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Classification of the nucleolytic ribozymes based upon catalytic mechanism.

Lilley DMJ.

F1000Res. 2019 Aug 19;8. pii: F1000 Faculty Rev-1462. doi: 10.12688/f1000research.19324.1. eCollection 2019. Review.


Effect of methylation of adenine N6 on kink turn structure depends on location.

Ashraf S, Huang L, Lilley DMJ.

RNA Biol. 2019 Oct;16(10):1377-1385. doi: 10.1080/15476286.2019.1630797. Epub 2019 Jun 24.


Structure and ligand binding of the glutamine-II riboswitch.

Huang L, Wang J, Watkins AM, Das R, Lilley DMJ.

Nucleic Acids Res. 2019 Aug 22;47(14):7666-7675. doi: 10.1093/nar/gkz539.


Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes.

Wilson TJ, Liu Y, Li NS, Dai Q, Piccirilli JA, Lilley DMJ.

J Am Chem Soc. 2019 May 15;141(19):7865-7875. doi: 10.1021/jacs.9b02141. Epub 2019 May 2.


Junction resolving enzymes use multivalency to keep the Holliday junction dynamic.

Zhou R, Yang O, Déclais AC, Jin H, Gwon GH, Freeman ADJ, Cho Y, Lilley DMJ, Ha T.

Nat Chem Biol. 2019 Mar;15(3):269-275. doi: 10.1038/s41589-018-0209-y. Epub 2019 Jan 21.


Structure-guided design of a high-affinity ligand for a riboswitch.

Huang L, Wang J, Wilson TJ, Lilley DMJ.

RNA. 2019 Apr;25(4):423-430. doi: 10.1261/rna.069567.118. Epub 2019 Jan 4.


The role of RNA structure in translational regulation by L7Ae protein in archaea.

Huang L, Ashraf S, Lilley DMJ.

RNA. 2019 Jan;25(1):60-69. doi: 10.1261/rna.068510.118. Epub 2018 Oct 16.


A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1.

Liu Y, Freeman AD, Déclais AC, Lilley DMJ.

Nucleic Acids Res. 2018 Nov 16;46(20):11089-11098. doi: 10.1093/nar/gky863.


Structure and ligand binding of the SAM-V riboswitch.

Huang L, Lilley DMJ.

Nucleic Acids Res. 2018 Jul 27;46(13):6869-6879. doi: 10.1093/nar/gky520.


Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes.

Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ.

Methods Enzymol. 2018;600:543-568. doi: 10.1016/bs.mie.2017.11.021. Epub 2018 Feb 1.


The kink-turn in the structural biology of RNA.

Huang L, Lilley DMJ.

Q Rev Biophys. 2018 Jan;51:e5. doi: 10.1017/S0033583518000033. Review.


Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.

Liu Y, Lilley DMJ.

Biophys J. 2017 Dec 5;113(11):2336-2343. doi: 10.1016/j.bpj.2017.10.002.


Structure of the Guanidine III Riboswitch.

Huang L, Wang J, Wilson TJ, Lilley DMJ.

Cell Chem Biol. 2017 Nov 16;24(11):1407-1415.e2. doi: 10.1016/j.chembiol.2017.08.021. Epub 2017 Oct 5.


Sequence determinants of the folding properties of box C/D kink-turns in RNA.

Ashraf S, Huang L, Lilley DMJ.

RNA. 2017 Dec;23(12):1927-1935. doi: 10.1261/rna.063453.117. Epub 2017 Sep 27.


Control of box C/D snoRNP assembly by N6-methylation of adenine.

Huang L, Ashraf S, Wang J, Lilley DM.

EMBO Rep. 2017 Sep;18(9):1631-1645. doi: 10.15252/embr.201743967. Epub 2017 Jun 16.


How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes.

Lilley DMJ.

Biochem Soc Trans. 2017 Jun 15;45(3):683-691. doi: 10.1042/BST20160158. Review.


Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations.

Füchtbauer AF, Preus S, Börjesson K, McPhee SA, Lilley DMJ, Wilhelmsson LM.

Sci Rep. 2017 May 24;7(1):2393. doi: 10.1038/s41598-017-02453-1.


