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Ferré-D'Amaré Lab Publications


132. Trachman, R.J. & Ferré-D'Amaré, A.R. Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers. Q. Rev. Biophys. 52:e8 (2019). [abstract]

131. Trachman, R.J. III, Stagno, J.R., Conrad, C., Jones, C.P., Fischer, P., Meents, A., Wang, Y.X., & Ferré-D'Amaré, A.R. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Crystallogr. F 75, 547-551 (2019). [abstract]

130. Jones, C., Tran, B., Conrad, C., Stagno, J., Trachman R. III, Fischer, P., Meents, A., & Ferré-D'Amaré, A. Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser. Acta Crystallogr. F 75, 496-500 (2019). [abstract]

129. Jones, C.P., Panja, S., Woodson, S.A. & Ferré-D'Amaré, A.R. Monitoring co-transcriptional folding of riboswitches through helicase unwinding. Meth. Enzymol. 623, 209-227 (2019). [abstract]

128. Sjekloca, L & Ferré-D'Amaré, A.R. Binding between G-quadruplexes at the homodimer interface of the Corn RNA aptamer strongly activates thioflavin T fluorescence. Cell Cehm. Biol. 26, 1159-1168 (2019). [abstract]

127. Truong, L., & Ferré-D'Amaré, A.R. From fluorescent proteins to fluorogenic RNAs: tools for imaging cellular macromolecules. Protein Sci. 28, 134-1386 (2019). [abstract]

126. Tippana, R., Chen, M.C., Demeshkina, N.A., Ferré-D'Amaré, A.R., & Myong. S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat. Commun. 10: 1855 (2019). [abstract]

125. Trachman, R.J. III, Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov. R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J. & Ferré-D'Amaré, A.R. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nature Chem. Biol. 15, 472-479 (2019). [abstract]

124. Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H. Sinniah, R.S., Barchi, J.J., Ferré-D'Amaré, A.R., & Schneekloth Jr., J.S. Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure. Nat. Commun. 10, 1501 (2019). [abstract]

123. Jones, C.P., Piszczek, G., & Ferré-D'Amaré, A.R. Isothermal titration calorimetry measurements of riboswitch-ligand interactions. Meth. Mol. Biol. 1964, 75-87 (2019). [abstract]

122. Niessen, K.A., Xu, M., George, D.K., Chen, M.C., Ferré-D'Amaré, A.R., Snell, E.H., Cody, V., Pace, J. Schmidt, M., Markelz, A.G. Protein and RNA dynamical fingerprinting. Nat. Commun. 10, 1026 (2019). [abstract]

121. Chen, M.C., Tippana, R., Demeshkina, N.A., Murat, P., Balasubramanian, S., Myong, S., & Ferré-D'Amaré, A.R. Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558,465-469 (2018). [abstract]

120. Bachas, S.T. & Ferré-D'Amaré, A.R. Convergent use of heptacoordination for cation selectivity by RNA and protein metalloregulators. Cell Chem. Biol. 25, 962-973 (2018). [abstract]

119. Trachman, R.J. III, Abdolahzadeh, A., Andreoni, A., Cokocaru, R., Knutson, J.R., Ryckelynck, M., Unrau, P.J., & Ferré-D'Amaré, A.R. Crystal structures of the Mango-II RNA aptamer reveal heterogeneous fluorophore binding and guide engineering of variants with improved selectivity and brightness. Biochemistry 57, 3544-3548 (2018). [abstract]


118. Chen, M.C. & Ferré-D'Amaré, A.R. Structural basis of DEAH/RNA helicase activity. Crystals 7, 253 (2017) [abstract]

117. Warner, K.D., Sjekloca, L., Song, W., Filonov, G.S., Jaffrey, S.R. & Ferré-D'Amaré, A.R. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nature Chem. Biol. 13, 1195-1201 (2017). [abstract]

