| Year |
Citation |
Score |
| 2023 |
Han Z, Moore GA, Mitter R, Lopez Martinez D, Wan L, Dirac Svejstrup AB, Rueda DS, Svejstrup JQ. DNA-directed termination of RNA polymerase II transcription. Molecular Cell. 83: 3253-3267.e7. PMID 37683646 DOI: 10.1016/j.molcel.2023.08.007 |
0.33 |
|
| 2022 |
Cawte AD, Iino H, Unrau PJ, Rueda DS. Single-Molecule RNA Imaging Using Mango II Arrays. Methods in Molecular Biology (Clifton, N.J.). 2404: 267-280. PMID 34694614 DOI: 10.1007/978-1-0716-1851-6_14 |
0.409 |
|
| 2020 |
Cawte AD, Unrau PJ, Rueda DS. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nature Communications. 11: 1283. PMID 32152311 DOI: 10.1038/S41467-020-14932-7 |
0.401 |
|
| 2018 |
Autour A, C Y Jeng S, D Cawte A, Abdolahzadeh A, Galli A, Panchapakesan SSS, Rueda D, Ryckelynck M, Unrau PJ. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nature Communications. 9: 656. PMID 29440634 DOI: 10.1038/S41467-018-02993-8 |
0.486 |
|
| 2018 |
Ghoneim M, Lin C, McCormack EA, Wigley DB, Rueda D. Dynamics of Eukaryotic Histone Exchange with Single Molecule Resolution Biophysical Journal. 114: 446a. DOI: 10.1016/J.Bpj.2017.11.2464 |
0.36 |
|
| 2018 |
Cawte A, Jeng S, Autour A, Ryckelynck M, Unrau P, Rueda D. Cellular Imaging of Small RNAs using Fluorescent RNA-Mango Aptamers Biophysical Journal. 114: 215a-216a. DOI: 10.1016/J.Bpj.2017.11.1203 |
0.477 |
|
| 2017 |
Liyanage PS, Walker AR, Brenlla A, Cisneros GA, Romano LJ, Rueda D. Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations. Scientific Reports. 7: 17383. PMID 29234107 DOI: 10.1038/S41598-017-17643-0 |
0.368 |
|
| 2017 |
Vámosi G, Rueda D. DNA Bends the Knee to Transcription Factors. Biophysical Journal. PMID 29229184 DOI: 10.1016/J.Bpj.2017.10.047 |
0.313 |
|
| 2017 |
Rueda FO, Bista M, Newton MD, Goeppert AU, Cuomo ME, Gordon E, Kröner F, Read JA, Wrigley JD, Rueda D, Taylor BJM. Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease. Nature Communications. 8: 1610. PMID 29151576 DOI: 10.1038/S41467-017-01732-9 |
0.527 |
|
| 2017 |
Gahlon H, Romano LJ, Rueda D. Influence of DNA Lesions on Polymerase-mediated DNA Replication at Single-Molecule Resolution. Chemical Research in Toxicology. PMID 29020440 DOI: 10.1021/Acs.Chemrestox.7B00224 |
0.333 |
|
| 2017 |
Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A. Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nature Structural & Molecular Biology. PMID 28436944 DOI: 10.1038/Nsmb.3402 |
0.326 |
|
| 2017 |
Liang Z, Brown K, Carroll T, Taylor B, Ferreirós Vidal I, Hendrich B, Rueda D, Fisher AG, Merkenschlager M. A high-resolution map of transcriptional repression. Elife. 6. PMID 28318487 DOI: 10.7554/Elife.22767 |
0.301 |
|
| 2017 |
Paudel BP, Rueda D. Correction to "Molecular Crowding Accelerates Ribozyme Docking and Catalysis". Journal of the American Chemical Society. PMID 28318260 DOI: 10.1021/Jacs.7B02376 |
0.32 |
|
| 2017 |
Perez MEF, Bloznelyte K, Merkenschlager M, Rueda D. Visualizing CTCF mediated DNA looping at the single molecule level Biophysical Journal. 112: 1-9. DOI: 10.1016/J.Bpj.2016.11.937 |
0.344 |
|
| 2017 |
Cawte A, Jeng S, Unrau P, Rueda D. Live Cell Imaging of Genomic Loci using Fluorescent RNA Aptamers Biophysical Journal. 112: 69a. DOI: 10.1016/J.Bpj.2016.11.416 |
0.487 |
|
| 2016 |
Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR. Protein-RNA Dynamics In The Central Junction Control 30S Ribosome Assembly. Journal of Molecular Biology. PMID 27192112 DOI: 10.1016/J.Jmb.2016.05.010 |
0.718 |
|
| 2016 |
Abid Ali F, Renault L, Gannon J, Gahlon HL, Kotecha A, Zhou JC, Rueda D, Costa A. Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate. Nature Communications. 7: 10708. PMID 26888060 DOI: 10.1038/Ncomms10708 |
0.386 |
|
| 2016 |
Ma WK, Paudel BP, Xing Z, Sabath IG, Rueda D, Tran EJ. Recruitment, duplex unwinding and protein-mediated inhibition of the DEAD-box RNA Helicase Dbp2 at actively transcribed chromatin. Journal of Molecular Biology. PMID 26876600 DOI: 10.1016/J.Jmb.2016.02.005 |
0.512 |
|
| 2016 |
Börner R, Fiorini E, Paudel B, Rueda D, Sigel RKO. A macromolecular crowding study of RNA folding and activity: polymer pore size matters!(Conference Presentation) Proceedings of Spie. 9719: 971909. DOI: 10.1117/12.2209290 |
0.347 |
|
| 2015 |
Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nature Communications. 6: 10209. PMID 26681117 DOI: 10.1038/Ncomms10209 |
0.81 |
|
| 2015 |
Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda D. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET. Nucleic Acids Research. PMID 26503251 DOI: 10.1093/Nar/Gkv1011 |
0.497 |
|
| 2015 |
Brenlla A, Rueda D, Romano LJ. Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4. Nucleic Acids Research. PMID 26481355 DOI: 10.1093/Nar/Gkv1067 |
0.372 |
|
| 2015 |
Taylor MR, Špírek M, Chaurasiya KR, Ward JD, Carzaniga R, Yu X, Egelman EH, Collinson LM, Rueda D, Krejci L, Boulton SJ. Rad51 Paralogs Remodel Pre-synaptic Rad51 Filaments to Stimulate Homologous Recombination. Cell. 162: 271-86. PMID 26186187 DOI: 10.1016/J.Cell.2015.06.015 |
0.36 |
|
| 2014 |
Paudel BP, Rueda D. Molecular crowding accelerates ribozyme docking and catalysis. Journal of the American Chemical Society. 136: 16700-3. PMID 25399908 DOI: 10.1021/Ja5073146 |
0.532 |
|
| 2014 |
Warnasooriya C, Rueda D. Single-molecule fluorescence-based studies on the dynamics, assembly and catalytic mechanism of the spliceosome. Biochemical Society Transactions. 42: 1211-8. PMID 25110027 DOI: 10.1042/Bst20140105 |
0.421 |
|
| 2014 |
Mundigala H, Michaux JB, Feig AL, Ennifar E, Rueda D. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Nucleic Acids Research. 42: 7281-9. PMID 24813449 DOI: 10.1093/Nar/Gku332 |
0.427 |
|
| 2014 |
Alemán EA, de Silva C, Patrick EM, Musier-Forsyth K, Rueda D. Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle. The Journal of Physical Chemistry Letters. 5: 777-781. PMID 24803990 DOI: 10.1021/Jz4025832 |
0.833 |
|
| 2014 |
Brenlla A, Markiewicz RP, Rueda D, Romano LJ. Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment. Nucleic Acids Research. 42: 2555-63. PMID 24270793 DOI: 10.1093/Nar/Gkt1149 |
0.449 |
|
| 2014 |
Karunatilaka KS, Rueda D. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex. Rna (New York, N.Y.). 20: 16-23. PMID 24243115 DOI: 10.1261/Rna.041806.113 |
0.8 |
|
| 2014 |
Paudel B, Rueda D. RNA folding dynamics using laser-assisted single-molecule refolding. Methods in Molecular Biology (Clifton, N.J.). 1086: 289-307. PMID 24136611 DOI: 10.1007/978-1-62703-667-2_17 |
0.534 |
|
| 2014 |
Senavirathne G, Bertram J, Jaszczur M, Pham P, Mak C, Goodman MF, Rueda D. Watching Aid Scanning Single Stranded and Transcribed DNA with Single Molecule Resolution Biophysical Journal. 106: 692a. DOI: 10.1016/J.Bpj.2013.11.3828 |