The Structure of the Guanidine-II Riboswitch.

Huang L, Wang J, Lilley DMJ.

Cell Chem Biol. 2017 Jun 22;24(6):695-702.e2. doi: 10.1016/j.chembiol.2017.05.014. Epub 2017 May 18.


The structure of a nucleolytic ribozyme that employs a catalytic metal ion.

Liu Y, Wilson TJ, Lilley DMJ.

Nat Chem Biol. 2017 May;13(5):508-513. doi: 10.1038/nchembio.2333. Epub 2017 Mar 6.


The Guanidine Riboswitch-A Poor Orphan No Longer.

Lilley DMJ.

Cell Chem Biol. 2017 Feb 16;24(2):130-131. doi: 10.1016/j.chembiol.2017.01.010.


Holliday junction-resolving enzymes-structures and mechanisms.

Lilley DMJ.

FEBS Lett. 2017 Apr;591(8):1073-1082. doi: 10.1002/1873-3468.12529. Epub 2017 Jan 1. Review.


A quasi-cyclic RNA nano-scale molecular object constructed using kink turns.

Huang L, Lilley DM.

Nanoscale. 2016 Aug 18;8(33):15189-95. doi: 10.1039/c6nr05186c.


Analysis of the Intrinsically Disordered N-Terminus of the DNA Junction-Resolving Enzyme T7 Endonuclease I: Identification of Structure Formed upon DNA Binding.

Freeman AD, Stevens M, Declais AC, Leahy A, Mackay K, El Mkami H, Lilley DM, Norman DG.

Biochemistry. 2016 Aug 2;55(30):4166-72. doi: 10.1021/acs.biochem.6b00242. Epub 2016 Jul 18.


The Novel Chemical Mechanism of the Twister Ribozyme.

Wilson TJ, Liu Y, Domnick C, Kath-Schorr S, Lilley DM.

J Am Chem Soc. 2016 May 18;138(19):6151-62. doi: 10.1021/jacs.5b11791. Epub 2016 May 6.


A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.

Huang L, Wang J, Lilley DM.

Nucleic Acids Res. 2016 Jun 20;44(11):5390-8. doi: 10.1093/nar/gkw201. Epub 2016 Mar 25.


Editorial overview: Nucleic acids and their protein complexes.

Lilley DM, Pyle AM.

Curr Opin Struct Biol. 2016 Feb;36:vii-viii. doi: 10.1016/ Epub 2016 Mar 2. No abstract available.


The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

Shi X, Huang L, Lilley DM, Harbury PB, Herschlag D.

Nat Chem Biol. 2016 Mar;12(3):146-52. doi: 10.1038/nchembio.1997. Epub 2016 Jan 4.


Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.

Liu Y, Freeman ADJ, Déclais AC, Wilson TJ, Gartner A, Lilley DMJ.

Cell Rep. 2015 Dec 22;13(11):2565-2575. doi: 10.1016/j.celrep.2015.11.042. Epub 2015 Dec 10.


The Kink Turn, a Key Architectural Element in RNA Structure.

Huang L, Lilley DMJ.

J Mol Biol. 2016 Feb 27;428(5 Pt A):790-801. doi: 10.1016/j.jmb.2015.09.026. Epub 2015 Oct 29. Review.


Crystal structure of the Varkud satellite ribozyme.

Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA.

Nat Chem Biol. 2015 Nov;11(11):840-6. doi: 10.1038/nchembio.1929. Epub 2015 Sep 28.


RNA catalysis--is that it?

Wilson TJ, Lilley DM.

RNA. 2015 Apr;21(4):534-7. doi: 10.1261/rna.049874.115. No abstract available.


A critical base pair in k-turns that confers folding characteristics and correlates with biological function.

McPhee SA, Huang L, Lilley DM.

Nat Commun. 2014 Oct 29;5:5127. doi: 10.1038/ncomms6127.


GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes.

Freeman ADJ, Liu Y, Déclais AC, Gartner A, Lilley DMJ.

J Mol Biol. 2014 Dec 12;426(24):3946-3959. doi: 10.1016/j.jmb.2014.10.008. Epub 2014 Oct 12.


Crystal structure and mechanistic investigation of the twister ribozyme.

