Center-Authored Papers

Filters: Author is Ferré-D'Amaré, Adrian R  [Clear All Filters]
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2008
Xiao H, Edwards TE, Ferré-D'Amaré AR.  2008.  Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.. Chemistry & biology. 15(10):1125-37. Abstract
Xiao H, Murakami H, Suga H, Ferré-D'Amaré AR.  2008.  Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.. Nature. 454(7202):358-61. Abstract
2009
Klein DJ, Ferré-D'Amaré AR.  2009.  Crystallization of the glmS ribozyme-riboswitch.. Methods in molecular biology (Clifton, N.J.). 540:129-39. Abstract
Klein DJ, Edwards TE, Ferré-D'Amaré AR.  2009.  Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase.. Nature structural & molecular biology. 16(3):343-4. Abstract
Pitt JN, Ferré-D'Amaré AR.  2009.  Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.. Journal of the American Chemical Society. 131(10):3532-40. Abstract
Kulshina N, Baird NJ, Ferré-D'Amaré AR.  2009.  Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.. Nature structural & molecular biology. 16(12):1212-7. Abstract
2010
Ferré-D'Amaré AR, Scott WG.  2010.  Small self-cleaving ribozymes.. Cold Spring Harbor perspectives in biology. 2(10):a003574. Abstract
Baird NJ, Ferré-D'Amaré AR.  2010.  Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis.. RNA (New York, N.Y.). 16(3):598-609. Abstract
Pitt JN, Ferré-D'Amaré AR.  2010.  Rapid construction of empirical RNA fitness landscapes.. Science (New York, N.Y.). 330(6002):376-9. Abstract
Baird NJ, Kulshina N, Ferré-D'Amaré AR.  2010.  Riboswitch function: flipping the switch or tuning the dimmer? RNA biology. 7(3):328-32. Abstract
Ferré-D'Amaré AR.  2010.  Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.. Methods (San Diego, Calif.). 52(2):159-67. Abstract
Pitt JN, Rajapakse I, Ferré-D'Amaré AR.  2010.  SEWAL: an open-source platform for next-generation sequence analysis and visualization.. Nucleic acids research. 38(22):7908-15. Abstract
Zhang J, Lau MW, Ferré-D'Amaré AR.  2010.  Ribozymes and riboswitches: modulation of RNA function by small molecules.. Biochemistry. 49(43):9123-31. Abstract
Kulshina N, Edwards TE, Ferré-D'Amaré AR.  2010.  Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.. RNA (New York, N.Y.). 16(1):186-96. Abstract
Ferré-D'Amaré AR.  2010.  The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.. Quarterly reviews of biophysics. 43(4):423-47. Abstract
Ferré-D'Amaré AR.  2010.  RNA methods: from sequence to structure and dynamics.. Methods (San Diego, Calif.). 52(2):123-4.
Hamma T, Ferré-D'Amaré AR.  2010.  The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.. The Journal of biological chemistry. 285(2):805-9. Abstract
2011
Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferré-D'Amaré AR, Schiemann O, Sigurdsson ST.  2011.  Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.. Nucleic acids research. 39(10):4419-26. Abstract
Algorithms
Pitt JN, Ferré-D'Amaré AR.  2010.  Rapid construction of empirical RNA fitness landscapes.. Science (New York, N.Y.). 330(6002):376-9. Abstract
Amino Acyl-tRNA Synthetases
Xiao H, Murakami H, Suga H, Ferré-D'Amaré AR.  2008.  Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.. Nature. 454(7202):358-61. Abstract
Animals
Hamma T, Ferré-D'Amaré AR.  2010.  The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.. The Journal of biological chemistry. 285(2):805-9. Abstract
Baird NJ, Kulshina N, Ferré-D'Amaré AR.  2010.  Riboswitch function: flipping the switch or tuning the dimmer? RNA biology. 7(3):328-32. Abstract
Aptamers, Nucleotide
Kulshina N, Edwards TE, Ferré-D'Amaré AR.  2010.  Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.. RNA (New York, N.Y.). 16(1):186-96. Abstract
Xiao H, Edwards TE, Ferré-D'Amaré AR.  2008.  Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.. Chemistry & biology. 15(10):1125-37. Abstract
Ferré-D'Amaré AR.  2010.  Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.. Methods (San Diego, Calif.). 52(2):159-67. Abstract