Education

Ph.D. in Molecular Biophysics, The Rockefeller University, 1995

Current position

Senior Investigator, Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, NIH

Publications (since 2005)

1. Zhang, J. and Ferre-D'Amare, A. R. (2015). Structure and mechanism of the T-box riboswitches. Wiley Interdiscip Rev RNA 6(4): 419-433.
   
2. Liu, Y., Holmstrom, E., Zhang, J., Yu, P., Wang, J., Dyba, M. A., Chen, D., Ying, J., Lockett, S., Nesbitt, D. J., Ferre-D'Amare, A. R., Sousa, R., Stagno, J. R. and Wang, Y. X. (2015). Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 522(7556): 368-372.
   
3. 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., Ferre-D'Amare, 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., Peselis, 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. and Westhof, E. (2015). RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21(6): 1066-1084.
   
4. Ferre-D'Amare, A. R. (2015). On the shoulders of giants. RNA 21(4): 504-505.
   
5. Jones, C. P. and Ferre-D'Amare, A. R. (2015). RNA quaternary structure and global symmetry. Trends Biochem Sci 40(4): 211-220.
   
6. Chen, M. C., Murat, P., Abecassis, K., Ferre-D'Amare, A. R. and Balasubramanian, S. (2015). Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase. Nucleic Acids Res 43(4): 2223-2231.
   
7. Zhang, J. and Ferre-D'Amare, A. R. (2014). A flexible, scalable method for preparation of homogeneous aminoacylated tRNAs. Methods Enzymol 549: 105-113.
   
8. Warner, K. D. and Ferre-D'Amare, A. R. (2014). Crystallographic analysis of TPP riboswitch binding by small-molecule ligands discovered through fragment-based drug discovery approaches. Methods Enzymol 549: 221-233.
   
9. Jones, C. P. and Ferre-D'Amare, A. R. (2014). Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. EMBO J 33(22): 2692-2703.
   
10. Zhang, J. and Ferre-D'Amare, A. R. (2014). Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22(9): 1363-1371.
    
11. Warner, K. D., Chen, M. C., Song, W., Strack, R. L., Thorn, A., Jaffrey, S. R. and Ferre-D'Amare, A. R. (2014). Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 21(8): 658-663.
    
12. Zhang, J. and Ferre-D'Amare, A. R. (2014). Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol Cell 55(1): 148-155.
    
13. Zhang, J., Jones, C. P. and Ferre-D'Amare, A. R. (2014). Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta 1839(10): 1020-1029.
    
14. Warner, K. D., Homan, P., Weeks, K. M., Smith, A. G., Abell, C. and Ferre-D'Amare, A. R. (2014). Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol 21(5): 591-595.
    
15. Zhang, J. and Ferre-D'Amare, A. R. (2014). New molecular engineering approaches for crystallographic studies of large RNAs. Curr Opin Struct Biol 26: 9-15.
    
16. Baird, N. J. and Ferre-D'Amare, A. R. (2014). Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 1103: 211-225.
    
17. Lau, M. W. and Ferre-D'Amare, A. R. (2013). An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol 9(12): 805-810.
    
18. Zhang, J. and Ferre-D'Amare, A. R. (2013). Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500(7462): 363-366.
    
19. Posakony, J. J. and Ferre-D'Amare, A. R. (2013). Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme. J Org Chem 78(10): 4730-4743.
    
20. Ferré-D'Amaré, A. R. Riboswitches. (2013). In: Lennarz, W. J. and Lane, M. D. (eds). The Encyclopedia of Biological Chemistry. Academic Press, 4: 136-141.
    
21. Ferré-D'Amaré, A. R. (2013). Crystallization of RNA for structure determination by X-ray crystallography. In: Klostermeier D. and Hammann, C. (eds). Structure and folding of RNA. deGruyter, 319-333.
    
22. Baird, N. J. and Ferre-D'Amare, A. R. (2013). Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19(2): 167-176.
    
23. Wood, S., Ferre-D'Amare, A. R. and Rueda, D. (2012). Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem Biol 7(5): 920-927.
    
24. Baird, N. J., Zhang, J., Hamma, T. and Ferre-D'Amare, A. R. (2012). YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA 18(4): 759-770.
    
25. Gong, B., Klein, D. J., Ferre-D'Amare, A. R. and Carey, P. R. (2011). The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate. J Am Chem Soc 133(36): 14188-14191.
    
26. Edwards, T. E., Cekan, P., Reginsson, G. W., Shelke, S. A., Ferre-D'Amare, A. R., Schiemann, O. and Sigurdsson, S. T. (2011). Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Nucleic Acids Res 39(10): 4419-4426.
    
27. Ferre-D'Amare, A. R. (2011). Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos Trans R Soc Lond B Biol Sci 366(1580): 2942-2948.
    
