Publications

Preprint

• Structural Basis for Target Discrimination and Activation by Cas13d
  Citation: Chou, C. W., Sinan, S., Kuo, H. C., Arguello, C., Sahaya, D., Russell, R., & Finkelstein, I. J. (2025). Structural basis for target discrimination and activation by Cas13d. bioRxiv. https://doi.org/10.1101/2025.09.12.675955

2024

• Cas12a domain flexibility guides R-loop formation and forces RuvC resetting
  Citation: Strohkendl, I., Saha, A., Moy, C., Nguyen, A. H., Ahsan, M., Russell, R., Palermo, G., & Taylor, D. W. (2024). Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Molecular cell, 84(14), 2717–2731.e6. https://doi.org/10.1016/j.molcel.2024.06.007
• Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a
  Citation: Sinan, S., Appleby, N. M., Chou, C. W., Finkelstein, I. J., & Russell, R. (2024). Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. RNA (New York, N.Y.), 30(10), 1345–1355. https://doi.org/10.1261/rna.080088.124

2023

• Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations
  Citation: Templeton, C., Hamilton, I., Russell, R., & Elber, R. (2023). Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations. The journal of physical chemistry. B, 127(41), 8796–8808. https://doi.org/10.1021/acs.jpcb.3c04354

2022

• Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins
  Citation: Jarmoskaite, I., Helmers, A. E., & Russell, R. (2022). Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins. Methods in enzymology, 673, 53–76. https://doi.org/10.1016/bs.mie.2022.04.004
• A tweak and a peek: How Cas9 pries open double-stranded DNA to check its sequence
  Citation: Sinan, S., Russell, R. A tweak and a peek: How Cas9 pries open double-stranded DNA to check its sequence. Nat Struct Mol Biol 29, 286–288 (2022). https://doi.org/10.1038/s41594-022-00763-1
• Kinetics measurements of G-quadruplex binding and unfolding by helicases
  Citation: Chang-Gu, B., Venkatesan, S., & Russell, R. (2022). Kinetics measurements of G-quadruplex binding and unfolding by helicases. Methods (San Diego, Calif.), 204, 1–13. https://doi.org/10.1016/j.ymeth.2022.04.012
• Group II intron-like reverse transcriptases function in double-strand break repair
  Citation: Park, S. K., Mohr, G., Yao, J., Russell, R., & Lambowitz, A. M. (2022). Group II intron-like reverse transcriptases function in double-strand break repair. Cell, 185(20), 3671–3688.e23. https://doi.org/10.1016/j.cell.2022.08.014
• Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking
  Citation: Hamilton I, Gebala M, Herschlag D, Russell R. Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking. Journal of the American Chemical Society. 144 :1718-1728.

2021

• How to Kinetically Dissect an RNA Machine
  Citation: Das R, Russell R. How to Kinetically Dissect an RNA Machine. Biochemistry. 60 :3485-3490.
• Structural basis for template switching by a group II intron–encoded non-LTR-retroelement reverse transcriptase
  Citation: Lentzsch AM, Stamos JL, Yao J, Russell R, Lambowitz AM. Structural basis for template switching by a group II intron–encoded non-LTR-retroelement reverse transcriptase. Journal of Biological Chemistry. 297 :100971.
• Inhibition of CRISPR-Cas12a targeting by nucleosomes and chromatin
  Citation: Strohkendl I, Saifudden F, Gibson BA, Rosen MK, Russell R, Finkelstein IJ. Inhibition of CRISPR-Cas12a targeting by nucleosomes and chromatin. Science Advances. 7 :eabd6030.
• The DHX36-specific-motif (DSM) enhances specificity by accelerating recruitment of DNA G-quadruplex structures
  Citation: Chang-Gu B, Bradburn DA, Yangyuoru PM, Russell R. The DHX36-specific-motif (DSM) enhances specificity by accelerating recruitment of DNA G-quadruplex structures. Biological Chemistry. 402 :593-604.

2020

• ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme
  Citation: Jarmoskaite I, Tijerina P, Russell R. ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme. Journal of Biological Chemistry. 296 :100132.

2019

• Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-seq
  Citation: Lentzsch AM, Yao J, Russell R, Lambowitz AM. Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-seq. Journal of Biological Chemistry. 294 :19764-19784.

