Publications

Aristodemou AEN, Rueda DS, Taylor GP, Bangham CRM et al., 2023,

The transcriptome of HTLV-1-infected primary cells following reactivation reveals changes to host gene expression central to the proviral life cycle

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Belan O, Sebald M, Adamowicz M, Anand R, Vancevska A, Neves J, Grinkevich V, Hewitt G, Segura-Bayona S, Bellelli R, Robinson HMR, Higgins GS, Smith GCM, West SC, Rueda DS, Boulton SJ et al., 2022,

POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells., Mol Cell, Vol: 82, Pages: 4664-4680.e9

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Moore G, Han Z, Xu J, Oh J, Wang D, Svejstrup J, Rueda D et al., 2022,

Dynamic Backtracking Regulates Lesion Bypass by RNAPII

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Kaczmarczyk AP, Déclais A-C, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS et al., 2022,

Search and processing of Holliday junctions within long DNA by junction-resolving enzymes, Nature Communications, Vol: 13, Pages: 1-13

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Kaczmarczyk A, Déclais A-C, Newton M, Boulton S, Lilley D, Rueda D et al., 2022,

Search and Processing of Holliday Junctions within Long DNA by Junction-Resolving Enzymes

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Newton MD, Taylor BJ, Cuomo ME, Rueda DS et al., 2022,

CRISPR/Cas9 On- and Off-Target Activity Using Correlative Force and Fluorescence Single-Molecule Microscopy., Methods Mol Biol, Vol: 2478, Pages: 349-378

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Anand R, Buechelmaier E, Belan O, Newton M, Vancevska A, Kaczmarczyk A, Takaki T, Rueda DS, Powell SN, Boulton SJ et al., 2021,

HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51, Nature, Vol: 601, Pages: 268-273, ISSN: 0028-0836

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Rueda D, Cawte AD, Ino H, Unrau P et al., 2021,

Single-molecule RNA Imaging Using Mango II Arrays, Methods in Molecular Biology, Publisher: Humana Press

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Newton MD, Fairbanks SD, Thomas JA, Rueda DS et al., 2021,

A Minimal Load‐and‐Lock Ru II Luminescent DNA Probe, Angewandte Chemie, Vol: 133, Pages: 21120-21127, ISSN: 0044-8249

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Losito M, Smith QM, Newton MD, Cuomo ME, Rueda DS et al., 2021,

Cas12a target search and cleavage on force-stretched DNA, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 23, ISSN: 1463-9076

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Newton MD, Fairbanks SD, Thomas JA, Rueda DS et al., 2021,

A minimal load-and-lock Ru-II luminescent DNA probe, Angewandte Chemie International Edition, Vol: 60, Pages: 20952-20959, ISSN: 1433-7851

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Boulton S, Anand R, Buechelmaier E, Belan O, Newton M, Vancevska A, Kaczmarczyk A, Rueda D, Powell S et al., 2021,

HELQ is a dual function DSB repair enzyme modulated by RPA and RAD51

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Belan O, Moore G, Kaczmarczyk A, Newton MD, Anand R, Boulton SJ, Rueda DS et al., 2021,

Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis., STAR Protocols, Vol: 2, Pages: 1-18, ISSN: 2666-1667

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Belan O, Barroso C, Kaczmarczyk A, Anand R, Federico S, OReilly N, Newton MD, Maeots E, Enchev RI, Martinez-Perez E, Rueda DS, Boulton SJ et al., 2021,

Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins, Molecular Cell, Vol: 81, Pages: 1058-1073.e7, ISSN: 1097-2765 Abstract Open Access Link Cite JOURNAL ARTICLE

Belan O, Barroso C, Kaczmarczyk A, Anand R, Federico S, O'Reilly N, Newton MD, Enchev R, Martinez-Perez E, Rueda DS, Boulton S et al., 2021,

Single-Molecule Investigation of Rad-51 Presynaptic Filament Assembly and the Role of Mediator Proteins, 65th Annual Meeting of the Biophysical-Society (BPS), Publisher: CELL PRESS, Pages: 33A-33A, ISSN: 0006-3495 Author Web Link Cite CONFERENCE PAPER

