Publications

2022
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
Das R, Russell R. How to Kinetically Dissect an RNA Machine. Biochemistry. 60 :3485-3490.
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.
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.
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
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
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
Strohkendl I, Saifudden F, Rybarski JM, Finkelstein IJ, Russell R. Kinetic basis for DNA target specificity of CRISPR-Cas12a. Molecular Cell. 71 :816-824.
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.
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.
2016
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.Abstract
Structured RNAs fold through multiple pathways, but we have little understanding of the molecular features that dictate folding pathways and determine rates along a given pathway. Here, we asked whether folding of a complex RNA can be understood from its structural modules. In a two-piece version of the Tetrahymena group I ribozyme, the separated P5abc subdomain folds to local native secondary and tertiary structure in a linked transition and assembles with the ribozyme core via three tertiary contacts: a kissing loop (P14), a metal core-receptor interaction, and a tetraloop-receptor interaction, the first two of which are expected to depend on native P5abc structure from the local transition. Native gel, NMR, and chemical footprinting experiments showed that mutations that destabilize the native P5abc structure slowed assembly up to 100-fold, indicating that P5abc folds first and then assembles with the core by conformational selection. However, rate decreases beyond 100-fold were not observed because an alternative pathway becomes dominant, with nonnative P5abc binding the core and then undergoing an induced-fit rearrangement. P14 is formed in the rate-limiting step along the conformational selection pathway but after the rate-limiting step along the induced-fit pathway. Strikingly, the assembly rate along the conformational selection pathway resembles that of an isolated kissing loop similar to P14, and the rate along the induced-fit pathway resembles that of an isolated tetraloop-receptor interaction. Our results indicate substantial modularity in RNA folding and assembly and suggest that these processes can be understood in terms of underlying structural modules.
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.
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
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.
Ward WL, Russell R. Key points to consider when studying RNA remodeling by proteins. In: Boudvillian M RNA remodeling proteins. USA: Humana Press.
Russell R. Reflections on 20 years of RNA folding, dynamics, and structure. RNA. 21 :723-724.
Russell R. Unwinding the mechanisms of a DEAD-box RNA helicase in cancer. J. Mol. Biol. 427 :1797-1800.
2014
Russell R, Matouschek A. Chance and destiny in the mechanism of a AAA+ protease. Cell. 158 :479-480.

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