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Michael David Stone - Publications

Affiliations: 
Chemistry & Biochemistry University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
structure and function of the telomerase ribonucleoprotein
Website:
http://www.chemistry.ucsc.edu/faculty/singleton.php?&singleton=true&cruz_id=mds
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Cech TR, Rouskin S, Stone MD. Dissecting telomerase RNA structural heterogeneity in living human cells with DMS-MaPseq. Biorxiv : the Preprint Server For Biology. PMID 37873413 DOI: 10.1101/2023.10.04.560962  0.424
2023 Hentschel J, Badstübner M, Choi J, Bagshaw CR, Lapointe CP, Wang J, Jansson LI, Puglisi JD, Stone MD. Real-time detection of human telomerase DNA synthesis by multiplexed single-molecule FRET. Biophysical Journal. PMID 37515327 DOI: 10.1016/j.bpj.2023.07.019  0.687
2022 Chang TR, Long X, Shastry S, Parks JW, Stone MD. Single-Molecule Mechanical Analysis of Strand Invasion in Human Telomere DNA. Biochemistry. 61: 1554-1560. PMID 35852986 DOI: 10.1021/acs.biochem.1c00448  0.758
2021 Bagshaw CR, Hentschel J, Stone MD. The Processivity of Telomerase: Insights from Kinetic Simulations and Analyses. Molecules (Basel, Switzerland). 26. PMID 34946615 DOI: 10.3390/molecules26247532  0.655
2021 Chang T, Draper JM, Van den Bout A, Kephart E, Maul-Newby H, Vasquez Y, Woodbury J, Randi S, Pedersen M, Nave M, La S, Gallagher N, McCabe MM, Dhillon N, Bjork I, ... ... Stone MD, et al. A method for campus-wide SARS-CoV-2 surveillance at a large public university. Plos One. 16: e0261230. PMID 34919584 DOI: 10.1371/journal.pone.0261230  0.519
2021 Thornlow B, Hinrichs AS, Jain M, Dhillon N, La S, Kapp JD, Anigbogu I, Cassatt-Johnstone M, McBroome J, Haeussler M, Turakhia Y, Chang T, Olsen HE, Sanford J, Stone M, et al. A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. Biorxiv : the Preprint Server For Biology. PMID 33851162 DOI: 10.1101/2021.04.05.438352  0.535
2020 Palka C, Forino N, Hentschel J, Das R, Stone MD. Folding heterogeneity in the essential human telomerase RNA three-way junction. Rna (New York, N.Y.). PMID 32817241 DOI: 10.1261/Rna.077255.120  0.544
2019 Jansson LI, Stone MD. Single-Molecule Analysis of Reverse Transcriptase Enzymes. Cold Spring Harbor Perspectives in Biology. 11. PMID 31481455 DOI: 10.1101/Cshperspect.A032458  0.487
2019 Jansson LI, Hentschel J, Parks JW, Chang TR, Lu C, Baral R, Bagshaw CR, Stone MD. Telomere DNA G-quadruplex folding within actively extending human telomerase. Proceedings of the National Academy of Sciences of the United States of America. PMID 31019071 DOI: 10.1073/Pnas.1814777116  0.796
2018 Stone MD. Detailed view of human telomerase enzyme invites rethink of its structure. Nature. 557: 174-175. PMID 29730671 DOI: 10.1038/D41586-018-04756-3  0.444
2018 Shastry S, Steinberg-Neifach O, Lue N, Stone MD. Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain. Nucleic Acids Research. PMID 29474579 DOI: 10.1093/Nar/Gky117  0.575
2018 Long X, Chang T, Shastry S, Parks JW, Stone MD. Direct Measurement of Torque Induced Telomere Strand Invasion using Magnetic Tweezers Biophysical Journal. 114: 86a. DOI: 10.1016/J.Bpj.2017.11.515  0.494
