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The least-squares superposition of backbone a carbons corresponding to the RNA binding region of the bound M domain (E. coli residues 376 to 421), Thermus aquaticus [Protein Data Bank (PDB) accession number 2ffh], and human M domain (1QB2) were performed with LSQMAN [G. J. Kleywegt and T. A. Jones, CCP4 Newslett. 31, 9 (1994)]. The backbone root mean square deviation (rmsd) between the E. coli and T. aquaticus M domains is 0.68 Å, and 0.66 Å between the E. coli and human M domains.
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2-ethanol solution and incubation at 90°C for 1 min. The cleavage products were resolved by electrophoresis on a 12% denaturing polyacrylamide gel. The band intensities were quantified by phosphorimaging and the extent of interference determined as described [S. P. Ryder and S. A. Strobel, Methods 18, 38 (1999)].
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2-ethanol solution and incubation at 90°C for 1 min. The cleavage products were resolved by electrophoresis on a 12% denaturing polyacrylamide gel. The band intensities were quantified by phosphorimaging and the extent of interference determined as described [S. P. Ryder and S. A. Strobel, Methods 18, 38 (1999)].
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A number of other nucleotide analogs, including 2′ deoxyadenosine, diamino purine, inosine, and N-methyl guanosine, have also been used, and the results are consistent with the crystal structure.
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40
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0343307737
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The A39U point mutation in the context of the E4 construct was also tested and failed to support growth
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The A39U point mutation in the context of the E4 construct was also tested and failed to support growth.
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We thank S. Brown for providing the 4.55 RNA conditionally deficient strains of E. coli and helpful advice; C. Ogata for time and assistance at beamline X4A of the National Synchrotron Light Source, Brookhaven National Laboratory; T. Earnest for support at beamline 5.0.2 of the Advanced Light Source, Lawrence Berkeley National Laboratory; R. Hanna, J. Kieft, A. Luptak, and M. Talavera for help with beam-line data collection and useful discussions; P. Adams and L. Rice for assistance with the refinement; the staff of the Yale Center for Structural Biology for cristallographic and computational support; S. Strobel for providing the nucleotide analogs and for helpful discussions; S. Basu, J. Cate, J. Davis, T. Griffin, J. Ippolito, S. Ryder, P. Scamborova, P. Sigler, and T. Steitz for many helpful discussions; and J. Cate, J. Kieft, V. Rath, and S. Strobel for critically reading the manuscript. We are particularly indebted to A. Ferré-D'Amaré for excellent advice and support throughout this project. This project was funded in part by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fund for Medical Research (R.T.B.), a Howard Hughes Medical Institute (HHMI) summer fellowship (B.R.), and by support from the NIH, HHMI, and the David and Lucile Packard Foundation. J.A.D. is a Fellow of the David and Lucile Packard Foundation and an Assistant Investigator of HHMI. Coordinates of the SRP core and structure factor amplitudes have been deposited in the PDB (accession code 1DUL). Coordinates are also available at www.csb.yale.edu/ people/doudna/doudna_people.html.
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