Iino H, Abdolahzadeh A, Dolgosheina E, Poudevigne-Durance P, Moore G, Girvan P, Kaczmarczyk A, Zhang T, Newton MD, Unrau PJ, Rueda DS et al., 2021,

Rapid Clinical Diagnostic Viral Detection with Saliva by a Novel Single Step Nested Mango-NASBA Assay, 65th Annual Meeting of the Biophysical-Society (BPS), Publisher: CELL PRESS, Pages: 196A-196A, ISSN: 0006-3495 Author Web Link Cite CONFERENCE PAPER

Cawte AD, Unrau PJ, Rueda DS, 2020,

Live cell imaging of single RNA molecules with fluorogenic Mango II arrays, Nature Communications, Vol: 11, ISSN: 2041-1723

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Gutierrez-Escribano P, Newton MD, Llauro A,

Huber J, Tanasie L, Davy J, Aly I, Aramayo R, Montoya A, Kramer H, Stigler J, Rueda DS, Aragon L

et al., 2019, A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules, Science Advances, Vol: 5, Pages: 1-15, ISSN: 2375-2548

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Miura M, Dey S, Ramanayake S, Singh A, Rueda DS, Bangham CRM et al., 2019,

Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling, PLoS Pathogens, Vol: 15, ISSN: 1553-7366

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Cawte AD, Unrau PJ, Rueda DS, 2019,

Live Cell Imaging of Single RNA Molecules with Fluorogenic Mango II Arrays

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Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE, Nans A, Rueda DS, Cherepanov P, Costa A et al., 2019,

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer, Nature Communications, Vol: 10, ISSN: 2041-1723

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Bruno L, Ramlall V, Studer RA, Sauer S, Bradley D, Dharmalingam G, Carroll T, Ghoneim M, Chopin M, Nutt SL, Elderkin S, Rueda DS, Fisher AG, Siggers T, Beltrao P, Merkenschlager M et al., 2019,

Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system, Nature Immunology, Vol: 20, Pages: 1372-1380, ISSN: 1529-2908

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Newton MD, Taylor BJ, Driessen RPC, Roos L, Cvetesic N, Allyjaun S, Lenhard B, Cuomo ME, Rueda DS et al., 2019,

DNA stretching induces Cas9 off-target activity, Nature Structural and Molecular Biology, Vol: 26, Pages: 185-192, ISSN: 1545-9985

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Newton M, Taylor B, Driessen R, Roos L, Cvetesic N, Allyjaun S, Lenhard B, Cuomo ME, Rueda D et al., 2018,

DNA stretching induces Cas9 off-target binding and cleavage, Nature Structural and Molecular Biology, ISSN: 1545-9985

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Paudel BP, Fiorini E, Börner R, Sigel RKO, Rueda DS et al., 2018,

Optimal molecular crowding accelerates group II intron folding and maximizes catalysis, Proceedings of the National Academy of Sciences, Vol: 115, Pages: 11917-11922, ISSN: 0027-8424 Abstract Open Access Link Cite JOURNAL ARTICLE

Gahlon HL, Walker AR, Cisneros GA, Lamers MH, Rueda DS et al., 2018,

Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant, Physical Chemistry Chemical Physics, Vol: 20, Pages: 26892-26902, ISSN: 1463-9076

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Willhoft O, Ghoneim M, Lin C-L, Chua E, Wilkinson M, Chaban Y, Ayala R, McCormack E, Ocloo L, Rueda D, Wigley DB et al., 2018,

Structure and dynamics of the yeast SWR1:nucleosome complex, Science, Vol: 362, ISSN: 0036-8075

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Vamosi G, Rueda D, 2018,

DNA Bends the Knee to Transcription Factors, BIOPHYSICAL JOURNAL, Vol: 114, Pages: 2253-2254, ISSN: 0006-3495

Author Web Link Cite CITATIONS: 3 JOURNAL ARTICLE

Ayala R, Willhoft O, Aramayo R, Wilkinson M, McCormack E, Ocloo L, Wigley D, Zhang X et al., 2018,

