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Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA.
Ferré-D'Amaré AR, Doudna JA. Ferré-D'Amaré AR, et al. Nucleic Acids Res. 1996 Mar 1;24(5):977-8. doi: 10.1093/nar/24.5.977. Nucleic Acids Res. 1996. PMID: 8600468 Free PMC article. No abstract available.
X-ray crystallographic studies of eukaryotic transcription factors.
Burley SK, Clark KL, Ferré-D'Amaré A, Kim JL, Nikolov DB. Burley SK, et al. Cold Spring Harb Symp Quant Biol. 1993;58:123-32. doi: 10.1101/sqb.1993.058.01.016. Cold Spring Harb Symp Quant Biol. 1993. PMID: 7956022
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. Miao Z, et al. RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30. RNA. 2017. PMID: 28138060 Free PMC article.
Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.
Pitt JN, Ferré-D'Amaré AR. Pitt JN, et al. J Am Chem Soc. 2009 Mar 18;131(10):3532-40. doi: 10.1021/ja8067325. J Am Chem Soc. 2009. PMID: 19220054 Free PMC article.
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.
Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD. Wadkins TS, et al. RNA. 1999 Jun;5(6):720-7. doi: 10.1017/s1355838299990209. RNA. 1999. PMID: 10376872 Free PMC article.
RNA folds: insights from recent crystal structures.
Ferré-D'Amaré AR, Doudna JA. Ferré-D'Amaré AR, et al. Annu Rev Biophys Biomol Struct. 1999;28:57-73. doi: 10.1146/annurev.biophys.28.1.57. Annu Rev Biophys Biomol Struct. 1999. PMID: 10410795 Review.
Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme.
Lupták A, Ferré-D'Amaré AR, Zhou K, Zilm KW, Doudna JA. Lupták A, et al. J Am Chem Soc. 2001 Sep 5;123(35):8447-52. doi: 10.1021/ja016091x. J Am Chem Soc. 2001. PMID: 11525650
Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module.
Ferré-D'Amaré AR, Doudna JA. Ferré-D'Amaré AR, et al. J Mol Biol. 2000 Jan 21;295(3):541-56. doi: 10.1006/jmbi.1999.3398. J Mol Biol. 2000. PMID: 10623545
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor.
Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA. Basu S, et al. Nat Struct Biol. 1998 Nov;5(11):986-92. doi: 10.1038/2960. Nat Struct Biol. 1998. PMID: 9808044
Crystal structure of a hepatitis delta virus ribozyme.
Ferré-D'Amaré AR, Zhou K, Doudna JA. Ferré-D'Amaré AR, et al. Nature. 1998 Oct 8;395(6702):567-74. doi: 10.1038/26912. Nature. 1998. PMID: 9783582
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