2018 Palka C, Das R, Tzfati Y, Stone M. Investigating the Function of Conformational Heterogeneity in Telomerase RNA using Multi-dimensional Chemical Mapping and Single-Molecule Spectroscopy Biophysical Journal. 114: 215a. DOI: 10.1016/J.Bpj.2017.11.1201  0.384
2017 Musgrove C, Jansson LI, Stone MD. New perspectives on telomerase RNA structure and function. Wiley Interdisciplinary Reviews. Rna. PMID 29124890 DOI: 10.1002/Wrna.1456  0.512
2017 Parks JW, Stone MD. Single-Molecule Studies of Telomeres and Telomerase. Annual Review of Biophysics. PMID 28375735 DOI: 10.1146/Annurev-Biophys-062215-011256  0.469
2017 Parks JW, Kappel K, Das R, Stone MD. Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. Rna (New York, N.Y.). 23: 175-188. PMID 28096444 DOI: 10.1261/Rna.058743.116  0.479
2016 Long X, Parks JW, Stone MD. Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Methods (San Diego, Calif.). PMID 27320203 DOI: 10.1016/J.Ymeth.2016.06.009  0.507
2015 Jansson LI, Akiyama BM, Ooms A, Lu C, Rubin SM, Stone MD. Structural basis of template-boundary definition in Tetrahymena telomerase. Nature Structural & Molecular Biology. PMID 26436828 DOI: 10.1038/Nsmb.3101  0.8
2015 Akiyama BM, Parks JW, Stone MD. The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids. Nucleic Acids Research. 43: 5537-49. PMID 25940626 DOI: 10.1093/Nar/Gkv406  0.823
2015 Long X, Stone MD. Mechanical Properties and Strand Invasion of Duplex Telomere DNA Probed using Magnetic Tweezers Biophysical Journal. 108: 352a. DOI: 10.1016/J.Bpj.2014.11.1926  0.669
2014 Parks JW, Stone MD. Coordinated DNA dynamics during the human telomerase catalytic cycle. Nature Communications. 5: 4146. PMID 24923681 DOI: 10.1038/Ncomms5146  0.582
2014 Akiyama BM, Stone MD. Direct Visualization of DNA Dynamics During the Telomerase Catalytic Cycle Reveals the Function of a Conserved Telomerase Domain Biophysical Journal. 106: 429a-430a. DOI: 10.1016/J.Bpj.2013.11.2420  0.824
2013 Long X, Stone MD. Kinetic partitioning modulates human telomere DNA G-quadruplex structural polymorphism Plos One. 8. PMID 24367594 DOI: 10.1371/Journal.Pone.0083420  0.65
2013 Akiyama BM, Gomez A, Stone MD. A conserved motif in tetrahymena thermophila telomerase reverse transcriptase is proximal to the RNA template and is essential for boundary definition Journal of Biological Chemistry. 288: 22141-22149. PMID 23760279 DOI: 10.1074/Jbc.M113.452425  0.807
2013 Akiyama BM, Stone MD. Structural biology: A solution to the telomerase puzzle Nature. 496: 177-178. PMID 23552897 DOI: 10.1038/Nature12090  0.785
2013 Long X, Parks JW, Bagshaw CR, Stone MD. Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy. Nucleic Acids Research. 41: 2746-55. PMID 23303789 DOI: 10.1093/Nar/Gks1341  0.736
2012 Hengesbach M, Kim NK, Feigon J, Stone MD. Single-molecule FRET reveals the folding dynamics of the human telomerase rna pseudoknot domain Angewandte Chemie - International Edition. 51: 5876-5879. PMID 22544760 DOI: 10.1002/Anie.201200526  0.571
2012 Akiyama BM, Loper J, Najarro K, Stone MD. The C-terminal domain of Tetrahymena thermophila telomerase holoenzyme protein p65 induces multiple structural changes in telomerase RNA Rna. 18: 653-660. PMID 22315458 DOI: 10.1261/Rna.031377.111  0.775