Structure and regulation of the human INO80–nucleosome complex, Nature, Vol: 556, Pages: 391-395, ISSN: 0028-0836

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Rudan M, Dib PB, Musa M, Kanunnikau M, Sobocanec S, Rueda D, Warnecke T, Krisko A et al., 2018,

Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing, eLife, Vol: 7, ISSN: 2050-084X

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Walker A, Gahlon H, Rueda D, Cisneros G et al., 2018,

Effects of a single point mutation and mismatched base on DNA polymerase III holoenzyme proofreading, 255th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nexus of Food, Energy, and Water, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727

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Autour A, Jeng S, Cawte A, Abdolahzadeh A, Galli A, Panchapakesan SSS, Rueda DS, Ryckelynck M, Unrau PJ et al., 2018,

Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells, Nature Communications, Vol: 9, ISSN: 2041-1723

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Ghoneim M, Lin C-L, McCormack EA, Wigley DB, Rueda D et al., 2018, Dynamics of Eukaryotic Histone Exchange with Single Molecule Resolution, 62nd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 446A-446A, ISSN: 0006-3495

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Cawte A, Jeng S, Autour A, Ryckelynck M, Unrau P, Rueda D et al., 2018,

Cellular Imaging of Small RNAs using Fluorescent RNA-Mango Aptamers, 62nd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 215A-216A, ISSN: 0006-3495

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Liyanage PS, Walker AR, Brenlla A, Cisneros GA, Romano LJ, Rueda D et al., 2017,

Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations., Sci Rep, Vol: 7

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Zhang X, Aramayo RJ, Willhoft O, Ayala R, Bythell-Douglas R, Wigley DB et al., 2017,

CryoEM structures of the human INO80 chromatin remodelling complex, Nature Structural and Molecular Biology, Vol: 25, Pages: 37-44, ISSN: 1545-9985

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Lane DA, Lynch CJ, Millar C, Rueda D, Cawte A et al., 2017,

A common mechanism by which type 2A von Willebrand Disease mutations enhance ADAMTS13 proteolysis revealed with a von Willebrand Factor A2 domain FRET construct, PLoS ONE, Vol: 12, ISSN: 1932-6203

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Gahlon HL, Poudevigne-Durance P, Rueda D, 2017,

Absence of nuclease activity in commonly used oxygen-scavenging systems, BMC Research Notes, Vol: 10, ISSN: 1756-050

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Rueda FO, Bista M, Newton MD, Goeppert AU, Cuomo ME, Gordon E, Kroener F, Read JA, Wrigley JD, Rueda D, Taylor BJM et al., 2017,

Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease, Nature Communications, Vol: 8, ISSN: 2041-1723

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Gahlon HL, Romano LJ, Rueda D, 2017,

Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution., Chemical Research in Toxicology, Vol: 30, Pages: 1972-1983, ISSN: 0893-228X Abstract Author Web Link Open Access Link Cite JOURNAL ARTICLE

Billman MR, Rueda D, Bangham CRM, 2017,

Single-cell heterogeneity and cell-cycle-related viral gene bursts in the human leukaemia virus HTLV-1 [version 1; peer review: 2 approved, 1 approved with reservations], Wellcome Open Research, Vol: 2, Pages: 87-87, ISSN: 2398-502X

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Gahlon HL, Zhao G, Fernandez-Leiro R, Lamers MH, Rueda D et al., 2017,

Dynamic proofreading in bacterial DNA polymerase III, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S142-S142, ISSN: 0175-7571

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Newton MD, Driessen R, Taylor BJ, Cuomo E, Rueda D et al., 2017,

Force induced off-target binding of CRISPR/Cas9 with single molecule resolution, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S146-S146, ISSN: 0175-7571

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Cawte A, Jeng S, Autour A,

Abdolahzadeh A, Galli A, Ryckelynck M, Unrau P, Rueda D

et al., 2017, Cellular imaging of small RNAs using fluorescent RNA-Mango based aptamers, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S292-S292, ISSN: 0175-7571

