Preprints
Massively parallel kinetic profiling of natural and engineered CRISPR nucleases
Stephen K. Jones Jr.*, John A. Hawkins*, Nicole V. Johnson, Cheulhee Jung, Kuang Hu, James R. Rybarski, Janice S. Chen, Jennifer A. Doudna, William H. Press & Ilya J. Finkelstein; (* co-first authors)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/696393    
2020
58. DNA-dependent Protein Kinase Promotes DNA End Processing by MRN and CtIP
Rajashree Deshpande, Logan Myler, Michael Soniat, Nodar Makharashvili, Linda Lee, Susan Lees-Miller, Ilya Finkelstein & Tanya Paull
Science Advances. 6 (2): eaay0922
[PDF]    [Supplement]    DOI: 10.1126/sciadv.aay0922    PMID: 31934630    
2019
57. Human cohesin compacts DNA by loop extrusion
Yoori Kim*, Zhubing Shi*, Hongshan Zhang, Ilya J. Finkelstein† & Hongtao Yu† (* co-first authors) († co-corresponding)
Science.
[PDF]    [Supplement]    DOI: 10.1126/science.aaz4475    PMID: 31780627    
56. Systematic discovery of endogenous human ribonucleoprotein complexes
Anna L Mallam, Wisath Sae-Lee, Jeffrey M Schaub, Fan Tu, Anna Battenhouse, Yu Jin Jang, Jonghwan Kim, John B. Wallingford, Ilya J Finkelstein, Edward M Marcotte & Kevin Drew
Cell Reports. 29 (5): 1351-1368
[PDF]    [Supplement]    DOI: 10.1016/j.celrep.2019.09.060    PMID: 31665645    
55. Retrons and their applications in genome engineering
Anna J. Simon, Andrew D. Ellington & Ilya J. Finkelstein
Nucleic Acids Research. 47 (21): 11007-11019
[PDF]    [Supplement]    DOI: 10.1093/nar/gkz865    PMID: 31598685    
54. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome
Kevin J Forsberg, Ishan V Bhatt, Danica T. Schmidtke, Kamyab Javanmardi, Kaylee E Dillard, Barry L Stoddard, Ilya J Finkelstein, Brett K Kaiser & Harmit S Malik
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.46540    PMID: 31502535    
53. RPA phosphorylation inhibits DNA resection
Michael M. Soniat, Logan R. Myler, Tanya T. Paull & Ilya J. Finkelstein
Molecular Cell. 75 (1): 145-153
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2019.05.005    PMID: 31153714    
52. Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks
Marie-Christine Caron, Ajit K. Sharma, Julia O’Sullivan, Logan R. Myler, Maria Tedim Ferreira, Amélie Rodrigue, Yan Coulombe, Chantal Ethier, Jean-Philippe Gagné, Marie-France Langelier, John M. Pascal, Ilya J. Finkelstein, Michael J. Hendzel, Guy G. Poirier & Jean-Yves Masson
Nature Communications. 10 (1): 2954
[PDF]    [Supplement]    DOI: 10.1038/s41467-019-10741-9    PMID: 31273204    
51. Purification and Biophysical Characterization of the Mre11-Rad50-Nbs1 Complex.
Logan R. Myler, Michael M. Soniat, Xiaoming Zhang, Rajashree A. Deshpande, Tanya T. Paull & Ilya J. Finkelstein
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-4939-9520-2_20    PMID: 31147924    
50. Assembling the Human Resectosome on DNA Curtains.
Michael M. Soniat, Logan R. Myler & Ilya J. Finkelstein
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-4939-9500-4_14    PMID: 31127580    
49. Sortase-mediated fluorescent labeling of CRISPR complexes
Kaylee E. Dillard, Jeffrey M. Schaub, Maxwell W. Brown, Fatema A. Saifuddin, Yibei Xiao, Erik Hernandez, Samuel D. Dahlhauser, Eric v. Anslyn, Ailong Ke, Ilya J. Finkelstein
Methods in Enzymology.
[PDF]    DOI: 10.1016/bs.mie.2018.10.031    PMID: 30691654    
2018
48. Intrinsically disordered regions regulate both catalytic and noncatalytic activities of the MutLα mismatch repair complex.
Yoori Kim*, Christopher M. Furman*, Carol M. Manhart, Eric Alani†, and Ilya J. Finkelstein† (* co-first authors) († co-corresponding)
Nucleic Acids Research.
[PDF]    [Supplement]    DOI: 10.1093/nar/gky1244    PMID: 30541127    
47. Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase
Sudipta Bhattacharyyaa, Michael M. Soniat, David Walker, Sooin Janga, Ilya J. Finkelstein†, and Rasika M. Harshey† († co-corresponding)
Proc Natl Acad Sci USA.
[PDF]    [Supplement]    DOI: 10.1073/pnas.1816606115    PMID: 30487222    
46. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex.
Kaylee E. Dillard*, Maxwell W. Brown*, Nicole V. Johnson, Yibei Xiao, Adam Dolan, Erik Hernandez, Samuel Dahlhauser, Yoori Kim, Logan R. Myler, Eric Anslyn, Ailong Ke, and Ilya J. Finkelstein (* co-first authors)
Cell. 175 (1): 1-13
[PDF]    [Supplement]    DOI: 10.1016/j.cell.2018.09.039    PMID: 30343903    

