Publications

2022

Schuler G#, Hu C#, Ke A*.

Structural basis for RNA-guided DNA cleavage by Iscb-ωRNA and mechanistic comparison with Cas9.

Science. 2022 May 26;eabq7220

https://www.science.org/stoken/author-tokens/ST-517/full

Tan R, Krueger R, Gramelspacher M, Zhou X, Xiao Y, Ke A, Hou Z, Zhang Y*.

Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems.

Molecular Cell. 2022 Feb 17;82(4):852-867.e5

Huo Z, Hu C, Ke A*, Zhang Y*.

Introducing large genomic deletions in human pluripotent stem cells using CRISPR-Cas3.

Current Protocol. 2022 Feb;2(2):e361

2021

Lu C, Cai R, Grigg JC, Ke A*.

Using tRNA Scaffold to Assist RNA Crystallization.

Methods Mol Biol. 2021;2323:39-47.

Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ*, Ke A*.

Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas.

Nature. 2021 Sep 29. doi: 10.1038/s41586-021-03951-z.

Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE*, Kellogg EH*.

Structural basis for target site selection in RNA-guided DNA transposition systems.

Science. 2021 Aug 13;373(6556):768-774.

2020

Budhathoki JB, Xiao Y, Schuler G, Hu C, Cheng A, Ding F, Ke A*.

Real-time observation of CRISPR spacer acquisition by Cas1-Cas2 integrase.

Nature Structural & Molecular Biology. 2020 May;27(5):489-499.

2019

Robert A. Battaglia, Jason C. Grigg, Ailong Ke*.

Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators.

Nature Structural & Molecular Biology. (2019) doi:10.1038/s41594-019-0327-6. [Faculty1000 recommended.]

Rujie Cai, Ian R Price, Fran Ding, Feifei Wu, Ting Chen, Yunlong Zhang, Guangfeng Liu, Paul J Jardine, Changrui Lu*, Ailong Ke*.

ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.

Nucleic Acids Research. 2019 Oct 10;47(18):9818-9828.

Suddala KC^#, Price IR^#, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A*, Walter NG*.

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch.

Nature Communications. 2019 Sep 20;10(1):4304. [Faculty1000 recommended.]

Adam Dolan, Zhonggang Hou, Yibei Xiao, Max Gramelspacher, Jaewon Heo, Sara Howden, Peter Freddolino, Ailong Ke*, Yan Zhang*.

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas.

Molecular Cell. Jun 6;74(5):936-950.e5. Epub 2019 April 8.

Dillard KE, Schaub JM, Brown MW, Saifuddin FA, Xiao Y, Hernandez E, Dahlhauser SD, Anslyn EV, Ke A, Finkelstein IJ.

Sortase-mediated fluorescent labeling of CRISPR complexes.

Methods in Enzymology. 2019;616:43-59.

Xiao Y, Ke A*.

Reconstitution and biochemical characterization of ribonucleoprotein complexes in Type I-E CRISPR-Cas systems.

Methods in Enzymology. 2019;616:27-41.

2018

Kaylee Dillard, Maxwell Brown, Nicole Johnson, Yibei Xiao, Adam Dolan, Erik Hernadez, Samuel Dahlhauser, Yoori Kim, Logan Myler, Eric Anslyn, Ailong Ke, Ilya Finkelstein.

Assembly and translocation of a CRISPR-Cas Primed Acquisition Complex.

Cell. 2018 Nov 1;175(4):934-946.

Robert Battaglia, Ailong Ke*.

Guanidine‐sensing riboswitches: How do they work and what do they regulate?

Wiley Interdisciplinary Reviews: RNA 9 (5), e1482.

Yibei Xiao^#, Min Luo^#, Andam Dolan, Maofu Liao*, Ailong Ke*

Structure basis for RNA-guided DNA degradation by Cascade and Cas3.

Science. 2018 Jul 6;361(6397).

Bob Battaglia, Ailong Ke*.

Guanidine-sensing riboswitches: How do they work and what do they regulate?

Wiley Interdiscip Rev RNA. 2018 Apr 26:e1482.

Bob Battaglia, Ailong Ke*.

Acting in tandem.

Elife. 2018 Apr 23;7.

2017

Yibei Xiao, Sherwin Ng, Ki Hyun Nam, Ailong Ke*.

How Type II CRISPR-Cas establishes immunity through Cas1-Cas2 mediated spacer integration.

Nature. 2017 Oct 5;550(7674):137-141.

Hameed U, Price I, Ikram-Ul-Haq, Ke A, Wilson DB, Mirza O.

Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization.

Biochim Biophys Acta. 2017 Oct;1865(10):1237-1245.