116. Trachman, R.J. III, Truong, L., & Ferré-D'Amaré, A.R. Structural principles of fluorescent RNA aptamers. Trends Pharmacol. Sci. 38, 928-939 (2017) [abstract]

115. Trachman, R.J. III, Demeshkina, N.A., Lau, M.W.L., Panchapakesan, S.S.S., Jeng, S.C.Y., Unrau, P.J., & Ferré-D'Amaré, A.R. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nature Chem. Biol. 13, 807-813 (2017). [abstract]

114. Jones, C.P., & Ferré-D'Amaré, A.R. Long-range interactions in riboswitch control of gene expression. Annu. Rev. Biophys. 46, 455-481 (2017). [abstract]

113. Lau, M.W., Trachman, R.J., & Ferré-D'Amaré, A.R. A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a pre-existing non-specific metal ion binding site. RNA 23, 355-364 (2017). [abstract]

112. Lau, M.W., & Ferré-D'Amaré, A.R. Many activities, one structure: functional plasticity of ribozyme folds. Molecules 21: E1570. [abstract]

111. Stagno, J.R., Liu, Y., Bhandari, Y.R., Conrad, C.E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D.R., White, T.A. Coe, J.D., Wiedom, M.O., Knoska, J., Oberthuer, D., Tuckey, R.A., Yu, P., Dyba, M., Tarasov, S.G., Weierstall, U., Grant, T.D. Schwieters, C.D., Zhang, J., Ferré-D'Amaré, A.R., Fromme, P., Draper, D.E. Liang. M., Hunter, M.S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N.A., Chapman, H.N., Spence, J.C., Woodson, S.A. & Wang, Y.X. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541, 242-246 (2017). [abstract]

110. Ferré-D'Amaré, A.R. RNA binding: getting specific about specificity. Cell Chem. Biol. 23, 1177-1178 (2016). [abstract]

109. Zhang, J., & Ferré-D'Amaré, A.R. Trying on tRNA for size: RNase P and the T-box riboswitch as molecular rulers. Biomolecules (2016). [abstract]

108. Lau, M.W. & Ferré-D'Amaré, A.R. In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods (2016). [abstract]

107. Meyer P.A. et al. Data publication with the structural biology data grid supports live analysis. Nat. Commun. 7, 10882 (2016). [abstract]

106. Zhang, J., & Ferré-D'Amaré, A.R. The tRNA elbow in structure, recognition and evolution. Life 6 (2016), doi: 10.3390/life6010003. [abstract]

105. Zhang, J., & Ferré-D'Amaré, A.R. Post-crystallization improvement of RNA crystals by synergistic ion exchange and dehydration. Bio Protoc. 5(17) pii: e1578 (2015). [abstract]

104. Baird, N.J., Inglese, J., & Ferré-D'Amaré, A.R. Rapid RNA-ligand interaction analysis through high-information content conformational and stability landscapes. Nat. Commun. 6, 8898 (2015). [abstract]

103. Jones, C.P. & Ferré-D'Amaré, A.R. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nature Struct. Mol. Biol. 22, 679-685 (2015). [abstract]

102. Ferré-D'Amaré, A.R. Use of the U1A protein to facilitate crystallization and structure determination of large RNAs. Methods Mol. Biol. 1320, 67-76 (2015). [abstract]

101. Zhang, J., & Ferré-D'Amaré, A.R. Post-crystallization improvement of RNA crystal diffraction quality. Methods Mol. Biol. 1316, 13-24 (2015). [abstract]

100. Zhang, J., & Ferré-D'Amaré, A.R. Structure and mechanism of the T-box riboswitches. Wiley Interdiscip. Rev. RNA 6, 419-433 (2015). [abstract]

99. Liu, Y., Holmstron, E., Zhang, J., Yu, Ping., Wang, J., Dyba, M.A., Chen, D., Ying, J., Lockett, S., Nesbitt, D.J., Ferré-D'Amaré, A.R., Sousa, R., Stagno, J.R., Wang, Y.X. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 522, 368-372 (2015). [abstract]