Press:

45. Assessing Protein Dynamics on Low-Complexity Single-Stranded DNA Curtains.
Jeffrey M. Schaub, Hongshan Zhang, Michael M. Soniat, Ilya J. Finkelstein
Langmuir.
[PDF]    [Supplement]    DOI: 10.1021/acs.langmuir.8b01812    PMID: 30044093    
44. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a.
Isabel Strohkendl, Fatema A. Saifuddin, James R. Rybarski, Ilya J. Finkelstein, Rick Russell
Mol Cell.
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2018.06.043    PMID: 30078724    

Press:

43. Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability.
R A Greenstein, Stephen K Jones, Eric C Spivey, James R Rybarski, Ilya J Finkelstein, Bassem Al-Sady
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.32948    PMID: 30020075    
42. Indel-correcting DNA barcodes for high-throughput sequencing.
John A. Hawkins, Stephen K. Jones Jr., Ilya J. Finkelstein†, and William H. Press† († co-corresponding)
Proc Natl Acad Sci USA. 115 (27): E6217-26
[PDF]    [Supplement]    DOI: 10.1073/pnas.1802640115    PMID: 29925596    

Press:

41. Coordination of Rad1-Rad10 interactions with Msh2-Msh3, Saw1 and RPA is essential for functional 3' non-homologous tail removal.
Robin Eichmiller, Melisa Medina-Rivera, Rachel DeSanto, Eugen Minca, Christopher Kim, Cory Holland, Ja-Hwan Seol, Megan Schmit, Diane Oramus, Jessica Smith, Ignacio F Gallardo, Ilya J Finkelstein, Sang Eun Lee, Jennifer A Surtees
Nucleic Acids Research. 46 (10): 5075-5096
[PDF]    [Supplement]    DOI: 10.1093/nar/gky254    PMID: 29660012    
40. Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair.
Ja-Hwan Seol, Cory Holland, Xiaolei Li, Christopher Kim, Fuyang Li, Melisa Medina-Rivera, Robin Eichmiller, Ignacio F. Gallardo, Ilya J. Finkelstein, Paul Hasty, Eun Yong Shim, Jennifer A. Surtees & Sang Eun Lee
Nature Communications. 9 (1): 2025
[PDF]    [Supplement]    DOI: 10.1038/s41467-018-04327-0    PMID: 29795289    
39. A Microfluidic Device for Massively Parallel, Whole-lifespan Imaging of Single Fission Yeast Cells.
Stephen K Jones Jr, Eric C Spivey, James R Rybarski, and Ilya J Finkelstein
Bio-protocol. 8 (7): e2783
[PDF]    DOI: 10.21769/BioProtoc.2783    PMID: 29770351    
2017
38. Single-molecule imaging reveals how Mre11-Rad50-Nbs1 initiates DNA break repair
Logan R. Myler*, Ignacio F. Gallardo*, Michael M. Soniat, Rajashree A. Deshpande, Xenia B. Gonzalez, Yoori Kim, Tanya T. Paull†, Ilya J. Finkelstein† (* co-first authors; † co-corresponding)
Molecular Cell. 67 (5): 891-898
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2017.08.002    PMID: 28867292    