Yibei Xiao^#, Min Luo^#, Robert P Hayes, Jonathan Kim, Sherwin Ng, Fran Ding, Maofu Liao*, Ailong Ke*.

Structure basis for directional R-loop formation and substrate handover mechanisms in Type I CRISPR-Cas system.

Cell. 2017 Jun 29;170(1):48-60

Cheulhee Jung, John Hawkins, Stephen K.Jones Jr, Yibei Xiao, Jim R. Rybarski, Kaylee Dillard, Mashelfatema A Saifuddin, Cagri Savran, Andrew Ellington, Ailong Ke, William H. Press, ILya J. Finkelstein.*.

Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips.

Cell. 2017 Jun 29; 170(1):35-37.

Kevin Lewis, Ailong Ke*.

Building the Class 2 CRISPR-Cas Arsenal.

Mol Cell. 2017 Feb 2;65(3):377-379. doi: 10.1016/j.molcel.2017.01.024

Robert Battaglia, Ian Price, Ailong Ke*.

Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches.

RNA. 2017 Apr;23(4):578-585. doi: 10.1261/rna.060186.116. Epub 2017 Jan 17.

2016

Yibei Xiao, Ailong Ke*.

PIWI Takes a Giant Step.

Cell. 2016 Oct 6;167(2):310-312. doi: 10.1016/j.cell.2016.09.043.

Robert P. Hayes, Yibei Xiao, Fran Ding, Paul B. G. van Erp, Kanagalaghatta Rajashankar, Scott Bailey, Blake Wiedenheft, Ailong Ke*.

Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.

Nature. 2016 Feb 25;530(7591):499-503.

2015

Mizachi D, Chen Y, Liu J, Peng HM, Ailong Ke, Pollack L, Turner RJ, Auchus RJ, Delisa MP.

Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy.

Nat Commun. 2015 Apr 8;6:6826. doi: 10.1038/ncomms7826.

Price IR, Gaballa A, Ding F, Helmann JD, Ailong Ke*.

Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.

Molecular Cell. 2015 Mar 19;57(6):1110-23.

http://stke.sciencemag.org/content/8/371/ec84.abstract EDITORS' CHOICE

http://www.nature.com/nrmicro/journal/v13/n5/full/nrmicro3478.html RESEARCH HIGHLIGHT

Hayes RP, Ailong Ke*.

One more piece down to solve the III-A CRISPR puzzle.

J Mol Biol. 2015 Jan 30;427(2):228-30.

Jason Grigg, Ailong Ke*.

Structures of Large RNAs and RNA-Protein Complexes: Toward structure Determination of Riboswitches.

Methods in Enzymology. 2015;558:213-32. doi: 10.1016/bs.mie.2015.02.009.

Ki Hyun Nam, Matthew P. DeLisa*, Ailong Ke*.

Characterizing metal-dependent nucleases of CRISPR-Cas prokaryotic adaptive immunity systems.

Methods Mol Biol. 2015;1311:265-76. doi: 10.1007/978-1-4939-2687-9_17.

2014

Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ailong Ke*.

Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation.

Nat Struct Mol Biol. 2014 Sep;21(9):771-7.

http://news.chess.cornell.edu/articles/2014/Schuller140909b.html RESEARCH HIGHLIGHT

Price IR, Grigg JC, Ailong Ke*.

Common themes and differences in SAM recognition among SAM riboswitches.

Biochim Biophys Acta. 2014 May 23.

Christopher M. Johnson*, Yuqing Chen*, Heejin Le, Ailong Ke, Keith E. Weaver, and Gary M. Dunny.

Identification of a conserved branched RNA structure that functions as a factor-independent terminator.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3573-8.

Junjie Liu, Matt Bratkowski, Xueqi Liu, Ailong Ke*, Hong-Wei Wang*.

Visualization of Distinct Substrate Recruitment Pathways in the Yeast Exosome by Electron Microscopy.

Nat Struct Mol Biol. 2014 Jan;21(1):95-102.

2013

Grigg JC, Ailong Ke*.

Sequence, structure and stacking: specifics of tRNA anchoring to the T box riboswitch.

RNA Biol. 2013 Dec;10(12):1761-4. doi: 10.4161/rna.26996. Review.

Grigg JC, Ailong Ke*.

Structural determinants for geometry and information decoding of tRNA by T box leader RNA.

Structure. 2013 Oct 1;13: 346-348.

Grigg JC, Chen Y, Grundy FJ, Henkin TM, Pollack L, Ailong Ke*.

T box RNA decodes both the information content and geometry of tRNA to affect gene expression.

Proceedings of National Academy of Sciences U.S.A. 2013 Apr 15;110(18):7240-5.

Grigg JC, Ailong Ke*.

