2023
An intronic RNA element modulates Factor VIII exon-16 splicing
Victor Tse, Guillermo Chacaltana, Martin Gutierrez, Nicholas M. Forino, Arcelia G. Jimenez, Hanzhang Tao, Phong H. Do, Catherine Oh, Priyanka Chary, Isabel Quesada, Antonia Hamrick, Sophie Lee, Michael D. Stone, Jeremy R. Sanford Nucleic Acids Res. 2023 Nov 14
2021
The Processivity of Telomerase: Insights from Kinetic Simulations and Analyses
Clive R Bagshaw, Jendrik Hentschel, and Michael D Stone. Molecules. 2021 Dec 13;26(24):7532.
A method for campus-wide SARS-CoV-2 surveillance at a large public university
Single-molecule Mechanical Analysis of Strand Invasion in Human Telomere DNA
Terren Chang, Xi Long, Shankar Shastry, Joseph W. Parks, Michael D Stone. bioRxiv Jun 23, 2021.
Cryo-EM structures tell a tale of two telomerases
Nicholas Forino, Jendrik Hentschel, Michael D. Stone. Nat Struct Mol Biol. 2021 Jun;28(6):457-459.
Splicing factor SRSF1 expands the regulatory logic of microRNA expression
Marija Dargyte, Julia Philipp, Christina D. Palka, Michael D. Stone, Jeremy R. Sanford. bioRxiv May14, 2021.
A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
Bryan Thornlow, Angie S. Hinrichs, Miten Jain, Namrita Dhillon, Scott La, Joshua D. Kapp, Ikenna Anigbogu, Molly Cassatt-Johnstone, Jakob McBroome, Maximilian Haeussler, Yatish Turakhia, Terren Chang, Hugh E Olsen, Jeremy Sanford, Michael Stone, Olena Vaske, Isabel Bjork, Mark Akeson, Beth Shapiro, David Haussler, A. Marm Kilpatrick, Russell Corbett-Detig. bioRxiv April 6, 2021.
2020
Folding heterogeneity in the essential human telomerase RNA three-way junction
Christina Palka, Nicholas Forino, Jendrik Hentschel, Rhiju Das, and Michael D. Stone. RNA. Dec. 26, 2020 (12):1787-1800.
2019
Telomere DNA G-quadruplex folding within actively extending human telomerase
Reevaluation of the RNA binding properties of the Tetrahymena thermophila telomerase reverse transcriptase N-terminal domain
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2018
Single-molecule analysis of reverse transcriptase enzymes
Jansson, L.I. and Stone MD. The RNA World: New Tools for Deep Exploration. CSH Perspectives.
Detailed view of human telomerase enzyme invites rethink of its structure
Stone MD. Nature. 2018 May; 557(7704):174-175.
Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain
Shastry, S, Steinberg-Neifach O, Lue N, Stone MD. Nucleic Acids Res. 2018 Apr 6.
2017
New perspectives on telomerase RNA structure and function
Musgrove, C, Jansson LI, Stone MD. WIREs RNA. 2017 Nov 9.
Single-molecule studies of Telomeres and Telomerase
Parks, JW and Stone MD. Annual Review of Biophysics. 2017 March 22.
Single molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis
Parks, JW, Kappel, K, Das, R, Stone MD. RNA. 2017 Feb 23;(2):175-188.
2016
Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid
Long X, Parks JW, Stone MD. Methods. 2016 Aug 1;105:16-25.
2015
Structural Basis of Template Boundary Definition in Tetrahymena Telomerase
Jansson L.I., Akiyama B.M., Ooms A., Lu C., Rubin S.M., Stone M.D. Nat Struct Mol Bio. 2015.
The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids
Akiyama BM, Parks JW, Stone MD. Nucleic Acids Res. 2015
2014
Coordinated DNA dynamics during the human telomerase catalytic cycle
Parks J.W. and Stone M.D. Nat Commun. 2014.
Kinetic partitioning modulates human telomere DNA G-quadruplex structural polymorphism
Long, X. and Stone M.D. PLoS ONE 2014.
2013
A conserved motif in Tetrahymena thermophila telomerase reverse transcriptase is proximal to the RNA template and is essential for boundary definition
Akiyama B.M., Gomez A., Stone M.D. JBC. 2013.
Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy
Long, X., Parks, J.W., Bagshaw, C., Stone M.D. NAR. 2013.
2012
Single-Molecule FRET Reveals the Folding Dynamics of the Human Telomerase RNA Pseudoknot Domain
Hengesbach, M., Kim, N., Feigon, J., Stone, M.D. Angewandte Chemie. 2012.
The C-terminal domain of Tetrahymena thermophila telomerase holoenzyme protein p65 induces multiple structural changes in telomerase RNA
Akiyama B.M., Loper J., Najarro K., Stone M.D. RNA. 2012.
2011
The RNA accordion model for template positioning by telomerase RNA during telomeric DNA synthesis
Berman, A. J., Akiyama, B. M., Stone, M. D., Cech, T. R. Nature: Struct. & Molec. Biol. 2011.
Single-molecule analysis of telomerase structure and function
Hengesbach M, Akiyama BM, Stone M.D. Curr Opin Chem Biol. 2011.
2009
Dynamics of nucleosome remodelling by individual ACF complexes
Blosser, T.R., Yang, J.R., Stone, M.D., Narlikar, G.J., Zhuang, X. Nature. 2009.
Assembly of Complex RNAs by Splinted Ligation
Akiyama, B.M., Stone, M.D. (2009). Methods in Enzymology. Vol. 469, 27-46.
A single-molecule assay for telomerase structure-function analysis
Wu, J.Y., Stone, M.D., Zhuang, X. (2009). Nucleic Acids Research Advance Access published on November 17, 2009
Prior to 2009
Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein
Stone, M.D., Mihalusova, M., O’Connor C, M., Prathapam, R., Collins, K., and Zhuang, X. (2007). Nature 446, 458
Mechanochemical analysis of DNA gyrase using rotor bead tracking
Gore, J., Bryant, Z., Stone, M.D., Nollmann, M., Cozzarelli, N. R., and Bustamante, C. (2006). Nature 439, 100-104.
Structural transitions and elasticity from torque measurements on DNA
Bryant, Z., Stone, M.D., Gore, J., Smith, S. B., Cozzarelli, N. R., and Bustamante, C. (2003). Nature 424, 338-341.