Nucleic Acids Research, 1988, Vol. 16, No. 15 7351-7367
© 1988
Articles |
A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions
Department of Human Genetics, Cetus Corporation, Emeryville, CA 94608, USA 1Department of Biochemistry, U.C. Berkeley Berkeley, CA 94720, USA
Received May 19, 1988. Accepted July 8, 1988.
Specific, end-labeled DNA fragments can be simply and rapidly prepared using the polymerase chain reaction (PCR). Such fragments are suitable for use in DNase I protection footprint assays, chemical sequencing reactions, and for the production and analysis of paused RNA polymerase transcription complexes. Moreover, a general means of introducing a specific mutation at any position along the length of such PCR-generated fragments is described. These procedures, which can circumvent the need for large-scale phage or plasmid growths, preparative gel-electrophoresis and the screening of molecular clones, can facilitate the rapid study of sequence-specffic interactions of proteins and DNA. A rapid means of removing excess oligonucleotide primers from completed PCRs is also described.
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S. Iwai, D. Hanamoto, and S. Chaen A Point Mutation in the SH1 Helix Alters Elasticity and Thermal Stability of Myosin II J. Biol. Chem., October 13, 2006; 281(41): 30736 - 30744. [Abstract] [Full Text] [PDF]
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A. Liiv and M. O'Connor Mutations in the Intersubunit Bridge Regions of 23 S rRNA J. Biol. Chem., October 6, 2006; 281(40): 29850 - 29862. [Abstract] [Full Text] [PDF]
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J. Schelert, M. Drozda, V. Dixit, A. Dillman, and P. Blum Regulation of Mercury Resistance in the Crenarchaeote Sulfolobus solfataricus. J. Bacteriol., October 1, 2006; 188(20): 7141 - 7150. [Abstract] [Full Text] [PDF]
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D. Kerssen, E. Hambruch, W. Klaas, H. W. Platta, B. de Kruijff, R. Erdmann, W.-H. Kunau, and W. Schliebs Membrane Association of the Cycling Peroxisome Import Receptor Pex5p J. Biol. Chem., September 15, 2006; 281(37): 27003 - 27015. [Abstract] [Full Text] [PDF]
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S. Borghini, M. Vargiolu, M. Di Duca, R. Ravazzolo, and I. Ceccherini Nuclear Factor Y Drives Basal Transcription of the Human TLX3, a Gene Overexpressed in T-Cell Acute Lymphocytic Leukemia Mol. Cancer Res., September 1, 2006; 4(9): 635 - 643. [Abstract] [Full Text] [PDF]
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M.-X. Guo, D. Wang, H.-J. Shao, H.-L. Qiu, L. Xue, Z.-Z. Zhao, C.-G. Zhu, Y.-B. Shi, and W.-X. Li Transcription of Human Zinc Finger ZNF268 Gene Requires an Intragenic Promoter Element J. Biol. Chem., August 25, 2006; 281(34): 24623 - 24636. [Abstract] [Full Text] [PDF]
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M. Trujillo, P. Mauri, L. Benazzi, M. Comini, A. De Palma, L. Flohe, R. Radi, M. Stehr, M. Singh, F. Ursini, et al. The Mycobacterial Thioredoxin Peroxidase Can Act as a One-cysteine Peroxiredoxin J. Biol. Chem., July 21, 2006; 281(29): 20555 - 20566. [Abstract] [Full Text] [PDF]
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 J. R. Merchan, J. Tang, G. Hu, Y. Lin, W. Mutter, C. Tong, S. A. Karumanchi, S. J. Russell, and V. P. Sukhatme Protease activity of urokinase and tumor progression in a syngeneic mammary cancer model. J Natl Cancer Inst, June 7, 2006; 98(11): 756 - 764. [Abstract] [Full Text] [PDF]
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T. G. Wilkinson II, G. C. Kedar, C. Lee, E. C. Guzman, D. W. Smith, and J. W. Zyskind The Synchrony Phenotype Persists after Elimination of Multiple GATC Sites from the dnaA Promoter of Escherichia coli. J. Bacteriol., June 1, 2006; 188(12): 4573 - 4576. [Abstract] [Full Text] [PDF]
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L. J. Falomir-Lockhart, L. Laborde, P. C. Kahn, J. Storch, and B. Corsico Protein-Membrane Interaction and Fatty Acid Transfer from Intestinal Fatty Acid-binding Protein to Membranes: SUPPORT FOR A MULTISTEP PROCESS J. Biol. Chem., May 19, 2006; 281(20): 13979 - 13989. [Abstract] [Full Text] [PDF]