98. Miao, Z., Adamiak, R.W., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cheng, C., Chojnowski, G., Chou, F.C., Cordero, P., Cruz, J.A., Ferré-D'Amaré, A.R., Das, R., Ding, F., Dokholyan, N.V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T.H., Masquida, B., Matelska, D., Meyer, M., Paselis, A., Popenda, M., Purzycka, K.J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, J., Zhao, P., Zok, T., Westhof, E. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21, 1066-1084 (2015). [abstract]

97. Ferré-D'Amaré, A.R. On the shoulders of giants. RNA 21, 504-505 (2015). [abstract]

96. Jones, C.P., & Ferré-D'Amaré, A.R. RNA quaternary structure and global symmetry. Trends Biochem. Sci. 40, 211-220 (2015). [abstract]

95. Chen, M.C., Murat, P., Abecassis, K., Ferré-D'Amaré, A.R. & Balasubramanian, S. Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase. Nuclec Acids Res. 43, 2223-2231 (2015). [abstract]


94. Zhang, J., & Ferré-D'Amaré, A.R. A Flexible, Scalable Method for Preparation of Homogeneous Aminoacylated tRNAs. Meth. Enzymol. 549C, 105-113 (2014). [abstract]

93. Warner, K.D., & Ferré-D'Amaré, A.R. Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches. Meth. Enzymol. 549C, 221-233 (2014). [abstract]

92. Jones, C.P., & Ferré-D'Amaré, A.R. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. EMBO J. 33, 2692-2703 (2014). [abstract]

91. Zhang, J., & Ferré-D'Amaré, A.R. Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22, 1363-1371 (2014). [abstract]

90. Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., & Ferré-D'Amaré, A.R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature Struct. Mol. Biol. 21, 658-663 (2014). [abstract]

89. Zhang, J., & Ferré-D'Amaré, A.R. Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol. Cell. 55, 148-155 (2014). [abstract]

88. Zhang, J., Jones, C.P., & Ferré-D'Amaré, A.R. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim. Biophys. Acta 1839, 1020-1029 (2014). [abstract]

87. Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C. & Ferré-D'Amaré, A.R. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595 (2014). [abstract]

86. Zhang, J., & Ferré-D'Amaré, A.R. New molecular engineering approaches for crystallographic studies of large RNAs. Curr. Op. Struct. Biol. 26, 9-15 (2014). [abstract]

85. Baird, N.J., & Ferré-D'Amaré, A.R. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Meth. Mol. Biol. 1103, 211-225 (2014). [abstract]

84. Lau, M.W.L., & Ferré-D'Amaré, A.R. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nature Chem. Biol. 9, 805-810 (2013). [abstract]

83. Zhang, J., & Ferré-D'Amaré, A.R. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-366 (2013). [abstract]

82. Posakony, J.J., & Ferré-D'Amaré, A.R. Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme. J. Org. Chem. 78, 4730-4743 (2013). [abstract]

81. Ferré-D'Amaré, A.R. Riboswitches. In: Lennarz, W.J. and Lane, M.D. (eds.) The Encyclopedia of Biological Chemistry, Vol. 4, pp. 136-141. Waltham, Academic Press (2013).

80. Ferré-D'Amaré, A.R. Crystallization of RNA for structure determination by X-ray crystallography. In Structure and Folding of RNA. Klostermeier D. & Hammann, C. (eds). Berlin, deGruyter pp. 319-333 (2013).

