233-1240 (2011).

 

J. Ouellet, S. Schorr, A. Iqbal, T. J. Wilson, and D. M. J. Lilley  Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers. Biophys. J. 101, 1148-1154 (2011).

 

B.Aranda-Orgilles, Rutschow, R. Zeller, A. I. Karagiannidis, A. Köhler,  C. Chen, T. Wilson, S. Krause, S. Roepcke, D. M. J. Lilley, R. Schneider & S. Schweiger. The PP2A-specific ubiquitin ligase MID1 is a sequence-dependent regulator of translation efficiency controlling 3-phosphoinositide dependent protein kinase-1(PDPK-1) J. Biol. Chem. 286, 39945-39957 (2011).

 

A. D. J. Freeman, R. Ward, H. El Mkami, D. M. J. Lilley, D. G. Norman.  Analysis of conformational changes in the DNA junction-resolving enzyme T7 endonuclease I on binding a four-way junction using EPR. Biochemistry 50, 9963–9972 (2011).

 

L. Urnavicius, S. A. McPhee, D. M. J. Lilley, D. G. Norman  The structure of sulfoindocarbocyanine 3 terminally attached to dsDNA via a long, flexible tether. Biophys. J.  102, 561-569 (2012).

 

K. T. Schroeder, P. Daldrop, S. A. McPhee and D. M. J. Lilley.  Structure and folding of a rare, natural kink turn in RNA with an A•A pair at the 2b•2n position. RNA In the press.

 

 

 

Some reviews and commentaries

 

D M J Lilley Commentary: All change at Holliday junction. Proc. Natl. Acad. Sci. USA 94, 9513-9515 (1997).

 

D.M.J. Lilley Analysis of the global conformation of branched RNA species by a combined electrophoresis and fluorescence approach. Meth. Enzymol. 317, 368-393 (2000).

 

D.M.J. Lilley Structure, folding and catalysis in the small nucleolytic ribozymes. Current Opinion Structural Biology, 9, 330-338 (1999).

 

D.M.J. Lilley Structures of helical junctions in nucleic acids Quart. Rev. Biophys. 33, 109-159 (2000).

 

D.M.J. Lilley and T.J. Wilson Fluorescence resonance energy transfer as a structural tool for nucleic acids Curr. Opin. Chem. Biol. 4, 507-517 (2000).

 

D.M.J. Lilley and M.F. White Resolving the relationships of resolving enzymes. Proc. Natl. Acad. Sci. USA. 97, 9351-9353 (2000).

 

D.M.J. Lilley The ribosome functions as a ribozyme. ChemBioChem 2, 31-35 (2001).

 

D.M.J. Lilley and M.F. White The junction-resolving enzymes. Nature Reviews Molec. Cell Biol. 2, 433-443 (2001).

 

D.M.J. Lilley Origins of RNA catalysis in the hairpin ribozyme. ChemBioChem 2, 729-733 (2001).

 

C. Hammann and D.M.J. Lilley Folding and activity of the hammerhead ribozyme ChemBioChem 3, 690-700 (2002).

 

D. M. J. Lilley The origins of RNA catalysis in ribozymes Trends Biochem. Sciences 28, 495-501 (2003).

 

D.M.J. Lilley Ribozymes – a snip too far ? Nature Structural Biology 10, 672-673 (2003).

 

D.M.J. Lilley The Varkud satellite ribozyme RNA. 10, 151–158 (2004).

 

A.-C. Déclais and D. M. J. Lilley New insight into the recognition of branched DNA structure by junction-resolving enzymes Curr. Opin. Struct. Biol. 18, 86-95 (2008).

 

D. M.J. Lilley Analysis of branched nucleic acid structure using comparative gel electrophoresis Quart. Rev. Biophys. 41, 1-39 (2008).

 

T.J. Wilson and D. M. J. Lilley The evolution of chemistry in the ribozymes. Science 323, 1436-1438 (2009).

 

D. M. J. Lilley Comparative gel electrophoresis analysis of helical junctions in RNA. Method. Enzymol. (Ed D Herschlag) 469, 143-159 (2009).

 

D. M. J. Lilley The structure and folding of branched RNA analysed by fluorescence resonance energy transfer. Method. Enzymol. (Ed D Herschlag) 469, 159-188 (2009).

 

D. M. J. Lilley Catalysis by nucleolytic ribozymes. Biochem. Soc. Transac. 39, 641-646 (2011).

 

D. M. J. Lilley and J. D. Sutherland The chemical origins of life and its early evolution - an introduction. Philosoph. Transac. Roy. Soc B. 366, 2853–2856 (2011).