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Xie SQ, Rueda D, 2017, Imaging endogenous activation-induced cytidine deaminase (AID) regulation in mammalian B cells, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S371-S371, ISSN: 0175-7571

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Perez MEF, Bloznelyte K, Merkenschlager M, Rueda D et al., 2017,

Visualizing CTCF-mediated DNA looping at the single-molecule level, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S141-S141, ISSN: 0175-7571

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Wigley DB, Willhoft O, McCormack EA, Aramayo R, Bythell-Douglas R, Ocloo L, Zhang X et al., 2017,

Cross-talk within a functional INO80 complex dimer regulates nucleosome sliding, eLife, Vol: 6, ISSN: 2050-084X

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Barbieri M, Xie SQ, Triglia ET, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A et al., 2017,

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 24, Pages: 515-+, ISSN: 1545-9993

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Paudel BP, Rueda D, 2017,

Correction to “Molecular Crowding Accelerates Ribozyme Docking and Catalysis”, Journal of the American Chemical Society, Vol: 139, Pages: 4582-4582, ISSN: 0002-7863

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Liang Z, Brown KE, Carroll T, Taylor B, Vidal IF, Hendrich B, Rueda D, Fisher AG, Merkenschlager M et al., 2017,

A high-resolution map of transcriptional repression, ELIFE, Vol: 6, ISSN: 2050-084X

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Barbieri M, Xie SQ, Torlai Triglia E, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A et al., 2017,

Active and poised promoter states drive folding of the extended<i>HoxB</i>locus in mouse embryonic stem cells

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Perez MEF, Bloznelyte K, Merkenschlager M, Rueda D et al., 2017,

Visualizing CTCF mediated DNA looping at the single molecule level, 61st Annual Meeting of the Biophysical-Society, Publisher: Biophysical Society, Pages: 169A-170A, ISSN: 0006-3495

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Cawte A, Jeng S, Unrau P,

Rueda D

et al., 2017, Live cell imaging of genomic loci using fluorescent RNA aptamers, 61st Annual Meeting of the Biophysical-Society, Publisher: Biophysical Society, Pages: 69A-69A, ISSN: 0006-3495

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Gahlon HL, Zhao G, Fernandez-Leiro R, Lamers MH, Rueda D et al., 2017,

Dynamic proofreading in the bacterial DNA polymerase, 58th Annual Meeting of the Biophysical-Society, Publisher: Biophysical Society, Pages: 513A-514A, ISSN: 0006-3495

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Rees DM, Willhoft O, Lin C-L, Bythell-Douglas R, Wigley DB et al., 2017,

Production and Assay of Recombinant Multisubunit Chromatin Remodeling Complexes, DNA REPAIR ENZYMES: STRUCTURE, BIOPHYSICS, AND MECHANISM, Vol: 592, Pages: 27-47, ISSN: 0076-6879

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Willhoft O, Bythell-Douglas R, Mccormack EA, Wigley DB et al., 2016,

Synergy and antagonism in regulation of recombinant human INO80 chromatin remodeling complex, Nucleic Acids Research, Vol: 44, Pages: 8179-8188, ISSN: 1362-4962

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Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR et al., 2016,

Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly., Journal of Molecular Biology, ISSN: 1089-8638

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Ali FA, Renault L, Gannon J, Gahlon HL, Kotecha A, Zhou JC, Rueda D, Costa A et al., 2016,

Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate, Nature Communications, Vol: 7, ISSN: 2041-1723

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Ma WK, Paudel BP, Xing Z, Sabath IG, Rueda D, Tran EJ et al., 2016,

Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin, Journal of Molecular Biology, Vol: 428, Pages: 1091-1106, ISSN: 1089-8638

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Borner R, Fiorini E, Paudel B, Rueda D, Sigel RKO et al., 2016,

A macromolecular crowding study of RNA folding and activity: polymer pore size matters!, Conference on Biophysics, Biology, and Biophotonics - The Crossroads, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X

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Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda DS et al., 2015,

Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution, Nature Communications, Vol: 6, ISSN: 2041-1723

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Brenlla A, Rueda D, Romano LJ, 2015,

Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4, Nucleic Acids Research, Vol: 43, Pages: 9918-9927, ISSN: 1362-4962

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Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda DS et al., 2015,

Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET, Nucleic Acids Research, ISSN: 1362-4962

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Paudel BP, Rueda D, 2014,

Molecular Crowding Accelerates Ribozyme Docking and Catalysis, Journal of the American Chemical Society, Vol: 136, Pages: 16700-16703, ISSN: 1520-5126

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Warnasooriya C, Rueda D, 2014,

Single-molecule fluorescence-based studies on the dynamics, assembly and catalytic mechanism of the spliceosome, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 42, Pages: 1211-1218, ISSN: 0300-5127

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Aleman EA, de Silva C, Patrick EM, Musier-Forsyth K, Rueda D et al., 2014,

Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle, Journal of Physical Chemistry Letters, Vol: 5, Pages: 777-781, ISSN: 1948-7185

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Brenlla A, Markiewicz RP, Rueda D, Romano LJ et al., 2014,

Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment, Nucleic Acids Research, Vol: 42, Pages: 2555-2563, ISSN: 0305-1048

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Senavirathne G, Bertram J, Jaszczur M, Phuong P, Mak C, Goodman MF, Rueda D et al., 2014,

Watching Aid Scanning Single Stranded and Transcribed DNA with Single Molecule Resolution, 58th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 692A-692A, ISSN: 0006-3495

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Mundigala H, Michaux JB, Feig AL, Ennifar E, Rueda D et al., 2014,

HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 7281-7289, ISSN: 0305-1048

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Paudel B, Rueda D, 2014,

RNA Folding Dynamics Using Laser-Assisted Single-Molecule Refolding, RNA FOLDING: METHODS AND PROTOCOLS, Vol: 1086, Pages: 289-307, ISSN: 1064-3745 Cite JOURNAL ARTICLE

Karunatilaka KS, Rueda D, 2014,

Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex, RNA, Vol: 20, Pages: 16-23, ISSN: 1355-8382

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Vrtis KB, Markiewicz RP, Romano LJ, Rueda D et al., 2013,

Carcinogenic adducts induce distinct DNA polymerase binding orientations, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: 7843-7853, ISSN: 0305-1048

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Brenlla A, Romano L, Rueda D, 2013,

Single-Molecule FRET Studies of a Y-family Polymerase Provide New Insights into Nucleotide Binding Mechanism, 57th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 515A-515A, ISSN: 0006-3495

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Vrtis KB, Markiewicz R, Romano LJ, Rueda D et al., 2013,

Unveiling DNA Polymerase Synthesis, Proofreading, and Mutagenesis Activities - One Molecule at a Time, 57th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 176A-176A, ISSN: 0006-3495

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Mundigala HR, Michaux J, Feig A, Ennifar E, Rueda D et al., 2013,

A Novel Bent Intermediate in the Dimerization of HIV-1 DIS RNA, 57th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 411A-411A, ISSN: 0006-3495

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Koenig SLB, Liyanage PS, Sigel RKO, Rueda D et al., 2013,

Helicase-mediated changes in RNA structure at the single-molecule level, RNA BIOLOGY, Vol: 10, Pages: 133-148, ISSN: 1547-6286

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Zhao R, Rueda D, 2013,

Memory effects in RNA folding dynamics revealed by single-molecule fluorescence, Biophysics of RNA Folding, Pages: 117-133, ISBN: 9781461449539

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Saravanan M, Wuerges J, Bose D, McCormack EA, Cook NJ, Zhang X, Wigley DB et al., 2012,

Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 20883-20888, ISSN: 0027-8424

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Markiewicz RP, Vrtis KB, Rueda D, Romano LJ et al., 2012,

Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I, NUCLEIC ACIDS RESEARCH, Vol: 40, Pages: 7975-7984, ISSN: 0305-1048

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Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D et al., 2012,

Single-stranded DNA Scanning and Deamination by APOBEC3G Cytidine Deaminase at Single Molecule Resolution, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 287, Pages: 15826-15835