79. Baird, N.J., & Ferré-D'Amaré, A.R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19, 167-176 (2013). [abstract]

78. Wood, S., Ferré-D'Amaré, A.R. & Rueda, D. Allosteric tertiary interactions pre-organize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem. Biol. 7, 920-927 (2012). [abstract]

77. Baird, N.J., Zhang, J., Hamma, T., & Ferré-D'Amaré, A.R. YbxF and YlxQ are bacterial homologs of L7Ae, and bind K-turns but not K-loops. RNA 18, 759-770 (2012).[abstract]


76. Gong, B., Klein, D.J., Ferré-D'Amaré, A.R., & Carey P.R. The glmS ribozyme tunes the catalytically critical pKa of its coenzyme glucosamine-6-phosphate. J. Am. Chem. Soc. 133, 14188-14191 (2011). [abstract]

75. Edwards, T.E., Cekan, P., Reginsson, G.W., Shelke, S.A., Ferré-D'Amaré, A.R., Schiemann, O., & Sigurdsson, S.Th. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe (C-cedille). Nucleic Acids Res. 39, 4419-4426 (2011).[abstract]

74. Ferré-D'Amaré, A.R. Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Phil. Trans. R. Soc. B 366, 2942-2948 (2011). [abstract]

73. Ferré-D'Amaré, A.R. & Winkler W.C. The roles of metal ions in regulation by riboswitches. Met. Ions Life Sci. 9, 141-173 (2011). [abstract]

72. Deigan, K.E. & Ferré-D'Amaré, A.R. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc. Chem. Res. 44, 1329-1338 (2011). [abstract]

71. Ferré-D'Amaré, A.R. Protein synthesis: stop the nonsense. Nature 474, 289-290 (2011). [abstract]

70. Zhang, J., Lau, M. & Ferré-D'Amaré, A.R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49, 9123-9131 (2010). [abstract]

69. Pitt, J.N. & Ferré-D'Amaré, A.R. Rapid construction of empirical RNA fitness landscapes. Science 330, 376-379 (2010). [abstract]

68. Ferré-D'Amaré, A.R. & Scott, W.G. The small self-cleaving ribozymes. Cold Spring Harbor Persp. Biol. (published online September 15, 2010). [abstract]

67. Ferré-D'Amaré, A.R. The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA. Quarterly Rev. Biophys. 43, 423-447 (2010). [abstract]

66. Pitt, J.N., Rajapakse, I., & Ferré-D'Amaré, A.R. SEWAL: an open-source platform for next-generation sequence analysis and visualization. Nucleic Acids Res. 38, 7908-7915 (2010). [abstract]

65. Baird, N.J. & Ferré-D'Amaré, A.R. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA 16, 598-609 (2010). [abstract]

64. Kulshina, N., Edwards, T.E. & Ferré-D'Amaré, A.R. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA 16, 186-196 (2010). [abstract]

63. Ferré-D'Amaré, A.R. RNA methods: from sequence to structure and dynamics. Methods 52: 123-124 (2010). [abstract]

62. Ferré-D'Amaré, A.R. Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs Methods 52: 159-167 (2010). [abstract]

61. Baird, N.J., Kulshina, N., & Ferré-D'Amaré, A.R. Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol. 7: 328-332 (2010). [abstract]

60. Ferré-D'Amaré, A.R. An RNP switch raises a roadblock. Nature Chem. Biol. 6: 5-6 (2010). [abstract]

59. Hamma, T. & Ferré-D’Amaré, A.R. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J. Biol. Chem. 285, 805-809 (2010). [abstract]

58. Kulshina, N., Baird, N.J., & Ferré-D'Amaré, A.R. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nature Struct. Mol. Biol. 16, 1212-1217 (2009). [abstract]

57. Klein, D.J., Edwards, T.E. & Ferré-D'Amaré, A.R. Cocrystal structure of a class-I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nature Struct. Mol. Biol. 16, 343-344 (2009). [abstract]

56. Pitt, J.N. & Ferré-D'Amaré, A.R. Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J. Am. Chem. Soc. 131, 3532-3540 (2009). [abstract]

55. Mueller, E.G & Ferré-D’Amaré, A.R. Pseudouridine formation, the most common transglycosylation in RNA. In DNA and RNA Modification (ed. Grosjean, H.) Landes Bioscience, Austin pp 364-379 (2009).