28. Ferre-D'Amare, A. R. and Winkler, W. C. (2011). The roles of metal ions in regulation by riboswitches. Met Ions Life Sci 9: 141-173.
    
29. Deigan, K. E. and Ferre-D'Amare, A. R. (2011). Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res 44(12): 1329-1338.
    
30. Ferre-D'Amare, A. R. (2011). Protein synthesis: Stop the nonsense. Nature 474(7351): 289-290.
    
31. Zhang, J., Lau, M. W. and Ferre-D'Amare, A. R. (2010). Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49(43): 9123-9131.
    
32. Pitt, J. N. and Ferre-D'Amare, A. R. (2010). Rapid construction of empirical RNA fitness landscapes. Science 330(6002): 376-379.
    
33. Ferré-D'Amaré, A. R. and Scott, W. G. (2010). Small self-cleaving ribozymes. Cold Spring Harbor perspectives in biology 2(10): a003574.
    
34. Ferre-D'Amare, A. R. (2010). The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA. Q Rev Biophys 43(4): 423-447.
    
35. Pitt, J. N., Rajapakse, I. and Ferre-D'Amare, A. R. (2010). SEWAL: an open-source platform for next-generation sequence analysis and visualization. Nucleic Acids Res 38(22): 7908-7915.
    
36. Baird, N. J. and Ferre-D'Amare, A. R. (2010). Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA 16(3): 598-609.
    
37. Kulshina, N., Edwards, T. E. and Ferre-D'Amare, A. R. (2010). Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA 16(1): 186-196.
    
38. Ferre-D'Amare, A. R. (2010). RNA methods: from sequence to structure and dynamics. Methods 52(2): 123-124.
    
39. Ferre-D'Amare, A. R. (2010). Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs. Methods 52(2): 159-167.
    
40. Baird, N. J., Kulshina, N. and Ferre-D'Amare, A. R. (2010). Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol 7(3): 328-332.
    
41. Ferre-D'Amare, A. R. (2010). Synthetic biology: an RNP switch raises a roadblock. Nat Chem Biol 6(1): 5-6.
    
42. Hamma, T. and Ferre-D'Amare, A. R. (2010). The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem 285(2): 805-809.
    
43. Kulshina, N., Baird, N. J. and Ferre-D'Amare, A. R. (2009). Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16(12): 1212-1217.
    
44. Klein, D. J., Edwards, T. E. and Ferre-D'Amare, A. R. (2009). Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol 16(3): 343-344.
    
45. Pitt, J. N. and Ferre-D'Amare, A. R. (2009). Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J Am Chem Soc 131(10): 3532-3540.
    
46. Mueller, E. G and Ferré-D’Amaré, A. R. (2009). Pseudouridine formation, the most common transglycosylation in RNA. In: Grosjean, H. (ed). DNA and RNA modification landes bioscience. Austin, 364-379.
    
47. Klein, D. J. and Ferre-D'Amare, A. R. (2009). Crystallization of the glmS ribozyme-riboswitch. Methods Mol Biol 540: 129-139.
    
48. Xiao, H., Edwards, T. E. and Ferre-D'Amare, A. R. (2008). Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem Biol 15(10): 1125-1137.
    
49. Xiao, H., Murakami, H., Suga, H. and Ferre-D'Amare, A. R. (2008). Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454(7202): 358-361.
    
50. Ferré-D’Amaré, A. R. (2008). RNA-modifying enzymes. In: Rice, P. A. and Correll, C. C. (eds). Protein-nucleic acid interactions structural biology. Royal Society of Chemistry, 367-381.
    
51. Klein, D. J., Been, M. D. and Ferre-D'Amare, A. R. (2007). Essential role of an active-site guanine in glmS ribozyme catalysis. J Am Chem Soc 129(48): 14858-14859.
    
52. Klein, D. J., Wilkinson, S. R., Been, M. D. and Ferre-D'Amare, A. R. (2007). Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme. J Mol Biol 373(1): 178-189.
    
53. Edwards, T. E., Klein, D. J. and Ferre-D'Amare, A. R. (2007). Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol 17(3): 273-279.
    
54. Reichow, S. L., Hamma, T., Ferre-D'Amare, A. R. and Varani, G. (2007). The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res 35(5): 1452-1464.
    
55. Hoang, C., Chen, J., Vizthum, C. A., Kandel, J. M., Hamilton, C. S., Mueller, E. G. and Ferre-D'Amare, A. R. (2006). Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell 24(4): 535-545.
    
56. Klein, D. J. and Ferre-D'Amare, A. R. (2006). Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313(5794): 1752-1756.
    
57. Edwards, T. E. and Ferre-D'Amare, A. R. (2006). Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14(9): 1459-1468.
    
58. Hamma, T. and Ferre-D'Amare, A. R. (2006). Pseudouridine synthases. Chem Biol 13(11): 1125-1135.