We write summaries of select papers - you can find links to individual posts below in the relevant listings, or find them all on our Paper Summaries page.
2021
Genome oligopaint via local denaturation fluorescence in situ hybridization. Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T. (2021) Mol Cell 81(7):1566-1577.e8 PDF
Identifying Poly(ADP-ribose)-Binding Proteins with Photoaffinity-Based Proteomics. Dasovich M, Beckett MQ, Bailey S, Ong SE, Greenberg MM, Leung AKL. (2021) J Am Chem Soc. 143(8):3037-3042
Real-time observation of Cas9 postcatalytic domain motions. Wang Y, Mallon J, Wang H, Singh D, Hyun Jo M, Hua B, Bailey S, Ha T. (2021) Proc Natl Acad Sci U S A. 118(2):e2010650118
2020
Regulation of the RNA and DNA nuclease activities required for Pyrococcus furiosus Type III-B CRISPR-Cas immunity. Foster K, Grüschow S, Bailey S, White MF, Terns MP. (2020) Nucleic Acids Res. 48(8):4418-4434
Processing and integration of functionally oriented prespacers in the E. coli CRISPR system depends on bacterial host exonucleases. Ramachandran A, Summerville L, Learn BA, DeBell L, Bailey S. (2020) J Biol Chem. 295(11): 3403-3414 PDF Featured as an Editor’s Pick Highlight: A moonlighting nuclease puts CRISPR in its place
➤ Check out our related post: CRISPR spacers - asymmetry and orientation
2019
Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding. Okafor IC, Singh D, Wang Y, Jung M, Wang H, Mallon J, Bailey S, Lee JK, Ha T. (2019) Nucleic Acids Res. 47(22):11880-11888.
Preface: CRISPR-Cas Enzymes. Bailey S. (2019) Methods Enzymol. 616: xvii-xviii
Target sequence requirements of a type III-B CRISPR-Cas immune system. Johnson K, Learn BA, Estrella MA, Bailey S. (2019) J. Biol. Chem. 294(26): 10290-10299.
➤ Check out our related post: What makes a match? For CRISPR type III-B, it depends on location
2018
A c9orf72-CARM1 axis regulates lipid metabolism under glucose starvation-induced nutrient stress. Liu Y, Wang T, Ju Ji Y, Johnson K, Liu H, Johnson K, Bailey S, Suk Y, Lu Y-N, Liu M, Wang J (2018) Genes & Dev. 32(21-22): 1380-1387 PDF
Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Singh D, Wang Y, Mallon J, Yang O, Fei J, Poddar A, Ceylan D, Bailey S, Ha T (2018) Nat. Struct. Mol. Biol. 25: 347-354. PMC Author Manuscript
Real-time observation of DNA target interrogation and product release by the RNA-guided CRISPR endonuclease Cpf1 (Cas12a). Singh D, Mallon J, Poddar A, Wang Y, Tippana R, Yang O, Bailey S, Ha T (2018) Proc. Natl. Acad. Sci. USA 115(21):5444-5449. PMC PDF
2017
Microbiology: The case of the mysterious messenger. Johnson K, Bailey S. (2017) Nature. 548, 527-528. PDF
Mycobacrium abscessus L,D-transpeptidases are susceptible to inactivation by carbapenems and cephalosporins but not penicillins. Kumar P, Chauhan V, Silva JRA, d’Andrea F, Li, S, Ginell SL, Freundlich JS, Alves CN, Bailey S, Cohen KA, Lamichhane G. (2017) Antimicrob Agents Chemother. 61(10): e00866-17. PDF
2016
Memory Upgrade: insights into primed adaptation by CRISPR-Cas immune systems. Ramachandran A, Bailey S. (2016) Mol Cell. 64: 641-642. Free Full Text
Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E. (2016) Nucleic Acids Res. 44: 10849-10861. PMC PDF
A molecular arms race new insights into antiCRISPR mechanisms. Mallon J, Bailey S (2016) Nat. Struct. Mol. Biol. 23: 765-766. Free Full Text
Cas9, poised for DNA cleavage. Hongfan C, Bailey S (2016) Science 351: 811-812.