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Daher M, Rueda D, 2012,

Fluorescence Characterization of the Transfer RNA-like Domain of Transfer Messenger RNA in Complex with Small Binding Protein B, BIOCHEMISTRY, Vol: 51, Pages: 3531-3538, ISSN: 0006-2960

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Wood S, Ferre-D'Amare AR, Rueda D, 2012,

Allosteric Tertiary Interactions Preorganize the c-di-GMP Riboswitch and Accelerate Ligand Binding, ACS CHEMICAL BIOLOGY, Vol: 7, Pages: 920-927, ISSN: 1554-8929

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Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D et al., 2012,

Single-stranded DNA scanning and deamination by APOBEC3G with single-molecule resolution, 11th International Biorelated Polymer Symposium / 243rd National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727

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Salim N, Lamichhane R, Zhao R, Banerjee T, Philip J, Rueda D, Feig AL et al., 2012,

Thermodynamic and Kinetic Analysis of an RNA Kissing Interaction and Its Resolution into an Extended Duplex, BIOPHYSICAL JOURNAL, Vol: 102, Pages: 1097-1107, ISSN: 0006-3495

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Cardo L, Karunatilaka KS, Rueda D, Sigel RKO et al., 2012,

Single molecule FRET characterization of large ribozyme folding., Methods Mol Biol, Vol: 848, Pages: 227-251

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Aleman EA, Rueda D, 2011,

2-Aminopurine Single-Molecule Fluorescence, 55th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 474-474, ISSN: 0006-3495

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Wood S, Kulshina N, Ferre-D'Amare A, Rueda D et al., 2011,

Single Molecule Studies of the c-di-GMP Riboswitch, 55th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 177-177, ISSN: 0006-3495

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Lamichhane R, Baker KA, Cunningham PR, Rueda D et al., 2011,

Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly, 55th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 233-233, ISSN: 0006-3495

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Karunatilaka KS, Solem A, Pyle AM, Rueda D et al., 2010,

Single-molecule analysis of Mss116-mediated group II intron folding, NATURE, Vol: 467, Pages: 935-U75, ISSN: 0028-0836

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Lamichhane R, Solem A, Black W, Rueda D et al., 2010,

Single-molecule FRET of protein-nucleic acid and protein-protein complexes: Surface passivation and immobilization, METHODS, Vol: 52, Pages: 192-200, ISSN: 1046-2023

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Zhao R, Marshall M, Aleman EA, Lamichhane R, Feig A, Rueda D et al., 2010,

Laser-Assisted Single-Molecule Refolding (LASR), BIOPHYSICAL JOURNAL, Vol: 99, Pages: 1925-1931, ISSN: 0006-3495

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Hsieh J, Koutmou KS, Rueda D, Koutmos M, Walter NG, Fierke CA et al., 2010,

A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P., J Mol Biol, Vol: 400, Pages: 38-51

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Lamichhane R, Daubner GM, Thomas-Crusells J, Auweter SD, Manatschal C, Austin KS, Valniuk O, Allain FH-T, Rueda D et al., 2010,

RNA looping by PTB: Evidence using FRET and NMR spectroscopy for a role in splicing repression, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 4105-4110, ISSN: 0027-8424

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Karunatilaka KS, Solem A, Pyle A-M, Rueda D et al., 2010,

Single-Molecule Analysis of Mss116-Mediated Group II Intron Folding, Publisher: CELL PRESS, Pages: 472A-472A, ISSN: 0006-3495

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Christian T, Romano L, Rueda D, 2010,

Single-Molecule Measurements of Synthesis by DNA Polymerase with Base-Pair Resolution, Publisher: CELL PRESS, Pages: 437A-438A, ISSN: 0006-3495

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Aleman EA, Pedini HS, Rueda D, 2010,

Covalent-Bond-Based Immobilization Approaches for Single-Molecule Fluorescence, Publisher: CELL PRESS, Pages: 185A-185A, ISSN: 0006-3495

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Lamichhane R, Daubner GM, Thomas-Crusells J, Auweter SD, Manatchal C, Austin KS, Valniuk O, Allain FH-T, Rueda D et al., 2010,