54. Klein, D.J. & Ferré-D'Amaré, A.R. Crystallization of the glmS ribozyme-riboswitch. Meth. Molec. Biol. 540, 129-139 (2009). [abstract]


53. Xiao, H., Edwards, T.E. & Ferré-D'Amaré, A.R. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem. Biol. 15, 1125-1137 (2008). [abstract]

52. Xiao, H., Murakami, H., Suga, H. & Ferré-D'Amaré, A.R. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454, 358-361 (2008). [abstract]

51. Ferré-D’Amaré, A.R. RNA-modifying enzymes. In Protein-Nucleic Acid Interactions Structural Biology (ed. Rice, P.A. & Correll, C.C.) 367-381. Royal Society of Chemistry, Cambridge (2008).

50. Klein, D.J., Been, M.D. & Ferré-D'Amaré, A.R. Essential role of an active-site guanine in glmS ribozyme catalysis. J. Am. Chem. Soc. 129, 14858-14859 (2007). [abstract]

49. Klein, D.J., Wilkinson, S.R., Been., M.D. & Ferré-D'Amaré, A.R. Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme. J. Mol. Biol. 373, 178-189 (2007). [abstract]

48. Edwards, T.E., Klein, D.J. & Ferré-D’Amaré, A.R. Riboswitches: small molecule recognition by gene-regulatory RNAs. Curr. Op. Struct. Biol. 15, 273-279 (2007). [abstract]

47. Reichow, S.L., Hamma, T., Ferré-D’Amaré, A.R. & Varani, G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 35, 1452-1464 (2007). [abstract]

46. Hoang, C., Chen, J., Vizthum, C.A., Kandel, J.M., Hamilton, C.S. Mueller, E.G. & Ferré-D’Amaré, A.R. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol. Cell 24, 535-545 (2006). [abstract]

45. Klein, D.J., & Ferré-D’Amaré, A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313, 1752-1756 (2006). [abstract]

44. Edwards, T.E., & Ferré-D’Amaré, A.R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14, 1459-1468 (2006). [abstract]

43. Hamma, T. & Ferré-D’Amaré, A.R. Pseudouridine synthases. Chem. Biol. 13, 1125-1135 (2006). [abstract]


42. Hamma, T., Reichow, S.L., Varani, G., & Ferré-D’Amaré, A.R. The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nature Struct. Mol. Biol. 12, 1101-1107 (2005). [abstract]

41. Hoang, C., Hamilton, C.S., Mueller, E.G., & Ferré-D'Amaré, A.R. Precursor complex structure of pseudouridine synthase TruB suggest coupling of active site perturbations to an RNA-sequestering peripheral protein domain. Prot. Sci. 14, 2201-2206 (2005). [abstract]

40. Canizales-Quinteros, S., Aguilar-Salinas, C.A., Huertas-Vázquez, A., Ordóñez-Sánchez, M.L., Rodríguez-Torres, M., Venturas-Gallegos, J.L., Riba, L., Ramírez-Jiménez, S., Salas-Montiel, R., Medina-Palacios, G., Robles-Osorio, L., Miliar-García, A., Rosales-León, L., Ruíz-Ordaz, B.H., Zentella-Dehesa, A., Ferré-D'Amaré A., Gómez-Pérez, F.J., & Tusié-Luna M.T. novel ARH splice site mutation in a Mexican kindred with autosomal recessive hypercholesterolemia. Hum. Genet. 116, 114-120 (2005). [abstract]

39. Pitt, J.N. & Ferré-D'Amaré, A.R. How RNA closes a diel. Nature Struct. Mol. Biol. 12, 206-208 (2005). [abstract]

38. Hoang, C. & Ferré-D'Amaré, A.R. Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. RNA 10, 1026-1033 (2004). [abstract]

37. Hamma, T. & Ferré-D'Amaré, A.R. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 Å resolution. Structure 12, 893-903 (2004). [abstract]

36. Ferré-D'Amaré, A.R. The hairpin ribozyme. In Encyclopedia of Biological Chemistry (ed. Lennarz, W.J., & Lane, M.D.) Elsevier Science, New York 3, 743-746 (2004).