0.816 |
|
| 2013 |
Vrtis KB, Markiewicz RP, Romano LJ, Rueda D. Carcinogenic adducts induce distinct DNA polymerase binding orientations. Nucleic Acids Research. 41: 7843-53. PMID 23814187 DOI: 10.1093/Nar/Gkt554 |
0.358 |
|
| 2013 |
König SL, Liyanage PS, Sigel RK, Rueda D. Helicase-mediated changes in RNA structure at the single-molecule level. Rna Biology. 10: 133-48. PMID 23353571 DOI: 10.4161/Rna.23507 |
0.53 |
|
| 2013 |
Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D. Single-Stranded DNA Scanning and Deamination by APOBEC3G with Single-Molecule Resolution Biophysical Journal. 104: 177a. DOI: 10.1016/J.Bpj.2012.11.995 |
0.809 |
|
| 2013 |
Vrtis KB, Markiewicz R, Romano LJ, Rueda D. Unveiling DNA Polymerase Synthesis, Proofreading, and Mutagenesis Activities - One Molecule at a Time Biophysical Journal. 104: 176a. DOI: 10.1016/J.Bpj.2012.11.993 |
0.373 |
|
| 2013 |
Brenlla A, Romano L, Rueda D. Single-Molecule FRET Studies of a Y-family Polymerase Provide New Insights into Nucleotide Binding Mechanism Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2846 |
0.391 |
|
| 2013 |
Mundigala HR, Michaux J, Feig A, Ennifar E, Rueda D. A Novel Bent Intermediate in the Dimerization of HIV-1 DIS RNA Biophysical Journal. 104: 411a. DOI: 10.1016/J.Bpj.2012.11.2291 |
0.45 |
|
| 2012 |
Markiewicz RP, Vrtis KB, Rueda D, Romano LJ. Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I. Nucleic Acids Research. 40: 7975-84. PMID 22669904 DOI: 10.1093/Nar/Gks523 |
0.447 |
|
| 2012 |
Daher M, Rueda D. Fluorescence characterization of the transfer RNA-like domain of transfer messenger RNA in complex with small binding protein B. Biochemistry. 51: 3531-8. PMID 22482838 DOI: 10.1021/Bi201751K |
0.661 |
|
| 2012 |
Salim N, Lamichhane R, Zhao R, Banerjee T, Philip J, Rueda D, Feig AL. Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophysical Journal. 102: 1097-107. PMID 22404932 DOI: 10.1016/J.Bpj.2011.12.052 |
0.726 |
|
| 2012 |
Wood S, Ferré-D'Amaré AR, Rueda D. Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. Acs Chemical Biology. 7: 920-7. PMID 22380737 DOI: 10.1021/Cb300014U |
0.64 |
|
| 2012 |
Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D. Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution. The Journal of Biological Chemistry. 287: 15826-35. PMID 22362763 DOI: 10.1074/Jbc.M112.342790 |
0.805 |
|
| 2012 |
Cardo L, Karunatilaka KS, Rueda D, Sigel RK. Single molecule FRET characterization of large ribozyme folding. Methods in Molecular Biology (Clifton, N.J.). 848: 227-51. PMID 22315073 DOI: 10.1007/978-1-61779-545-9_15 |
0.804 |
|
| 2011 |
Alemán EA, Rueda D. 2-Aminopurine Single-Molecule Fluorescence Biophysical Journal. 100: 474a. DOI: 10.1016/J.Bpj.2010.12.2777 |
0.791 |
|
| 2011 |
Wood S, Kulshina N, Ferre-D'Amare A, Rueda D. Single Molecule Studies of the c-di-GMP Riboswitch Biophysical Journal. 100: 177a. DOI: 10.1016/J.Bpj.2010.12.1186 |
0.619 |
|
| 2010 |
Karunatilaka KS, Solem A, Pyle AM, Rueda D. Single-molecule analysis of Mss116-mediated group II intron folding. Nature. 467: 935-9. PMID 20944626 DOI: 10.1016/J.Bpj.2009.12.2568 |
0.823 |
|
| 2010 |
Zhao R, Marshall M, Alemán EA, Lamichhane R, Feig A, Rueda D. Laser-assisted single-molecule refolding (LASR). Biophysical Journal. 99: 1925-31. PMID 20858438 DOI: 10.1016/J.Bpj.2010.07.019 |