RNA Looping By PTB: Evidence Using Fret and NMR Spectroscopy and For a Role in Splicing Repression, Publisher: CELL PRESS, Pages: 72A-73A, ISSN: 0006-3495

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Christian TD, Romano LJ, Rueda D, 2009,

Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 106, Pages: 21109-21114, ISSN: 0027-8424

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Aleman EA, Pedini HS, Rueda D, 2009,

Covalent-Bond-Based Immobilization Approaches for Single-Molecule Fluorescence, CHEMBIOCHEM, Vol: 10, Pages: 2862-2866, ISSN: 1439-4227

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Guo Z, Karunatilaka KS, Rueda D, 2009,

Single-molecule analysis of protein-free U2-U6 snRNAs, Nature Structural and Molecular Biology, Vol: 16, Pages: 1154-1159, ISSN: 1545-9985

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Zhao R, Rueda D, 2009,

RNA folding dynamics by single-molecule fluorescence resonance energy transfer, METHODS, Vol: 49, Pages: 112-117, ISSN: 1046-2023

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Karunatilaka KS, Rueda D, 2009,

Single-molecule fluorescence studies of RNA: A decade's progress, CHEMICAL PHYSICS LETTERS, Vol: 476, Pages: 1-10, ISSN: 0009-2614

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Rueda D, Lamichhane R, Auweter SD, Manatchal C, Austin KS, Valniuk O, Allain F et al., 2009,

Evidence of RNA looping by PTB using Fluorescence Resonance Energy Transfer and NMR spectroscopy, Publisher: FEDERATION AMER SOC EXP BIOL, ISSN: 0892-6638

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Steiner M, Rueda D, Sigel RKO, 2009,

Ca2+ induces the formation of two distinct subpopulations of group II intron molecules., Angew Chem Int Ed Engl, Vol: 48, Pages: 9739-9742

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Coller J, Rueda D, 2009,

RNA research in the rustbelt., RNA Biol, Vol: 6, Pages: 9-11

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Aleman EA, Lamichhane R, Rueda D, 2008,

Exploring RNA folding one molecule at a time, CURRENT OPINION IN CHEMICAL BIOLOGY, Vol: 12, Pages: 647-654, ISSN: 1367-5931

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Ditzler MA, Rueda D, Mo J, Håkansson K, Walter NG et al., 2008,

A rugged free energy landscape separates multiple functional RNA folds throughout denaturation., Nucleic Acids Res, Vol: 36, Pages: 7088-7099

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Steiner M, Karunatilaka KS, Sigel RKO, Rueda D et al., 2008,

Single-molecule studies of group II intron ribozymes (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 37, (13853-13858) DOI: 10.1073/pnas.0804034105), Proceedings of the National Academy of Sciences of the United States of America, Vol: 105, ISSN: 0027-8424

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Zhang X, Wigley DB, 2008,

The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA plus proteins, Nature Structural and Molecular Biology, Vol: 15, Pages: 1223-1227, ISSN: 1545-9985

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Steiner M, Karunatilaka KS, Sigel RKO, Rueda D et al., 2008,

Single-molecule studies of group II intron ribozymes, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 13853-13858, ISSN: 0027-8424

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Ditzler MA, Alemán EA, Rueda D, Walter NG et al., 2007,

Focus on function: single molecule RNA enzymology., Biopolymers, Vol: 87, Pages: 302-316, ISSN: 0006-3525

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Bobeck MJ, Rueda D, Walter NG, Glick GD et al., 2007,

Structural modeling of sequence specificity by an autoantibody against single-stranded DNA., Biochemistry, Vol: 46, Pages: 6753-6765, ISSN: 0006-2960

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Gondert ME, Tinsley RA, Rueda D, Walter NG et al., 2006,

Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core., Biochemistry, Vol: 45, Pages: 7563-7573, ISSN: 0006-2960

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Rueda D, Walter NG, 2006,

Fluorescent energy transfer readout of an aptazyme-based biosensor., Methods Mol Biol, Vol: 335, Pages: 289-310, ISSN: 1064-3745