2018

• Kinetic basis for DNA target specificity of CRISPR-Cas12a
  Citation: Strohkendl I, Saifudden F, Rybarski JM, Finkelstein IJ, Russell R. Kinetic basis for DNA target specificity of CRISPR-Cas12a. Molecular Cell. 71 :816-824.
• Hidden structural modules in a cooperative RNA folding transition
  Citation: Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden structural modules in a cooperative RNA folding transition. Cell Reports. 22 :3240-3250.
• The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism
  Citation: Yangyuoru PM, Bradburn DA, Liu Z, Xiao TS, Russell R. The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism. J. Biol. Chem. 293 :1924-32.

2017

• Distinct RNA unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs
  Citation: Gilman B, Tijerina P, Russell R. Distinct RNA unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs. Biochem Soc Trans. 45 :1313-21.
• The DEAD-box protein CYT-19 uses arginine residues in its C-tail to tether RNA substrates
  Citation: Busa V, Rector M, Russell R. The DEAD-box protein CYT-19 uses arginine residues in its C-tail to tether RNA substrates. Biochemistry. 56 :3571-8.

2016

• RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly
  Citation: Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. J Mol Biol. 428 (20) :3972-3985.
• Modulation of local RNA folding allows control of RNA assembly pathway and rate
  Citation: Gracia B, Xue Y, Bisaria N, Al-Hashimi HM, Russell R. Modulation of local RNA folding allows control of RNA assembly pathway and rate. J. Mol Biol. 428 :3972-3985.
• Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch
  Citation: Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat. Commun. 7 :11768.

2015

• Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations
  Citation: Cannon B, Kachroo A, Jayaram M, Russell R. Hexapeptides that inhibit processing of branched DNA structures induce a dynamic ensemble of Holliday junction conformations. J. Biol. Chem. 290 :22734-22746.
• Key points to consider when studying RNA remodeling by proteins
  Citation: Ward WL, Russell R. Key points to consider when studying RNA remodeling by proteins. In: Boudvillian M RNA remodeling proteins. USA: Humana Press.
• Reflections on 20 years of RNA folding, dynamics, and structure
  Citation: Russell R. Reflections on 20 years of RNA folding, dynamics, and structure. RNA. 21 :723-724.
• Unwinding the mechanisms of a DEAD-box RNA helicase in cancer
  Citation: Russell R. Unwinding the mechanisms of a DEAD-box RNA helicase in cancer. J. Mol. Biol. 427 :1797-1800.

2014

• Chance and destiny in the mechanism of a AAA+ protease
  Citation: Russell R, Matouschek A. Chance and destiny in the mechanism of a AAA+ protease. Cell. 158 :479-480.
• DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA
  Citation: Jarmoskaite I, Bhaskaran H, Seifert S, Russell R. DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA. Proc. Natl. Acad. Sci. U.S.A. 111 :E2928-2936.
• Folding pathways of theTetrahymena ribozyme
  Citation: Mitchell D, Russell R. Folding pathways of theTetrahymena ribozyme. J. Mol. Biol. 426 :2300-2312.
• Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET, and single molecule TPM
  Citation: Ma CH, Liu YT, Savva CG, Rowley PA, Cannon B, Russell R, Holzenberg A, Jayaram M. Organization of DNA partners and strand exchange mechanisms during Flp site-specific recombination analyzed by difference topology, single molecule FRET, and single molecule TPM. J. Mol. Biol. 426 :793-815.
• RNA helicase proteins as chaperones and remodelers
  Citation: Jarmoskaite I, Russell R. RNA helicase proteins as chaperones and remodelers. Ann. Rev. Biochem. 83 :697-725.
• DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture.
  Citation: Pan C, Potratz JP, Cannon B, Simpson ZB, Ziehr JL, Tijerina P, Russell R. DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture. PLoS Biology [Internet].  Publisher’s Version