Liu Y, Wilson TJ, McPhee SA, Lilley DM.

Nat Chem Biol. 2014 Sep;10(9):739-44. doi: 10.1038/nchembio.1587. Epub 2014 Jul 20.


FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.

Pennell S, Déclais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ.

Cell Rep. 2014 Jul 10;8(1):84-93. doi: 10.1016/j.celrep.2014.06.001. Epub 2014 Jun 26.


The K-turn motif in riboswitches and other RNA species.

Lilley DM.

Biochim Biophys Acta. 2014 Oct;1839(10):995-1004. doi: 10.1016/j.bbagrm.2014.04.020. Epub 2014 May 4. Review.


The k-junction motif in RNA structure.

Wang J, Daldrop P, Huang L, Lilley DM.

Nucleic Acids Res. 2014 Apr;42(8):5322-31. doi: 10.1093/nar/gku144. Epub 2014 Feb 14.


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

Huang L, Lilley DM.

Nucleic Acids Res. 2014 Apr;42(7):4734-40. doi: 10.1093/nar/gku087. Epub 2014 Jan 29.


Measurement of the change in twist at a helical junction in RNA using the orientation dependence of FRET.

Fessl T, Lilley DM.

Biophys J. 2013 Nov 5;105(9):2175-81. doi: 10.1016/j.bpj.2013.09.042.


A mechanistic comparison of the Varkud satellite and hairpin ribozymes.

Wilson TJ, Lilley DM.

Prog Mol Biol Transl Sci. 2013;120:93-121. doi: 10.1016/B978-0-12-381286-5.00003-2.


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

Huang L, Lilley DM.

RNA. 2013 Dec;19(12):1703-10. doi: 10.1261/rna.041517.113. Epub 2013 Oct 22.


Cooperative control of holliday junction resolution and DNA repair by the SLX1 and MUS81-EME1 nucleases.

Castor D, Nair N, Déclais AC, Lachaud C, Toth R, Macartney TJ, Lilley DM, Arthur JS, Rouse J.

Mol Cell. 2013 Oct 24;52(2):221-33. doi: 10.1016/j.molcel.2013.08.036. Epub 2013 Sep 26.


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

Daldrop P, Masquida B, Lilley DM.

RNA Biol. 2013 Mar;10(3):445-52. doi: 10.4161/rna.23673. Epub 2013 Jan 30.


The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment.

Daldrop P, Lilley DM.

RNA. 2013 Mar;19(3):357-64. doi: 10.1261/rna.036657.112. Epub 2013 Jan 16.


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

Wang J, Fessl T, Schroeder KT, Ouellet J, Liu Y, Freeman AD, Lilley DM.

Biophys J. 2012 Dec 19;103(12):2541-8. doi: 10.1016/j.bpj.2012.11.006. Epub 2012 Dec 18.


The importance of the N-terminus of T7 endonuclease I in the interaction with DNA junctions.

Freeman AD, Déclais AC, Lilley DM.

J Mol Biol. 2013 Jan 23;425(2):395-410. doi: 10.1016/j.jmb.2012.11.029. Epub 2012 Dec 1.


The structure and folding of kink turns in RNA.

Lilley DM.

Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):797-805. doi: 10.1002/wrna.1136. Epub 2012 Sep 13. Review.


General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.

Kath-Schorr S, Wilson TJ, Li NS, Lu J, Piccirilli JA, Lilley DM.

J Am Chem Soc. 2012 Oct 10;134(40):16717-24. doi: 10.1021/ja3067429. Epub 2012 Sep 25.


Structure and folding of a rare, natural kink turn in RNA with an A*A pair at the 2b*2n position.

Schroeder KT, Daldrop P, McPhee SA, Lilley DM.

RNA. 2012 Jun;18(6):1257-66. doi: 10.1261/rna.032409.112. Epub 2012 Apr 26.


The structure of sulfoindocarbocyanine 3 terminally attached to dsDNA via a long, flexible tether.

Urnavicius L, McPhee SA, Lilley DM, Norman DG.

Biophys J. 2012 Feb 8;102(3):561-8. doi: 10.1016/j.bpj.2012.01.001. Epub 2012 Feb 7.

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