0.803 |
|
| 2010 |
Lamichhane R, Solem A, Black W, Rueda D. Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization. Methods (San Diego, Calif.). 52: 192-200. PMID 20554047 DOI: 10.1016/J.Ymeth.2010.06.010 |
0.689 |
|
| 2010 |
Hsieh J, Koutmou KS, Rueda D, Koutmos M, Walter NG, Fierke CA. 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. Journal of Molecular Biology. 400: 38-51. PMID 20434461 DOI: 10.1016/J.Jmb.2010.04.050 |
0.617 |
|
| 2010 |
Lamichhane R, Daubner GM, Thomas-Crusells J, Auweter SD, Manatschal C, Austin KS, Valniuk O, Allain FH, Rueda D. 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. 107: 4105-10. PMID 20160105 DOI: 10.1073/Pnas.0907072107 |
0.742 |
|
| 2010 |
Lamichhane R, Daubner GM, Thomas-Crusells J, Auweter SD, Manatchal C, Austin KS, Valniuk O, Allain FH-, Rueda D. RNA Looping By PTB: Evidence Using Fret and NMR Spectroscopy and For a Role in Splicing Repression Biophysical Journal. 98: 72. DOI: 10.1016/J.Bpj.2009.12.411 |
0.743 |
|
| 2009 |
Karunatilaka KS, Rueda D. Single-Molecule Fluorescence Studies of RNA: A Decade's Progress. Chemical Physics Letters. 476: 1-10. PMID 20161154 DOI: 10.1016/J.Cplett.2009.06.001 |
0.84 |
|
| 2009 |
Christian TD, Romano LJ, Rueda D. 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. 106: 21109-14. PMID 19955412 DOI: 10.1073/Pnas.0908640106 |
0.429 |
|
| 2009 |
Steiner M, Rueda D, Sigel RK. Ca2+ induces the formation of two distinct subpopulations of group II intron molecules. Angewandte Chemie (International Ed. in English). 48: 9739-42. PMID 19924747 DOI: 10.1002/Anie.200903809 |
0.383 |
|
| 2009 |
Alemán EA, Pedini HS, Rueda D. Covalent-bond-based immobilization approaches for single-molecule fluorescence. Chembiochem : a European Journal of Chemical Biology. 10: 2862-6. PMID 19911404 DOI: 10.1002/Cbic.200900640 |
0.76 |
|
| 2009 |
Guo Z, Karunatilaka KS, Rueda D. Single-molecule analysis of protein-free U2-U6 snRNAs. Nature Structural & Molecular Biology. 16: 1154-9. PMID 19881500 DOI: 10.1038/Nsmb.1672 |
0.822 |
|
| 2009 |
Zhao R, Rueda D. RNA folding dynamics by single-molecule fluorescence resonance energy transfer. Methods (San Diego, Calif.). 49: 112-7. PMID 19409995 DOI: 10.1016/J.Ymeth.2009.04.017 |
0.54 |
|
| 2009 |
Coller J, Rueda D. RNA research in the rustbelt. Rna Biology. 6: 9-11. PMID 19098455 DOI: 10.4161/Rna.6.1.7459 |
0.388 |
|
| 2009 |
Zhao R, Alemán E, Rueda D. Laser Assisted Single-molecule Refolding Biophysical Journal. 96: 9a. DOI: 10.1016/J.Bpj.2008.12.941 |
0.816 |
|
| 2009 |
Aleman EA, Pedini HS, Rueda D. Immobilization of Single Biomolecules Using Covalent-Bond Linkages for Fluorescence Single-Molecule Experiments Biophysical Journal. 96: 288a. DOI: 10.1016/J.Bpj.2008.12.1426 |
0.775 |
|
| 2008 |
Ditzler MA, Rueda D, Mo J, Håkansson K, Walter NG. A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Research. 36: 7088-99. PMID 18988629 DOI: 10.1093/Nar/Gkn871 |
0.821 |
|
| 2008 |
Alemán EA, Lamichhane R, Rueda D. Exploring RNA folding one molecule at a time. Current Opinion in Chemical Biology. 12: 647-54. PMID 18845269 DOI: 10.1016/J.Cbpa.2008.09.010 |
0.828 |
|
| 2008 |