 

D. M. J. Lilley Mechanisms of RNA catalysis. Philosoph. Transac. Roy. Soc B. 366, 2910–2917 (2011).

 

 

Book

 

Ribozymes and RNA Catalysis Eds. D M J Lilley and F Eckstein, Royal Society of Chemistry (2008).

 

Some significant older papers

 

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

 

D M J Lilley In vivo consequences of plasmid topology. Nature 292, 380-382 (1981).

 

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

 

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

 

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

 

K M Sullivan & D M J Lilley A dominant influence of flanking sequences on a local structural transition in DNA. Cell 47, 817-827 (1986)

 

S M H Richardson, C F Higgins & D M J Lilley DNA supercoiling and the leu-500 mutation of Salmonella typhimurium. EMBO J. 7, 1863-1869 (1988).

 

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

 

A I H Murchie, R M Clegg, E von Kitzing, D R Duckett, S Diekmann, & D M J Lilley Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763-766 (1989).

 

D R Duckett, A I H Murchie & D M J Lilley The role of metal ions in the conformation of the four-way DNA junction. EMBO J. 9, 583-590 (1990).

 

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

 

R Clegg, A I H Murchie, A Zechel, C Carlberg, S Diekmann & D M J Lilley Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Biochemistry 31, 4846-4856 (1992).

 

F A Riordan, A Bhattacharyya, S McAteer & D M J Lilley Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element. J. Molec. Biol. 226, 305-310 (1992).

 

D Chen, R Bowater, C J Dorman & D M J Lilley Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc Natl Acad Sci USA 89, 8784-8788 (1992).

 

R Clegg, A I H Murchie, A Zechel & D M J Lilley Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc Natl Acad Sci USA 90, 2994-2998 (1993).

 

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

 

D Chen, R Bowater & D M J Lilley Activation of the leu-500 promoter: A topological domain generated by divergent transcription in a plasmid. Biochemistry, 32, 13162-13170 (1993).

 

R M Clegg, A I H Murchie & D M J Lilley The solution structure of the four-way DNA junction at low salt conditions; a fluorescence resonance energy transfer analysis. Biophys. J. 66, 99-109 (1994).

 

N E Møllegaard, A I H Murchie, D M J Lilley & P E Nielsen Uranyl photoprobing of a four-way DNA junction: Evidence of specific metal ion binding. EMBO J. 13, 1508-1516 (1994).

 

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

 

F Aboul-ela, A I H Murchie, D G Norman & D M J Lilley Solution structure of a parallel-stranded tetraplex formed by d(TG₄T) in the presence of sodium ions by nuclear magnetic resonance spectroscopy. J. Molec. Biol. 243, 458-471 (1994).

 

R P Bowater, D Chen and D M J Lilley Modulation of tyrT promoter activity by template supercoiling in vivo. EMBO J. 13, 5647-5655 (1994).

 

C Gohlke, A I H Murchie, D M J Lilley and R M Clegg The bending of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energytransfer. Proc. Natl. Acad. Sci. USA 91, 11660-11664 (1994).

 

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

 

J B Welch, F Walter & D M J Lilley Two inequivalent folding isomers of the three-way DNA junction with unpaired bases: sequence-dependence of the folded conformation J. Molec. Biol. 251, 507-519 (1995).

 

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

 

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

 

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

 

J R G Pöhler, M-J E Giraud-Panis and D M J Lilley T4 endonuclease VII selects and alters the structure of the four-way DNA junction; binding of a resolution-defective mutant enzyme J Molec Biol 260, 687-696 (1996).

 

M F White and D M J Lilley The resolving enzyme CCE1 of yeast opens the structure of the four-way DNA junction J Molec Biol 266 122-134 (1997).

 

M-J E Giraud-Panis and D M J Lilley Near-simultaneous DNA cleavage by the subunits of the junction-resolving enzyme T4 endonuclease VII. EMBO J. 16, 2528 - 2534 (1997).

 

K. Phillips, Z. Dauter, A.I.H. Murchie, D.M.J. Lilley and B. Luisi The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J Molec Biol 273, 171-182 (1997).

 

F Stühmeier, J B Welch, A I H Murchie, D M J Lilley and R M Clegg The global structure of three-way DNA junctions with and without bulges: Fluorescence studies. Biochemistry 36, 13530-13538 (1997).

 

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