Highlights:

37. Eukaryotic resectosomes: A single-molecule perspective.
Logan R. Myler and Ilya J. Finkelstein
Progress in Biophysics and Molecular Biology.
[PDF]    DOI: 10.1016/j.pbiomolbio.2016.08.001    PMID: 27498169    
36. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips
Cheulhee Jung*, John A. Hawkins*, Stephen K. Jones, Jr.*, Yibei Xiao, James R. Rybarski, Kaylee E. Dillard, Jeffrey Hussmann, Fatema A. Saifuddin, Cagri A. Savran, Andrew D. Ellington, Ailong Ke, William H. Press, Ilya J. Finkelstein (* co-first authors)
Cell. 170 (1): 35-47.e13
[PDF]    [Supplement]    DOI: 10.1016/j.cell.2017.05.044    PMID: 28666121    

Press:

35. Efficient modification of λ-DNA substrates for single-molecule studies.
Yoori Kim, Armando de la Torre, Andrew A. Leal & Ilya J. Finkelstein
Sci Rep. 7 (1): 2071
[PDF]    [Supplement]    DOI: 10.1038/s41598-017-01984-x    PMID: 28522818    
34. An aging-independent replicative lifespan in a symmetrically dividing eukaryote.
Eric C. Spivey, Stephen K. Jones, James R. Rybarski, Fatema A. Saifuddin, and Ilya J. Finkelstein
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.20340    PMID: 28139976    
33. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.
Michael M. Soniat, Logan R. Myler, Jeffrey M. Schaub, Yoori Kim, Ignacio F. Gallardo, Ilya J. Finkelstein
Methods in Enzymololgy.
[PDF]    DOI: 10.1016/bs.mie.2017.03.011    PMID: 28668123    
32. Inserting Extrahelical Structures into Long DNA Substrates for Single-Molecule Studies of DNA Mismatch Repair.
Maxwell W. Brown, Armando de la Torre, and Ilya J. Finkelstein
Methods in Enzymology.
[PDF]    DOI: 10.1016/bs.mie.2016.08.006    PMID: 28062036    
2016
31. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome.
Houqing Yu, Amit K. Singh Gautam, Shameika R. Wilmington, Dennis Wylie, Kirby Martinez-Fonts, Grace Kago, Marie Warburton, Sreenivas Chavali, Tomonao Inobe, Ilya J. Finkelstein, M. Madan Babu and Andreas Matouschek
J Biol Chem. 291 (28): 14526-39
[PDF]    [Supplement]    DOI: 10.1074/jbc.M116.727578    PMID: 27226608    
30. Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins.
Logan R. Myler, Ignacio F. Gallardo, Yi Zhou, Fade Gong, Soo-Hyun Yang, Marc S. Wold, Kyle M. Miller, Tanya T. Paull, and Ilya J. Finkelstein
Proc Natl Acad Sci USA. 113 (9): E1170-9
[PDF]    [Supplement]    DOI: 10.1073/pnas.1516674113    PMID: 26884156    

Press:

29. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions.
Maxwell W. Brown, Yoori Kim, Gregory M. Williams, John D. Huck, Jennifer A. Surtees & Ilya J. Finkelstein
Nature Communications.
[PDF]    [Supplement]    DOI: 10.1038/ncomms10607    PMID: 26837705    
2015
28. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging.
Ignacio F. Gallardo, Praveenkumar Pasupathy, Maxwell Brown, Carol M. Manhart, Dean P. Neikirk, Eric Alani, and Ilya J. Finkelstein.
Langmuir. 31 (37): 10310-7
[PDF]    [Supplement]    DOI: 10.1021/acs.langmuir.5b02416    PMID: 26325477    
2014
27. High-throughput single-molecule studies of protein-DNA interactions.
Aaron D. Robison and Ilya J. Finkelstein
FEBS Lett. 588 (19): 3539-46
[PDF]    DOI: 10.1016/j.febslet.2014.05.021    PMID: 24859086    
26. 3D-printed microfluidic microdissector for high-throughput studies of cellular aging.
Eric C. Spivey, Blerta Xhemalce, Jason B. Shear, and Ilya J. Finkelstein
Anal Chem. 86 (15): 7406-12
[PDF]    [Supplement]    DOI: 10.1021/ac500893a    PMID: 24992972    
25. From cradle to grave: high-throughput studies of aging in model organisms.
Eric C. Spivey and Ilya J. Finkelstein
Mol Biosyst. 10 (7): 1658-67
[PDF]    DOI: 10.1039/c3mb70604d    PMID: 24535099    
24. Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA.
Ja YilLee, Ilya J.Finkelstein, Lidia K.Arciszewska, David J.Sherratt, Eric C.Greene
Mol Cell. 54 (5): 832-43
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2014.03.033    PMID: 24768536    
23. Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging.
Aaron D. Robison and Ilya J. Finkelstein
Anal Chem. 86 (9): 4157-63
[PDF]    [Supplement]    DOI: 10.1021/ac500267v    PMID: 24734940    
22. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.
Justin W. Leung, Poonam Agarwal, Marella D. Canny, Fade Gong, Aaron D. Robison, Ilya J. Finkelstein, Daniel Durocher, Kyle M. Miller
PLoS Genet.
[PDF]    DOI: 10.1371/journal.pgen.1004178    PMID: 24603765    
2013
21. Molecular traffic jams on DNA.
Ilya J. Finkelstein and Eric C. Greene
Annu Rev Biophys.
[PDF]    DOI: 10.1146/annurev-biophys-083012-130304    PMID: 23451891    
20. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion.
Feng Wang, Sy Redding, Ilya J Finkelstein, Jason Gorman, David R Reichman & Eric C Greene
Nat Struct Mol Biol. 20 (2): 174-81
[PDF]    [Supplement]    DOI: 10.1038/nsmb.2472    PMID: 23262491    
2012
19. Single-stranded DNA curtains for real-time single-molecule visualization of protein-nucleic acid interactions.
Bryan Gibb, Tim D. Silverstein, Ilya J. Finkelstein, and Eric C. Greene
Anal Chem. 84 (18): 7607-12
[PDF]    DOI: 10.1021/ac302117z    PMID: 22950646    
18. Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK.
Ja Yil Lee*, Ilya J. Finkelstein*, Estelle Crozat, David J. Sherratt, and Eric C. Greene (* co-first authors)
Proc Natl Acad Sci USA. 109 (17): 6531-6
[PDF]    [Supplement]    DOI: 10.1073/pnas.1201613109    PMID: 22493241    
2011
17. Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies.
Ilya J. Finkelstein and Eric C. Greene
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-61779-129-1_26    PMID: 21660710    
2010
16. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase.
Ilya J. Finkelstein, Mari-Liis Visnapuu, and Eric C. Greene
Nature. 468 (7326): 983-7
[PDF]    [Supplement]    DOI: 10.1038/nature09561    PMID: 21107319    
2009
15. XPD helicase speeds through a molecular traffic jam.
Ilya J. Finkelstein and Eric C. Greene
Mol Cell. 35 (5): 549-50
[PDF]    DOI: 10.1016/j.molcel.2009.08.012    PMID: 19748351    
2008