Steiner M, Karunatilaka KS, Sigel RK, Rueda D. Single-molecule studies of group II intron ribozymes. Proceedings of the National Academy of Sciences of the United States of America. 105: 13853-8. PMID 18772388 DOI: 10.1073/Pnas.0804034105 |
0.811 |
|
| 2008 |
Steiner M, Karunatilaka KS, Sigel RKO, Rueda D. 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. 105: 18071. DOI: 10.1073/pnas.0809940105 |
0.764 |
|
| 2007 |
Ditzler MA, Alemán EA, Rueda D, Walter NG. Focus on function: single molecule RNA enzymology. Biopolymers. 87: 302-16. PMID 17685395 DOI: 10.1002/Bip.20819 |
0.82 |
|
| 2007 |
Bobeck MJ, Rueda D, Walter NG, Glick GD. Structural modeling of sequence specificity by an autoantibody against single-stranded DNA. Biochemistry. 46: 6753-65. PMID 17503778 DOI: 10.1021/Bi700212S |
0.556 |
|
| 2007 |
Guo Z, Zhao R, Rueda D. Single molecule semiconductor nanoparticle-based biosensors Nanomedicine: Nanotechnology, Biology and Medicine. 3: 345. DOI: 10.1016/J.Nano.2007.10.046 |
0.496 |
|
| 2006 |
Rueda D, Walter NG. Fluorescent energy transfer readout of an aptazyme-based biosensor. Methods in Molecular Biology (Clifton, N.J.). 335: 289-310. PMID 16785635 DOI: 10.1385/1-59745-069-3:289 |
0.643 |
|
| 2006 |
Gondert ME, Tinsley RA, Rueda D, Walter NG. Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core. Biochemistry. 45: 7563-73. PMID 16768452 DOI: 10.1021/Bi052116J |
0.816 |
|
| 2005 |
Rueda D, Walter NG. Single molecule fluorescence control for nanotechnology. Journal of Nanoscience and Nanotechnology. 5: 1990-2000. PMID 16430133 DOI: 10.1166/Jnn.2005.505 |
0.563 |
|
| 2005 |
Rueda D, Hsieh J, Day-Storms JJ, Fierke CA, Walter NG. The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry. 44: 16130-9. PMID 16331973 DOI: 10.1021/Bi0519093 |
0.632 |
|
| 2004 |
Rueda D, Bokinsky G, Rhodes MM, Rust MJ, Zhuang X, Walter NG. Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proceedings of the National Academy of Sciences of the United States of America. 101: 10066-71. PMID 15218105 DOI: 10.1073/Pnas.0403575101 |
0.8 |
|
| 2003 |
Rueda D, Wick K, McDowell SE, Walter NG. Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core. Biochemistry. 42: 9924-36. PMID 12924941 DOI: 10.1021/Bi0347757 |
0.744 |
|
| 2003 |
Bokinsky G, Rueda D, Misra VK, Rhodes MM, Gordus A, Babcock HP, Walter NG, Zhuang X. Single-molecule transition-state analysis of RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 100: 9302-7. PMID 12869691 DOI: 10.1073/Pnas.1133280100 |
0.787 |
|
| 2003 |
Jeong S, Sefcikova J, Tinsley RA, Rueda D, Walter NG. Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence. Biochemistry. 42: 7727-40. PMID 12820882 DOI: 10.1021/Bi034627G |
0.79 |
|
| 2002 |
Sekella PT, Rueda D, Walter NG. A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. Rna (New York, N.Y.). 8: 1242-52. PMID 12403463 DOI: 10.1017/S1355838202028066 |
0.632 |
|
| 2002 |
Harris DA, Rueda D, Walter NG. Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry. 41: 12051-61. PMID 12356305 DOI: 10.1021/Bi026101M |
0.765 |
|
| 2002 |
Pereira MJ, Harris DA, Rueda D, Walter NG. Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry. 41: 730-40. PMID 11790094 DOI: 10.1021/Bi011963T |
0.791 |
|
| 2001 |
Walter NG, Harris DA, Pereira MJ, Rueda D. In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs. Biopolymers. 61: 224-42. PMID 11987183 DOI: 10.1002/Bip.10144 |
0.818 |
|
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