RNA activated DNA cleavage by the Type III-B CRISPR-Cas effector complex. Estrella MA, Kuo FT, Bailey S (2016) Genes & Dev. 30(4): 460-470. PDF
➤ Check out our related post: Solving a targeting puzzle: Type III-B DNA cleavage
Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Hayes RP, Xiao Y, Ding F, van Erp PBG, Rajashankar K, Bailey S, Wiedenheft B, Ke A (2016) Nature 530(7591): 499-503. PMC Author Manuscript
2015
Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. van Erp PBG, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B (2015) Nucleic Acids Res. 43: 8381-8392. Free Full Text
Metalloprotease NleC suppresses host NF-kB/inflammatory responses by cleaving p65 and interfering with the p65/RPS3 interaction. Hodgson A, Wier EM, Fu K, Sun X, Yu H, Zheng W, Sham HP, Johnson K, Bailey S, Vallance BA, Wan F (2015) PLoS Pathog. 11(3):e1004705. PDF
2014
Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. Mulepati S, Heroux A, Bailey S (2014) Science 345: 1479-1484.
➤ Check out our related post: Viewing a Cascade
Independent Cut Site Selection by the Two Nuclease Domains of the Cas9 RNA-guided Endoribonuclease. Chen H, Choi J, Bailey S (2014) J. Biol. Chem. 289: 13284-13294. PDF
2013
The Cmr complex: an RNA-guided Endoribonuclease. Bailey S (2013) Biochem. Soc. Trans. 41: 1459-1463.
Dematin, a human erythrocyte cytoskeletal protein, is a substrate for a recombinant FIKK kinase from Plasmodium falciparum. Brandt SG, Bailey S (2013) Mol. Biochem. Parasitol. 191: 20-23.
In vitro Reconstitution of the Escherichia coli RNA-guided Immune System Reveals Unidirectional, ATP-dependent degradation of DNA target. Mulepati S, Bailey S (2013) J. Biol. Chem. 288: 22184-22192. PDF
2012
Crystal Structure of the Largest Subunit of a Bacterial RNA-guided Immune Complex and its Role in DNA Target Binding. Mulepati S, Orr A, Bailey S. (2012) J. Biol. Chem. 287: 22445-22449. PDF
Hidden iron-sulfur clusters. Bailey S. (2012) Nat. Chem. Biol. 8: 24-25.
2011
Structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 3 (Cas3). Mulepati S, Bailey S. (2011) J. Biol. Chem. 286: 31896-31903. PDF
➤ Check out our related post: A look at a Cas3 HD domain
2009
Structure of the RAG1 nonamer binding domain with DNA reveals a dimmer that mediates DNA synapsis. Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. (2009) Nat. Struct. Mol. Biol 16: 499-508. PMC Author Manuscript
2008
The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation. Durniak KJ, Bailey S. Steitz TA. (2008). Science 322: 553-557. PMC Author Manuscript
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit. Wing RA, Bailey S, Steitz TA. (2008). J. Mol. Biol. 382: 859-86 PMC Author Manuscript
The structure of LepA, the ribosomal back translocase. Evans RN, Blaha G, Bailey S, Steitz TA. (2008) Proc. Natl. Acad. Sci. USA 105: 4673-4678. PDF
2007
Structure of Hexameric DnaB Helicase and its Complex with a Domain of DnaG Primase. Bailey S, Eliason WA, Steitz TA. (2007). Science 318: 459-463. PDF
The Crystal Structure of the Thermus aquaticus DnaB Helicase Monomer. Bailey S, Eliason WA, Steitz TA. (2007). Nucleic Acids Res. 35: 4728-4736. Free Full Text
2006
The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases. Bailey S, Wing RA, Steitz TA. (2006). Cell 126: 893-904. Free Full Text
2003
Structural analysis of Bacillus subtilis SPP1 phage helicase loader protein G39P. Bailey S, Sedelnikova SE, Mesa P, Ayora S, Waltho JP, Aschroft AE, Baron AJ, Alonso JC, Rafferty JB. (2003) J. Biol. Chem. 278: 15304-15312. PDF
Crystallization of the Bacillus subtilis SPP1 bacteriophage helicase loader protein G39P. Bailey S, Sedelnikova SE, Mesa P, Ayora S, Alonso JC, Rafferty JB. (2003). Acta. Crystallogr. D59: 1090-1092.
Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans. Abdelghany HM, Bailey S, Blackburn GM, Raffertry JB, McLennan AG. (2003). J. Biol. Chem. 278: 4435-4439. PDF
2002
The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms. Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, Baker PJ, McLennan AG, Rafferty JB. (2002). Structure. 10: 589-600. Free Full Text
Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA. Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, McLennan AG. Rafferty JB. (2002). Acta. Crystallogr. D58: 526-528.
2001
Cloning, characterization and crystallization of a diadenosine 5’5”’-P1,P4-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans. Abdelghany HM. Gasmi L, Cartwright JL, Bailey S, Rafferty JB, McLennan AG. (2001) Biochem. Biophys. Acta. 1550: 27-36.