One Platform, Five Brands: How Nature Cuts the Cost on Riboswitches.

Journal of Molecular Biology. 2013 May 27;425(10):1593-5.

2012

Nam KH, Huang Q, Ailong Ke*.

Nucleic Acid Binding Surface and Dimer Interface Revealed by CRISPR-associated CasB Protein Structures.

FEBS Letters. 2012 Nov 16;586(22):3956-61.

Nam KH, Ding F, Haitjema C, Huang Q, Delisa MP, Ailong Ke*.

Double-stranded Endonuclease Activity in B. halodurans Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas2 Protein.

Journal of Biological Chemistry. 2012 Oct 10; 287: 35943-35952.

[Featured on the Cover of JBC]

Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A*.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System.

Structure. 2012 Sep 5; 20(9):1574-1564. [Featured on the Cover of Structure] [See "Commentary (Previews)" by Structure.]

Zhao W, Saha M, Ailong Ke, Morais MC, Jardine PJ, Grimes S*.

Three-helix junction is the interface between two functional domains of prohead RNA in {square}29 DNA packaging.

Journal of Virology. 2012 Aug 15. [Epub ahead of print]

Lee G, Bratkowski MA, Ding F, Ailong Ke, Ha T*.

Elastic coupling between RNA degradation and unwinding by an exoribonuclease.

Science. 2012 Jun 29;336(6089):1726-9.

Karlsson AJ, Lim HK, Xu H, Rocco MA, Bratkowski MA, Ailong Ke, DeLisa MP*.

Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins.

Journal of Molecular Biology. 2012 Feb 10;416(1):94-107. 2011

2011

Nam KH, Kurinov I, and Ailong Ke*.

Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

Journal of Biological Chemistry. 2011 Sep 2; 286: 30759-30768.

[Featured on the Cover of JBC] [Selected as a"Paper of the Week" by JBC.] [Selected as a "JBC Best of 2011" (12/4000)]

Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM, Ailong Ke*.

Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch.

Journal of Molecular Biology. 2011 Jun 24;409(5):786-99.

Ding F, Lu C, Zhao W, Rajashankar KR, Anderson DL, Jardine PJ, Grimes S, Ailong Ke*.

Structure and assembly of the essential RNA ring component of a viral DNA packaging motor.

Proceedings of National Academy of Sciences U.S.A. 2011 May 3;108(18):7357-62.

Ataide SF, Schmitz N, Shen K, Ailong Ke, Shan SO, Doudna JA, Ban N.

The crystal structure of the signal recognition particle in complex with its receptor.

Science. 2011 Feb 18;331(6019):881-6.

Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ailong Ke*, DeLisa MP*.

Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli.

Molecular Microbiology. 2011 Feb;79(3):584-99. [Commented in the same issue.]

2010

Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ailong Ke*.

SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch.

Journal of Molecular Biology. 2010 Dec 17;404(5):803-18.

Lu C, Ding F, Ailong Ke*.

Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

PLoS One. 2010 Jan 15;5(1):e8739.

2007-09

Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ailong Ke*.

Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.

Nature Structure and Molecular Biology. 2008 Oct;15(10):1076-83.

Wang HW, Wang J, Ding F, Callahan K, Bratkowski MA, Butler JS, Nogales E, Ailong Ke*.

Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.

Proceedings of National Academy of Sciences U.S.A. 2007 Oct 23;104(43):16844-9.

Before Joining Cornell:

Ke A, Ding F, Batchelor JD, Doudna JA.

Structural roles of monovalent cations in the HDV ribozyme.

Structure. 2007 Mar;15(3):281-7.

Wu S, Ke A, Doudna JA.

A fast and efficient procedure to produce scFvs specific for large macromolecular complexes.

J Immunol Methods. 2007 Jan 10;318(1-2):95-101.

Spanggord RJ, Siu F, Ke A, Doudna JA.

RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.

Nature Structure and Molecular Biology. 2005 Dec;12(12):1116-22.

Ke A, Doudna JA.

Catalytic strategies of self-cleaving ribozymes: Relics of an RNA world?

The RNA World, 3rd Edition. 2005 (Book chapter).

Ke A, Doudna JA.

Crystallization of RNA and RNA-protein complexes.

Methods. 2004 Nov;34(3):408-14. Review.

Ke A, Zhou K, Ding F, Cate JH, Doudna JA.

A conformational switch controls hepatitis delta virus ribozyme catalysis.

Nature. 2004 May 13;429(6988):201-5.

Ke A, Wolberger C.

Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.

Protein Science. 2003 Feb;12(2):306-12.

Ke A, Mathias JR, Vershon AK, Wolberger C.

Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2.

Structure. 2002 Jul;10(7):961-71.