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Feigon Lab PUBLICATIONS |
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Complete Publication List: 142) C.A. Theimer, B.E. Jady, N. Chim, P. Richard, K.E. Breece, T. Kiss, and J. Feigon: “Structural and functional characterization of human telomerase RNA processing and Cajal Body localization signals” Molecular Cell 27, 869-881 (2007) [abstract] 141) K. Januszyk, P.W. Li, V. Villareal, D. Branciforte, H. Wu, Y. Xie, J. Feigon, J.A. Loo, S.L. Martin, and R.T. Clubb: "Identification and solution structure of a highly conserved C-terminal domain required for the retrotransposition of Long Interspersed Nuclear Element-1" J. Biol. Chem. 282, 24893-24904 (2007) [abstract] 140) H. Wu and J. Feigon: "H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification" PNAS 104, 6655-6660 (2007). [abstract] 139) R.J. Richards, H. Wu, L. Trantirek, C.M. O'Connor, k. Collins, and J. Feigon: "Structural study of elements of Tetrahymena telomerase RNA stem-loop IV domain important for function" RNA 12, 1475-1485 (2006). [abstract] 138) C.A. Theimer and J. Feigon: "Structure and function of telomerase RNA", Curr. Opin. Struct. Biol. 16, 307-318 (2006). [abstract] 137) R.J. Richards, C.A. Theimer, L.D. Finger, and J. Feigon: "Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element", Nucleic Acids Res. 34, 816-825 (2006). [abstract] 136) M. Khanna, H. Wu, C. Johansson, M. Caizergues-Ferrer, and J. Feigon, "Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA", RNA 12, 40-52 (2006) [abstract] 135) A.J. Dingley, R.D. Peterson, S. Grzesiek, and J. Feigon, "Characterization of the cation and temperature dependence of DNA quadruplex hydrogen bond properties using high-resolution NMR", J. Am. Chem. Soc. 127, 14466-72 (2005). [abstract] 134) A.K. Henras, M. Sam, S.L. Hiley, H. Wu, J. Feigon, T.R. Hughes, and G.F. Chanfreau: “Biochemical and genomic and analysis of substrate recognition by the double stranded RNA binding domain of yeast RNase III”, RNA 11, 1225-1237 (2005). [abstract] 133) P.Z. Qin, J. Feigon, and W. Hubbell: “Site-directed spin labeling studies reveal a coupled mechanism in the formation of the GAAA tetraloop/receptor RNA tertiary interaction”, J. Mol. Biol. 351, 1-8 (2005). [abstract] 132) H. Wu, L.D. Finger, J. Feigon: “Structure determination of Protein/RNA complexes by NMR”, in Methods in Enzymol. (T.L. James, ed.) Academic Press, 394, 525-545 (2005). [abstract] 131) C.A. Theimer, C.A. Blois, and J. Feigon: “Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function”, Mol. Cell 17, 671-682 (2005). [abstract] 130) M. Kamionka and J. Feigon: "Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction", Protein Science, 13, 2370-2377 (2004). [abstract] 129) J. Feigon and C. Bustamante: “Nucleic acids – controlling biology and controlled by biophysics” Curr. Opin. Struct. Biol., 14, 333-334 (2004). 128) L.D. Finger, C. Johansson, B. Rinaldi, P. Bouvet, and J. Feigon "Contributions of the RBDs and linker domains and RNA structure to the specificity and affinity of the nucleolin RBD12/NRE interaction" Biochemistry, 43, 6937-6947 (2004). [abstract] 127) H. Wu, A. Henras, G. Chanfreau, and J. Feigon: “Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA binding domain of Rnt1p Rnase III”, Proc. Natl. Acad. Sci. USA, 101, 8307-8312 (2004). [abstract] 126) C. Johansson, L.D. Finger, L. Trantirek, T.D. Mueller, S. Kim, I.A. Laird-Offringa, and J. Feigon: “Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target”, J. Mol. Biol., 337, 799-816 (2004). [abstract] 125) T.D. Mueller, M. Kamionka, and J. Feigon: “Specificity of the interaction between UBA domains and ubiquitin”, J. Biol. Chem., 279, 11926-11936 (2004). [abstract] 124) R. Stefl, H. Wu, S. Ravindranathan, V. Sklenár, and J. Feigon: “DNA A-tract bending in three dimensions: Solving the dA4T4 versus dT4A4 conundrum”, Proc. Natl. Acad. Sci. USA, 101, 1177-1182 (2004). [abstract] 