35. Rupert, P.B. & Ferré-D'Amaré, A.R. Crystallization of the hairpin ribozyme: illustrative protocols. Meth. Mol. Biol. 252, 303-311 (2004). [abstract]

34. Ferré-D'Amaré, A.R. The hairpin ribozyme. Biopolymers 73, 71-78 (2004). [abstract]

33. Rupert, P.B., Xiao, H., & Ferré-D'Amaré, A.R. U1A RNA binding domain at 1.8 Å resolution. Acta Crystallogr. D 59, 1521-1524 (2003). [abstract]

32. Ferré-D'Amaré, A.R. RNA-modifying enzymes. Curr. Op. Struct. Biol. 13, 49-55 (2003). [abstract]


31. Rupert, P.B., Massey, A., Sigurdsson, S.Th. & Ferré-D'Amaré, A.R. Transition state stabilization by a catalytic RNA. Science 298, 1421-1424 (2002). [abstract]

30. Ferré-D'Amaré, A.R. & Rupert, P.B. The hairpin ribozyme: from crystal structure to function. Trans. Biochem. Soc. 30, 1105-1109 (2002). [abstract]

29. Hoang, C. & Ferré-D'Amaré, A.R. Cocrystal structure of a tRNA Ψ55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107, 929-939 (2001). [abstract]

28. Rupert, P.B. & Ferré-D’Amaré, A.R. Crystal structure of a hairpin ribozyme- inhibitor complex with implications for catalysis. Nature 410, 780-786 (2001). [abstract]

27. Lupták, A., Ferré-D’Amaré, A.R., Zhou, K., Zilm, K.W. & Doudna, J.A. Direct pKa measurement of the active site cytosine in a genomic HDV ribozyme. J. Am. Chem. Soc. 123, 8447-8452 (2001). [abstract]

26. Ferré-D'Amaré, A.R. & Doudna, J.A. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein as U1A as a crystallization module. J. Mol. Biol. 295, 541-556 (2000). [abstract]

25. Rupert, P.B. & Ferré-D’Amaré, A.R. SRPrises in RNA–protein recognition. Structure 8, 99-104 (2000). [abstract]

24. Ferré-D'Amaré, A.R. & Doudna, J.A. Methods to crystallize RNA. In Curent Protocols in Nucleic Acid Chemistry (ed Beaucage, S.L., Bergstrom, D.E., Glick, G.D., & Jones, R.A.) 7.6.1-7.6.10, Wiley, New York (2000). [abstract]

A.R. Ferré-D'Amaré publications 1985-1999

23. Wadkins, T.S., Perrotta, A.T., Ferré-D’Amaré, A.R., Doudna, J.A. & Been, M.D. A nested double-pseudoknot is required for self-cleavage activity of both the genomic and antigenomic HDV ribozymes. RNA 5, 720-727 (1999). [abstract]

22. Ferré-D’Amaré, A.R. Crystallization of biological macromolecules. RNA 5, 847-848 (1999).

21. Ferré-D'Amaré, A.R. & Doudna, J.A. RNA folds: insights from recent crystal structures. Annu. Rev. Biophys. Biomolec. Struct. 28, 57-73 (1999). [abstract]

20. Ferré-D'Amaré, A.R., Zhou, K. & Doudna, J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998). [abstract]

19. Basu, S., Rambo, R.P., Strauss-Soukup, J., Cate, J.H., Ferré-D'Amaré, A.R., Strobel, S.A. & Doudna, J.A. A specific monovalent metal ion integral to the A-A platform of the RNA tetraloop receptor. Nature Struct. Biol. 5, 986-992 (1998). [abstract]

18. Ferré-D'Amaré, A.R., Zhou, K. & Doudna, J.A. A general module for RNA crystallization. J. Mol. Biol. 279, 621-631 (1998). [abstract]

17. Párraga, A., Bellsolell, L., Ferré-D'Amaré, A.R. & Burley, S.K. Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 Å resolution. Structure 6, 661-672 (1998).