2013

• Enhanced group II intron retrohoming in magnesium-deficientE. coli via selection of mutations in the ribozyme core
  Citation: Truong DM, Sidote DJ, Russell R, Lambowitz AM. Enhanced group II intron retrohoming in magnesium-deficientE. coli via selection of mutations in the ribozyme core. Proc. Natl. Acad. Sci. U.S.A. 110 :E3800-3809.
• Group II intron-ribosome association protects intron RNA from degradation
  Citation: Contreras L, Smith D, Potratz JP, Russell R, Belfort M. Group II intron-ribosome association protects intron RNA from degradation. RNA. 19 :1497-1509.
• Introduction and overview
  Citation: Russell R. Introduction and overview. In: Russell R Biophysics of RNA folding. NY: Springer.
• The long-range P3 helix of theTetrahymena ribozyme is disrupted during folding between the native and misfolded conformations
  Citation: Mitchell D, Jarmoskaite I, Seval N, Seifert S, Russell R. The long-range P3 helix of theTetrahymena ribozyme is disrupted during folding between the native and misfolded conformations. J. Mol. Biol. 425 :2670-2686.
• RNA Catalytic Activity as a Probe of Chaperone-mediated RNA Folding
  Citation: Gracia B, Russell R. RNA Catalytic Activity as a Probe of Chaperone-mediated RNA Folding. In: Waldsich C RNA Folding- Methods and Protocols. NY: Springer.
• The roles of chaperones in RNA folding
  Citation: Tijerina P, Russell R. The roles of chaperones in RNA folding. In: Biophysics of RNA folding. NY: Springer.
• Toward a molecular understanding of RNA remodeling by DEAD-box proteins
  Citation: Russell R, Jarmoskaite I, Lambowitz A. Toward a molecular understanding of RNA remodeling by DEAD-box proteins. RNA Biol. 10 :43-54.
• Visualization of local DNA unwinding by MRN using single molecule FRET
  Citation: Cannon B, Kuhnlein J, Yang SH, Cheng A, Stark JM, Russell R, Paull TT. Visualization of local DNA unwinding by MRN using single molecule FRET. Proc. Natl. Acad. Sci. U.S.A. 110 :18868-18873.

2012

• A dual-mode single molecule fluorescence assay for the detection of expanded CGG repeats in Fragile X syndrome
  Citation: Cannon B, Pan C, Chen L, Hadd AG, Russell R. A dual-mode single molecule fluorescence assay for the detection of expanded CGG repeats in Fragile X syndrome. Molecular Biotechnology. 53 :19-28.
• RNA catalysis as a probe for chaperone activity of DEAD-box helicase proteins
  Citation: Potratz JP, Russell R. RNA catalysis as a probe for chaperone activity of DEAD-box helicase proteins. Methods Enzymol. 511 :111-130.
• Zeptomole detection of DNA nanoparticles by single-molecule fluorescence with magnetic field-directed localization
  Citation: Cannon B, Campos AR, Lewitz Z, Willets KA, Russell R. Zeptomole detection of DNA nanoparticles by single-molecule fluorescence with magnetic field-directed localization. Anal. Biochem. 431 :40-47.

2011

• ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicingin vitro andin vivo
  Citation: Potratz JP, Del Campo M, Wolf RZ, Lambowitz AM, Russell R. ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicingin vitro andin vivo. J. Mol. Biol. 411 :661-679.
• DEAD-box proteins as RNA helicases and RNA chaperones
  Citation: Jarmoskaite I, Russell R. DEAD-box proteins as RNA helicases and RNA chaperones. WIREs: RNA. 2 :135-152.
• The Azoarchusgroup I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins
  Citation: Sinan S, Yuan X, Russell R. The Azoarchusgroup I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins. J. Biol. Chem. 286 :37304-37312.
• Enhanced specificity against misfolding in a thermostable mutant of theTetrahymena ribozyme
  Citation: Wan Y, Russell R. Enhanced specificity against misfolding in a thermostable mutant of theTetrahymena ribozyme. Biochemistry. 50 :864-874.
• Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail
  Citation: Mallam AL, Jarmoskaite I, Tijerina P, Del Campo M, Seifert S, Guo L, Russell R, Lambowitz AM. Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail. Proc. Natl. Acad. Sci. U.S.A. 108 :12254-12259.