123) R.D. Peterson, C.A. Theimer, H. Wu, and J. Feigon: “New Applications of 2D Filtered/Edited NOESY for Assignment and Structure Elucidation of RNA and RNA-Protein Complexes”, J. Biomol. NMR, 28, 59-67 (2004). [abstract] 122) C.A. Theimer, L.D, Finger, and J. Feigon: “YNMG tetraloop formation by a dyskeratosis congenita mutation in human telomerase RNA”, RNA, 9, 1446-1455 (2003). [abstract] 121) L.D. Finger, L. Trantirek, C. Johansson, and J. Feigon: “Solution structures of stem-loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin”, Nucleic Acids Res., 31, 6461-6472 (2003). [abstract] 120) T.M. Mueller and J. Feigon: “Structural determinants for the binding of ubiquitin-like domains to the proteasome”, EMBO J., 22, 4634-4645 (2003). [abstract] 119) P.Z. Qin, K. Hideg, J. Feigon, and W.L. Hubbell: "Monitoring RNA base structure and dynamics using site-directed spin labeling", Biochemistry, 42, 6772-6783 (2003). [abstract] 118) C.A. Theimer, L.D. Finger, L. Trantirek, and J. Feigon: "Mutations linked to dyskeratosis congenita cause dynamic changes in telomerase RNA structure", Proc. Natl. Acad. Sci. USA 100, 449-454 (2003). [abstract] 117) J.E. Masse, B. Wong, Y-M. Yen, F.H.-T. Allain, R.C. Johnson, and J. Feigon: " The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding", J. Mol. Biol., 323, 263-284 (2002). [abstract] 116) N.V. Hud and J. Feigon: "Characterization of divalent cation localization in the minor groove of AnTn and TnAn DNA sequence elements by 1H NMR spectroscopy and manganese(II)", Biochemistry, 41, 9900-9910 (2002). [abstract] 115) T.D. Mueller and J. Feigon: "Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions", J. Mol. Biol., 319, 1243-1255 (2002). [abstract] 114) L. Trantirek, R. Stefl, J.E. Masse, J. Feigon, and V. Sklenar: "Determination of the glycosidic torsion angles in uniformly 13C-labeled nucleic acids from vicinal coupling constants 3JC2/4-H1 and 3JC6/8-H1", J. Biomol. NMR, 23, 1-12 (2002). [abstract] 113) B. Wong, J.E. Masse, Y.-M. Yen, P. Giannikopolous, J. Feigon, and R.C. Johnson: "Binding to cisplatin-modified DNA by the S. cervisiae HMGB proteinNhp6A", Biochemistry, 41, 5404-5414 (2002). [abstract] 112) H. Wu, Pok K. Yang, S.E. Butcher, S. Kang, G. Chanfreau, and J. Feigon: "A novel family of RNA tetraloop structure forms the recognition site for S. cerevisiae RNase III", EMBO J., 20, 7240-7249 (2001). [abstract] 111) L. Zidek,H. Wu, J. Feigon, and V. Sklenar: "Measurement of small scalar and dipolar couplings in purine and pyrimidine bases" , J. Biomol. NMR 21, 153-160 (2001). [abstract] 110) J. Feigon, S.E. Butcher, L.D. Finger, and N.V. Hud: "Solution NMR probing of cation binding sites on nucleic acids", in Methods in Enzymology (T.L. James, V. Dötsch, and U. Schmitz, eds.), Academic Press, 338, 400-420 (2001). 109) D.M.J. Lilley and J. Feigon: "Nucleic Acids: From single molecules to ensembles - cations, junctions, folding, and catalysis" (editorial) Curr. Opin. Struct. Biol., 11, 273-274 (2001). 108) P.Z. Qin, S.E. Butcher, J. Feigon, and W.L. Hubbell: "Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: A site-directed spin-labeling study", Biochemistry, 40, 6929-6936 (2001). [abstract] 107) P. Bouvet, F. H.-T. Allain, L.D. Finger, T. Dieckmann, and J. Feigon, "Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin", J. Mol. Biol., 309, 763-775 (2001). [abstract] 106) M. Barfield, A.J. Dingley, J. Feigon, and S. Grzesiek: "A DFT Study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA triplex", J. Am. Chem. Soc., 123, 4014-4022 (2001). [abstract] 105) S. Ravindranathan, S.E. Butcher, and J. Feigon: "Adenine protonation in domain B of the hairpin ribozyme", Biochemistry, 39, 16026-16032 (2000). [abstract] 104) F. H.-T. Allain, P. Bouvet, T. Dieckmann, and J. Feigon: "Molecular basis of sequence specific recognition of pre-ribosomal RNA by nucleolin", EMBO J., 19, 6870-6881 (2000). [abstract] 103) D. Rovnyak, M. Baldus, G. Wu, N.V. Hud, J. Feigon, and R.G. Griffin: "Localization of 23Na+ in a DNA Quadruplex by High Field Solid State NMR", J. Am. Chem Soc., 122, 11423-11429 (2000). 