(12) United States Patent (10) Patent No.: US 6,555,349 B1 O'donnell (45) Date of Patent: Apr
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USOO6555349B1 (12) United States Patent (10) Patent No.: US 6,555,349 B1 O'Donnell (45) Date of Patent: Apr. 29, 2003 (54) METHODS FOR AMPLIFYING AND Xiao et al., “DNA Polymerase III Accessory Proteins. III. SEQUENCING NUCLEIC ACID MOLECULES HolC and holD Encoding X and up,” J. Biol. Chem. USING ATHREE COMPONENT 268: 11779–84 (1993). POLYMERASE Xiao et al., “DNA Polymerase III Accessory Proteins. IV. Characterization of X and up,” J. Biol. Chem. 268: 11773-78 (75) Inventor: Michael E. O'Donnell, (1993). Hastings-on-Hudson, NY (US) Studwell-Vaughan et al., “DNA Polymerase III Accessory (73) Assignees: Cornell Research Foundation, Inc., Proteins. V. 0 Encoded by holE,” J. Biol. Chem. Ithaca, NY (US); The Rockefeller 268:11785-91 (1993). University, New York, NY (US) Carter et al., “Molecular Cloning, Sequencing, and Overex pression of the Structural Gene Encoding the Ó Subunit of E. (*) Notice: Subject to any disclaimer, the term of this Coli DNA Polymerase III Holoenzyme,” J. Bacteriol. patent is extended or adjusted under 35 174:7013-25 (1993). U.S.C. 154(b) by 0 days. Carter et al., “Identification, Isolation, and Characterization of the Structural Gene Encoding the ÖN Subunit of E. Coli DNA Polymerase III Holoenzyme,” J. Bacteriol, (21) Appl. No.: 09/325,067 175:3812–22 (1993). Carter et al., “Isolation, Sequencing, and Overexpression of (22) Filed: Jun. 3, 1999 the Gene Encoding the 0 Subunit of DNA Polymerase III Related U.S. Application Data Holoenzyme,” Nuc. Acids Res. 21:3281–86 (1993). Carter et al., “Identification, Isolation, and Overexpression (63) Continuation-in-part of application No. 08/828,323, filed on of the Gene Encoding the I? Subunit of DNA Polymerase III Mar. 28, 1997, which is a continuation of application No. Holoenzyme,” J. Bacteriol. 175:5604–10 (1993). 08/279,058, filed on Jul. 22, 1994, now Pat. No. 5,668,004, which is a continuation-in-part of application No. 07/826, Carter et al., “Identification, Molecular Cloning and Char 926, filed on Jan. 22, 1993, now abandoned, application No. acterization of the Gene Encoding the X. Subunit of DNA 09/325,067, which is a continuation-in-part of application Polymerase III Holoenzyme of E. coli,' Mol. Gen. Genet. No. 09/282,917, filed on Mar. 31, 1999, now Pat. No. 6,221,642, which is a division of application No. 08/696, 241:399-408 (1993). 651, filed on Aug. 14, 1996, which is a continuation of Tomasiewicz et al., “Sequence Analysis of the Escherichia application No. 08/298.945, filed on Aug. 31, 1994, now Pat. No. 5,583,026. coli dnaE Gene,” J. Bacteriol. 169:5735–44 (1987). Ohmori et al., “Structural Analysis of the dnaA and dnaN (51) Int. Cl. ........................... C12Q 1/68; C12P 19/34; Genes of Escherichia coli,” Gene 28:159–170) (1984). C07H 21/02; CO7H 21/04 Flower et al., “The Adjacent dnaZ and dnaX Genes of (52) U.S. Cl. ........................... 435/91.2, 435/6; 435/7.1; Escherichia coli are Contained Within One Continuous 435/91.1; 435/194; 530/350; 536/23.1; Open Reading Frame,” Nuc. Acids Res, 14:8091-8101 536/24.3; 536/24.31; 536/24.32; 536/24.33; 536/22.1 (1986). (58) Field of Search ............................ 435/6, 7.1, 91.1, Yin et al., “Nucleotide Sequence of the Escherichia coli 435/912; 530/350, 22.1; 536/23.1, 24.3, Replication Gene dnaZX,” ibid. pp. 6541-6549. 24.31-33 Maki et al., “Structural and Expression of the dnaO Mutator and the RNase H Genes of Escherichia coli. Overlap of the Promoter Regions.” Proc. Natl. Acad. Sci. USA 80:7137–41 (56) References Cited (1983). U.S. PATENT DOCUMENTS Lasken et al., “The BSubunit Dissociates Readily from the Escherichia coli DNA Polymerase III Holoenzyme,” J. Biol. 4,394,443 A 7/1983 Weissman et al. 5,583,026 A 12/1996 O'Donnell Chem. 262:1720–24 (1987). 5,668,004 A 9/1997 O'Donnell Studwell-Vaughan et al., “Constitution of the Twin Poly merase of DNA Polymerase III Holoenzyme,” J. Biol. FOREIGN PATENT DOCUMENTS Chem. 266(29):19833–41 (1991). WO WO 93/15115 8/1993 WO WO-99/13060 A1 * 3/1999 (List continued on next page.) OTHER PUBLICATIONS Primary Examiner Jeffrey Siew (74) Attorney, Agent, or Firm Nixon Peabody LLP Young et al Biochemistry vol. 21 No. 27 pp. 8675-8690 1992.* (57) ABSTRACT Onrust et al., “DNA Polymerase III Accessory Proteins. II. The present invention is directed to a method for amplifying Characterization of 8 and ÖN,” J. Biol. Chem. 268: 11766-72 or Sequencing a nucleic acid molecule with a three compo (1993). nent polymerase comprising a DNA polymerase component, Dong et al., “DNA Polymerase III Accessory Proteins. I. a sliding clamp component, and a clamp loader component. HolA and holB Encoding 8 and ÖN,” J. Biol. 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