14. Single molecule studies of homologous recombination.
Ilya J. Finkelstein and Eric C. Greene
Mol Biosyst. 4 (11): 1094-104
[PDF]    DOI: 10.1039/b811681b    PMID: 18931785    
2007
13. Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy.
Haruto Ishikawa, Ilya J. Finkelstein, Seongheun Kim, Kyungwon Kwak, Jean K. Chung, Keisuke Wakasugi, Aaron M. Massari, and Michael D. Fayer
Proc Natl Acad Sci USA. 2007 (104): 41
[PDF]    DOI: 10.1073/pnas.0707718104    PMID: 17916624    
12. Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach.
Kyungwon Kwak, Sungnam Park, Ilya J. Finkelstein, and M. D. Fayer
J Chem Phys. 127 (12): 124503
[PDF]    DOI: 10.1063/1.2772269    PMID: 17902917    
11. Viscosity-Dependent Protein Dynamics
Ilya J. Finkelstein, Aaron M. Massari, M.D. Fayer
Biophys J. 92 (10): 3652-62
[PDF]    [Supplement]    DOI: 10.1529/biophysj.106.093708    
10. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy.
Ilya J. Finkelstein, Junrong Zheng, Haruto Ishikawa, Seongheun Kim, Kyungwon Kwaka and Michael D. Fayer
Phys Chem Chem Phys. 9 (13): 1533-49
[PDF]    DOI: 10.1039/b618158a    PMID: 17429547    
9. Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy.
Ilya J. Finkelstein, Haruto Ishikawa, Seongheun Kim, Aaron M. Massari, and M. D. Fayer
Proc Natl Acad Sci USA. 104 (8): 2637-42
[PDF]    DOI: 10.1073/pnas.0610027104    PMID: 17296942    
2006
8. Cytochrome c552 mutants: structure and dynamics at the active site probed by multidimensional NMR and vibration echo spectroscopy.
Aaron M. Massari, Brian L. McClain, Ilya J. Finkelstein, Andrew P. Lee, Heather L. Reynolds, Kara L. Bren, and Michael D. Fayer
J Phys Chem B. 110 (38): 18803-10
[PDF]    [Supplement]    DOI: 10.1021/jp054959q    PMID: 16986870    
7. Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy.
Aaron M. Massari, Ilya J. Finkelstein, and Michael D. Fayer
J Am Chem Soc. 128 (12): 3990-7
[PDF]    [Supplement]    DOI: 10.1021/ja058745y    PMID: 16551107    
2005
6. The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations.
Aaron M. Massari, Ilya J. Finkelstein, Brian L. McClain, Anne Goj, Xin Wen, Kara L. Bren, Roger F. Loring, and Michael D. Fayer
J Am Chem Soc. 127 (41): 14279-89
[PDF]    [Supplement]    DOI: 10.1021/ja053627w    PMID: 16218622    
5. Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations.
Ilya J. Finkelstein, Anne Goj, Brian L. McClain, Aaron M. Massari, Kusai A. Merchant, Roger F. Loring, and M. D. Fayer
J Phys Chem B. 109 (35): 16959-66
[PDF]    DOI: 10.1021/jp0517201    PMID: 16853158    
2004
4. Dynamics of hemoglobin in human erythrocytes and in solution: influence of viscosity studied by ultrafast vibrational echo experiments.
Brian L. McClain, Ilya J. Finkelstein, and M. D. Fayer
J Am Chem Soc. 126 (48): 15702-10
[PDF]    DOI: 10.1021/ja0454790    PMID: 15571392    
3. Fifth-order contributions to ultrafast spectrally resolved vibrational echoes: heme-CO proteins.
Ilya J. Finkelstein, Brian L. McClain, and M. D. Fayer
J Chem Phys. 121 (2): 877-85
[PDF]    DOI: 10.1063/1.1758940    PMID: 15260618    
2. Vibrational echo experiments on red blood cells: Comparison of the dynamics of cytoplasmic and aqueous hemoglobin.
Brian L. McClain, Ilya J. Finkelstein, M.D. Fayer
Chem Phys Lett. 392 (4-6): 324-329
[PDF]    DOI: 10.1016/j.cplett.2004.05.080    
2003
1. Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.
Kusai A. Merchant, W. G. Noid, Ryo Akiyama, Ilya J. Finkelstein, Alexei Goun, Brian L. McClain, Roger F. Loring, and M. D. Fayer
J Am Chem Soc. 125 (45): 13804-18
[PDF]    [Supplement]    DOI: 10.1021/ja035654x    PMID: 14599220