102) E. Withers-Ward, T.D. Mueller, I.S.Y. Chen, and J. Feigon: "Biochemical and Structural Analysis of the Interaction between the UBA(2) Domain of the DNA Repair Protein HHR23A and HIV-1 Vpr", Biochemistry, 39, 14103-14112 (2000). [abstract] 101)L. Trantírek, M. Urbásek, R. Stefl, J. Feigon, and V. Sklenár: "A Method for Direct Determination of Helical Parameters in Nucleic Acids Using Residual Dipolar Couplings", J. Am. Chem. Soc., 122, 10454-10455 (2000). 100) F. H.-T. Allain, D.E. Gilbert, P. Bouvet, and J. Feigon: "Solution Structure of the Two N-Terminal RNA-Binding Domains of Nucleolin and NMR Study of the Interaction With its RNA Target", J. Mol. Biol., 303, 227-241 (2000). [abstract] 99) A.J. Dingley, J.E. Masse, J. Feigon, and S. Grzesiek: "Characterization of the Hydrogen Bond Network in Guanosine Quartets by Internucleotide 3hJNC’ and 2hJNN Scalar Couplings", J. Biomol. NMR, 16, 279-289 (2000). [abstract] 98) S.E. Butcher, F.H.-T. Allain, and J. Feigon: "Determination of Metal Ion Binding Sites Within the Hairpin Ribozyme Domains by NMR", Biochemistry, 39, 2174-2182 (2000). [abstract] 97) P. Schultze, F.W. Smith, N.V. Hud, and J. Feigon: "The Effect of Sodium, Potassium, and Ammonium Ions on the Conformation of the Dimeric Quadruplex formed by the Oxytricha nova Telomere Repeat Oligonucleotide d(G4T4G4)", Nucleic Acids Res., 27, 3018-3028 (1999). [abstract] 96) A.J. Dingley, J.E. Masse, R.D. Peterson, M. Barfield, J. Feigon, and S. Grzesiek: "Internucleotide Scalar Couplings Across Hydrogen Bonds in Watson-Crick and Hoogsteen Base Pairs of a DNA Triplex", J. Am. Chem. Soc., 121, 6019-6027 (1999). 95) D.E. Gilbert and J. Feigon: "Multi-Stranded DNA Structures", Curr. Opin. Struct. Biol., 9, 305-314 (1999). [abstract] 94) F.H-T. Allain, Y-M. Yen, J.E. Masse, P. Schultze, T. Dieckmann, R.C. Johnson, and J. Feigon: "Solution Structure of the HMG Protein NHP6A and its Interaction with DNA Reveals the Structural Determinants for Non-Sequence Specific Binding", EMBO J., 18, 2563-2579 (1999). [abstract] 93) J.E. Masse, F. H-T. Allain, Y-M. Yen, R.C. Johnson, and J. Feigon: "Use of 13C,15N-Labeled DNA in a Sequence Specific Protein-DNA Complex Resolves Ambiguous Assignments of Intermolecular NOEs", J. Am. Chem. Soc., 121, 3547-3548 (1999). 92) V. Sklenár, J. E. Masse, and J. Feigon: "HCCCH Experiment for Through-Bond Correlation of Thymine Resonances in C-13 Labeled DNA Oligonucleotides", J. Magn. Reson.,137, 345-349 (1999). [abstract] 91) S.E. Butcher, F.H.-T. Allain, and J. Feigon: "Solution Structure of the Loop B Domain From the Hairpin Ribozyme", Nature Struct. Biol., 6, 212-216 (1999). [abstract] 90) E. Wang and J. Feigon: "Structures of Nucleic Acid Triplexes", in Oxford Handbook of Nucleic Acid Structures (S. Neidle ed.) Oxford University Press, Inc., New York, pp. 355 (1999). 89) N.V. Hud, V. Sklenár , and J. Feigon: "Localization of Ammonium Ions in the Minor Groove of DNA Duplexes in Solution and the Origin of DNA A-Tract Bending", J. Mol. Biol. 286, 651-660 (1999). [abstract] 88) N.V. Hud, P. Schultze, V. Sklenár, and J. Feigon: "Binding Sites and Dynamics of Ammonium Ions in a Telomere Repeat DNA Quadruplex", J. Mol. Biol. 285, 233-243 (1999). [abstract] 87) T. Dieckmann, E. Withers-Ward, M.A. Jarosinski, C-F. Liu, I.S.Y. Chen, and J. Feigon: "Structure of a human DNA repair protein UBA domain that interacts with HIV-1 Vpr", Nature Struct. Biol. 5, 1042-1047 (1998). [abstract] 86) M.R. Wall, T. Dieckmann, J. Feigon, and D. Neuhauser: "Two-Dimensional Filter-Diagonalization: Spectral Inversion of 2D NMR Time-Correlation Signals Including Degeneracies", Chem. Phys. Lett. 291, 465-470 (1998). 85) N.V. Hud, P. Schultze, and J. Feigon: "Ammonium Ion as an NMR Probe for Monovalent Cation Coordination Sites of DNA Quadruplexes", J. Am. Chem. Soc. 120, 6403-6404 (1998). |