2012 Hengesbach M, Stone MD. Single Molecule Analysis of Human Telomerase RNA Pseudoknot Folding and Dynamics Biophysical Journal. 102: 644a. DOI: 10.1016/J.Bpj.2011.11.3507  0.528
2012 Wu JY, Mihalusova M, Stone MD, Zhuang X. Single-Molecule Analysis of the Functional Structure of Telomerase RNP Biophysical Journal. 102: 421a. DOI: 10.1016/J.Bpj.2011.11.2302  0.719
2011 Berman AJ, Akiyama BM, Stone MD, Cech TR. The RNA accordion model for template positioning by telomerase RNA during telomeric DNA synthesis. Nature Structural & Molecular Biology. 18: 1371-5. PMID 22101935 DOI: 10.1038/Nsmb.2174  0.817
2011 Hengesbach M, Akiyama BM, Stone MD. Single-molecule analysis of telomerase structure and function Current Opinion in Chemical Biology. 15: 846-852. PMID 22057212 DOI: 10.1016/J.Cbpa.2011.10.008  0.79
2009 Akiyama BM, Stone MD. Assembly of complex RNAs by splinted ligation. Methods in Enzymology. 469: 27-46. PMID 20946783 DOI: 10.1016/S0076-6879(09)69002-9  0.771
2009 Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. Dynamics of nucleosome remodelling by individual ACF complexes Nature. 462: 1022-1027. PMID 20033040 DOI: 10.1038/Nature08627  0.786
2009 Wu JY, Stone MD, Zhuang X. A single-molecule assay for telomerase structure-function analysis Nucleic Acids Research. 38: e16.1-e16.11. PMID 19920121 DOI: 10.1093/Nar/Gkp1033  0.688
2009 Blosser TR, Stone MD, Yang J, Narlikar G, Zhuang X. Nucleosome Sliding by ACF is Processive and Bidirectional Biophysical Journal. 96: 566a. DOI: 10.1016/J.Bpj.2008.12.3713  0.8
2009 Mihalusova M, Stone MD, Wu JY, Zhuang X. Conformation of Telomerase RNP Established through Footprinting and Single-Molecule FRET Biophysical Journal. 96: 416a. DOI: 10.1016/J.Bpj.2008.12.2127  0.717
2009 Wu JY, Stone MD, Mihalusova M, Zhuang X. Caught in the Act: Single Molecule Structure-Function Studies of Telomerase Biophysical Journal. 96: 416a. DOI: 10.1016/J.Bpj.2008.12.2126  0.731
2007 Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, Hong SC, Mitelheiser S, Maxwell A, Bustamante C, Cozzarelli NR. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nature Structural & Molecular Biology. 14: 264-71. PMID 17334374 DOI: 10.1038/Nsmb1213  0.761
2007 Stone MD, Mihalusova M, O'Connor CM, Prathapam R, Collins K, Zhuang X. Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein Nature. 446: 458-461. PMID 17322903 DOI: 10.1038/Nature05600  0.631
2006 Gore J, Bryant Z, Stone MD, Nöllmann M, Cozzarelli NR, Bustamante C. Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature. 439: 100-4. PMID 16397501 DOI: 10.1038/Nature04319  0.674
2004 Hardy CD, Crisona NJ, Stone MD, Cozzarelli NR. Disentangling DNA during replication: a tale of two strands. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 359: 39-47. PMID 15065655 DOI: 10.1098/Rstb.2003.1363  0.801
2003 Bryant Z, Stone MD, Gore J, Smith SB, Cozzarelli NR, Bustamante C. Structural transitions and elasticity from torque measurements on DNA. Nature. 424: 338-41. PMID 12867987 DOI: 10.1038/Nature01810  0.66
2003 Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, Bustamante C, Cozzarelli NR. Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proceedings of the National Academy of Sciences of the United States of America. 100: 8654-9. PMID 12857958 DOI: 10.1073/Pnas.1133178100  0.656
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