2010

• Mechanisms of DEAD-box proteins in ATP-dependent processes
  Citation: Potratz J, Tijerina P, Russell R. Mechanisms of DEAD-box proteins in ATP-dependent processes. In: Jankowsky E RNA Helicases. Cambridge: RSC Publishing.
• Multiple unfolding events during folding of theTetrahymena group I ribozyme
  Citation: Wan Y, Suh H, Russell R, Herschlag D. Multiple unfolding events during folding of theTetrahymena group I ribozyme. J. Mol. Biol. 400 :1067-1077.
• Predicting RNA structure by multiple template homology modeling
  Citation: Flores SC, Wan Y, Russell R, Altman RB. Predicting RNA structure by multiple template homology modeling. Pac. Symp. Biocomput. :216-227.
• Protein roles in group I intron RNA folding: The tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics.
  Citation: Chadee AB, Bhaskaran H, Russell R. Protein roles in group I intron RNA folding: The tyrosyl-tRNA synthetase CYT-18 stabilizes the native state relative to a long-lived misfolded structure without compromising folding kinetics. J. Mol. Biol. 395 :656-670.
• Roles of DEAD-box Proteins in RNA and RNP Folding
  Citation: Pan C, Russell R. Roles of DEAD-box Proteins in RNA and RNP Folding. RNA Biol. 7 :667-767.

2009

• Catalytic activity as a probe of native RNA folding
  Citation: Wan Y, Mitchell D, Russell R. Catalytic activity as a probe of native RNA folding. Methods Enzymol. 468 :195-218.
• Mapping of the functional boundaries and secondary structure of the Murine Mammary Tumor Virus Rem-responsive element
  Citation: Mertz JA, Chadee AB, Byun H, Russell R, Dudley JP. Mapping of the functional boundaries and secondary structure of the Murine Mammary Tumor Virus Rem-responsive element. J. Biol. Chem. 284 :25642-25652.

2008

• DEAD-box proteins can completely separate an RNA duplex using a single ATP
  Citation: Chen Y, Potratz JP, Tijerina P, Del Campo M, Lambowitz AM, Russell R. DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proc. Natl. Acad. Sci. U.S.A. 105 :20203-20208.
• Editorial overview: Exploring the vast dynamic range of RNA dynamics
  Citation: Bevilacqua PC, Russell R. Editorial overview: Exploring the vast dynamic range of RNA dynamics. Curr. Opin. Chem. Biol. 12 :601-603.
• RNA misfolding and the action of chaperones
  Citation: Russell R. RNA misfolding and the action of chaperones. Frontiers in Bioscience. 13 :1-20.

2007

• Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme
  Citation: Russell R, Tijerina P, Chadee AB, Bhaskaran H. Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme. Biochemistry. 46 :4951-4961.
• DMS footprinting of structured RNAs and RNA-protein complexes
  Citation: Tijerina P, Mohr S, Russell R. DMS footprinting of structured RNAs and RNA-protein complexes. Nature Protocols. 2 :2608-2623.
• Do DEAD-box proteins promote group II intron splicing without unwinding RNA?
  Citation: Del Campo M, Tijerina P, Bhaskaran H, Mohr S, Yang Q, Jankowsky E, Russell R, Lambowitz AM. Do DEAD-box proteins promote group II intron splicing without unwinding RNA?. Molecular Cell. 28 :159-166.
• Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone
  Citation: Bhaskaran H, Russell R. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature. 449 :1014-1018.
• Probing the mechanisms of DEAD-box proteins as general RNA chaperones: The C-terminal domain of CYT-19 mediates general recognition of RNA
  Citation: Grohman JK, Del Campo M, Bhaskaran H, Tijerina P, Lambowitz AM, Russell R. Probing the mechanisms of DEAD-box proteins as general RNA chaperones: The C-terminal domain of CYT-19 mediates general recognition of RNA. Biochemistry. 46 :3013-3022.

2006

• Non-specific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone
  Citation: Tijerina P, Bhaskaran H, Russell R. Non-specific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone. Proc. Natl. Acad. Sci. U.S.A. 103 :16698-16703.
• The paradoxical behavior of a highly structured misfolded intermediate in RNA folding
  Citation: Russell R, Das R, Suh H, Travers K, Laederach A, Engelhardt M, Hershlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363 :531-544.
• The UAA/GAN internal loop motif: A new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions
  Citation: Lee JC, Gutell RR, Russell R. The UAA/GAN internal loop motif: A new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J. Mol. Biol. 360 :978-988.

2005

• Structural specificity conferred by a group I RNA peripheral element
  Citation: Johnson TH, Tijerina P, Chadee AB, Herschlag D, Russell R. Structural specificity conferred by a group I RNA peripheral element. Proc. Natl. Acad. Sci. U.S.A. 102 :10176-10181.