16. Steingrímsson, E., Favor, J., Ferré-D'Amaré, A.R., Copeland, N.G. & Jenkins, N.A. Mitfmi-enu122 is a missense mutation in the HLH dimerization domain. Mammalian Genome 9, 250-252 (1998). [abstract]

15. Ferré-D'Amaré, A.R. & Burley, S.K. Dynamic light scattering in evaluating crystallizability of macromolecules. Meth. Enzymol. 276, 157-166 (1997).

14. Ferré-D'Amaré, A.R. & Doudna, J.A. Establishing suitability of RNA preparations for crystallization. Determination of polydispersity. In Ribozyme Protocols (ed. Turner, P.C.) 371-378, Humana Press, Totowa, N.J. (1997). [abstract]

13. Ferré-D'Amaré, A.R. & Doudna, J.A. Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 24, 977-978 (1996). [abstract]

12. Steingímsson, E., Nii, A., Fisher, D.F., Ferré-D'Amaré, A.R., McCormick, R.J., Russell, L.B., Burley, S.K., Ward, J.M., Jenkins, N.A. & Copeland, N.G. The semidominant Mib mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization. EMBO J. 15, 6280-6289 (1996).

11. Canne, L.E., Ferré-D'Amaré, A.R., Burley, S.K. & Kent, S.B.H. Total chemical synthesis of a unique transcription factor protein: cMyc-Max. J. Am. Chem. Soc. 117, 2998-3007 (1995).

10. Ferré-D'Amaré, A.R. Prospección ecológica de los arrecifes coralinos de Cayos Arcas y Triángulos, Campeche, México. Impacto ambiental de una década de actividades de la industria petrolera. Sian Ka'an Serie Documentos 4, 40-48 (1995).

9. Sha, M., Ferré-D'Amaré, A.R., Burley, S.K. & Goss, D.J. Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes. J. Biol. Chem. 270, 19325-19329 (1995). [abstract]

8. Ferré-D'Amaré, A.R. & Burley, S.K. DNA recognition by helix-loop-helix proteins. In Nucleic Acids and Molecular Biology (ed Eckstein, F. & Lilley, D.M.J.) 9, 285-298, Springer Verlag, Berlin (1995).

7. Cohen, S.L., Ferré-D'Amaré, A.R., Burley, S.K. & Chait, B.T. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 4, 1088-1099 (1995). [abstract]

6. Ferré-D'Amaré, A.R., Pognonec, P., Roeder, R.G. & Burley, S.K. Structure and function of the b/HLH/Z domain of USF. EMBO J. 13, 180-189 (1994). [abstract]

5. Ferré-D'Amaré, A.R. & Burley, S.K. Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure 2, 357-359, 567 (1994). [abstract]

4. Steingrímsson, E., Moore, K.J., Lamoreux, M.L., Ferré-D'Amaré, A.R., Burley, S.K., Sanders Zimring, D.C., Skow, L.C., Hodgkinson, C.A., Arnheiter, H., Copeland, N.G. & Jenkins, N.A. Molecular basis of mouse microphthalmia (mi) mutations helps explain their developmental and phenotypic consequences. Nature Genet. 8, 256-268 (1994). [abstract]

3. Ferré-D'Amaré, A.R., Prendergast, G.C., Ziff, E.B. & Burley, S.K. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38- 45 (1993). [abstract]

2. Burley, S.K., Clark, K.L., Ferré-D'Amaré, A., Kim, J.L. & Nikolov, D.B. X-ray crystallographic studies of eukaryotic transcription factors. Cold Spring Harbor Symp. Quant. Biol. 58, 123-132 (1993). [abstract]

1. Ferré-D'Amaré, A.R. Coral reefs of the Mexican Atlantic: a review. Proc. Fifth Intl. Coral Reef Congress 6, 349-354 (1985).