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N. Devroede, N. Huysveld, and D. Charlier Mutational Analysis of Intervening Sequences Connecting the Binding Sites for Integration Host Factor, PepA, PurR, and RNA Polymerase in the Control Region of the Escherichia coli carAB Operon, Encoding Carbamoylphosphate Synthase J. Bacteriol., May 1, 2006; 188(9): 3236 - 3245. [Abstract] [Full Text] [PDF]
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 J. Sambrook and D. W. Russell Site-specific Mutagenesis by Overlap Extension CSH Protocols, May 1, 2006; 2006(2): pdb.prot3468 - pdb.prot3468. [Full Text]
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J. D. Bloom, S. T. Labthavikul, C. R. Otey, and F. H. Arnold Protein stability promotes evolvability PNAS, April 11, 2006; 103(15): 5869 - 5874. [Abstract] [Full Text] [PDF]
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G. Lack, E. Homberger-Zizzari, G. Folkers, L. Scapozza, and R. Perozzo Recombinant Expression and Biochemical Characterization of the Unique Elongating beta-Ketoacyl-Acyl Carrier Protein Synthase Involved in Fatty Acid Biosynthesis of Plasmodium falciparum Using Natural and Artificial Substrates J. Biol. Chem., April 7, 2006; 281(14): 9538 - 9546. [Abstract] [Full Text] [PDF]
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H. Mizumoto, H.-o. Iwakawa, M. Kaido, K. Mise, and T. Okuno Cap-Independent Translation Mechanism of Red Clover Necrotic Mosaic Virus RNA2 Differs from That of RNA1 and Is Linked to RNA Replication. J. Virol., April 1, 2006; 80(8): 3781 - 3791. [Abstract] [Full Text] [PDF]
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 W. I.L. Tameling, J. H. Vossen, M. Albrecht, T. Lengauer, J. A. Berden, M. A. Haring, B. J.C. Cornelissen, and F. L.W. Takken Mutations in the NB-ARC Domain of I-2 That Impair ATP Hydrolysis Cause Autoactivation Plant Physiology, April 1, 2006; 140(4): 1233 - 1245. [Abstract] [Full Text] [PDF]
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M. Zielinski, S. Kahl, C. Standfuss-Gabisch, B. Camara, M. Seeger, and B. Hofer Generation of Novel-Substrate-Accepting Biphenyl Dioxygenases through Segmental Random Mutagenesis and Identification of Residues Involved in Enzyme Specificity. Appl. Envir. Microbiol., March 1, 2006; 72(3): 2191 - 2199. [Abstract] [Full Text] [PDF]
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Y. Honda and M. Kitaoka The First Glycosynthase Derived from an Inverting Glycoside Hydrolase J. Biol. Chem., January 20, 2006; 281(3): 1426 - 1431. [Abstract] [Full Text] [PDF]
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G. Rudolph, G. Semini, F. Hauser, A. Lindemann, M. Friberg, H. Hennecke, and H.-M. Fischer The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrhizobium japonicum Genes, Is a Target for the Irr Protein J. Bacteriol., January 15, 2006; 188(2): 733 - 744. [Abstract] [Full Text] [PDF]
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E. van de Vosse, R. A. de Paus, J. T. van Dissel, and T. H.M. Ottenhoff Molecular complementation of IL-12R{beta}1 deficiency reveals functional differences between IL-12R{beta}1 alleles including partial IL-12R{beta}1 deficiency Hum. Mol. Genet., December 15, 2005; 14(24): 3847 - 3855. [Abstract] [Full Text] [PDF]
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L. Moumne, M. Fellous, and R. A. Veitia Deletions in the polyAlanine-containing transcription factor FOXL2 lead to intranuclear aggregation Hum. Mol. Genet., December 1, 2005; 14(23): 3557 - 3564. [Abstract] [Full Text] [PDF]
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B. T. Vander Kooi, H. Onuma, J. K. Oeser, C. A. Svitek, S. R. Allen, C. W. Vander Kooi, W. J. Chazin, and R. M. O'Brien The Glucose-6-Phosphatase Catalytic Subunit Gene Promoter Contains Both Positive and Negative Glucocorticoid Response Elements Mol. Endocrinol., December 1, 2005; 19(12): 3001 - 3022. [Abstract] [Full Text] [PDF]
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F. Cargnin, A. Flora, S. D. Lascio, E. Battaglioli, R. Longhi, F. Clementi, and D. Fornasari PHOX2B Regulates Its Own Expression by a Transcriptional Auto-regulatory Mechanism J. Biol. Chem., November 11, 2005; 280(45): 37439 - 37448. [Abstract] [Full Text] [PDF]
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