References
- Watson JD. A structure for deoxyribose nucleic acid. Nature171, 737–738 (1953).
- Watson JD, Crick FH. Genetic implications of the structure of deoxyribonucleic acid. Nature171, 964–967 (1953).
- Bessman MJ, Kornberg A, Lehman IR et al. Enzymatic synthesis of deoxyribonucleic acid. Biochim. Biophys. Acta21, 197–198 (1956).
- Gefter ML, Molineux IJ, Kornberg T et al. Deoxyribonucleic acid synthesis in cell-free extracts III. Catalytic properties of deoxyribonucleic acid polymerase II. J. Biol. Chem.247, 3321–3326 (1972).
- Kornberg T, Gefter ML. Purification and DNA synthesis in cell-free extracts: properties of DNA polymerase II. Proc. Natl Acad. Sci. USA68, 761–764 (1971).
- Patel PH, Suzuki M, Adman E et al. Prokaryotic DNA polymerase I: evolution, structure, and “base flipping” mechanism for nucleotide selection. J. Mol. Biol.308, 823–837 (2001).
- Garg P, Burgers PMJ. DNA polymerases that propagate the eukaryotic DNA replication fork. Crit. Rev. Biochem. Mol. Biol.40, 115–128 (2005).
- Prakash S, Johnson RE, Prakash L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem.74, 317–353 (2005).
- Robins P, Pappin DJC, Wood RD et al. Structural and functional homology between mammalian DNase IV and the 5´-nuclease domain of Escherichia coli DNA polymerase I. J. Biol. Chem.269, 28535–28538 (1994).
- Kornberg T, Gefter ML. Deoxyribonucleic acid synthesis in cell-free extracts IV. Purification and catalytic properties of deoxyribonucleic acid polymerase III. J. Biol. Chem.247, 5369–5375 (1972).
- Kornberg A, Baker T. DNA Replication, 2nd Ed. WH Freeman and Co, NY, USA (1992).
- Delarue M, Poch O, Tordo N et al. An attempt to unify the structure of polymerases. Protein Eng.3, 461–467 (1990).
- Ohmori H, Friedberg EC, Fuchs RPP et al. The Y-family of DNA polymerases. Mol. Cell8, 7–8 (2001).
- Burgers PMJ, Koonin EV, Bruford E et al. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J. Biol. Chem.276, 43487–43490 (2001).
- Johnson R, Kondratick C, Prakash S et al. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science285, 263–265 (1999).
- Tang M, Shen X, Frank EG et al. UmuD´2C is an error-prone DNA polymerase, Escherichia coli Pol V. Proc. Natl Acad. Sci. USA96, 8919–8924 (1999).
- Wagner J, Gruz P, Kim SR et al. The dinB gene encodes a novel E. coli DNA polymerase, DNA Pol IV, involved in mutagenesis. Mol. Cell4, 281–286 (1999).
- Grabowski B, Kelman Z. Archeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol.57, 487–516 (2003).
- Steitz TA. DNA- and RNA-dependent DNA polymerases. Curr. Opin. Struct. Biol.3, 31–38 (1993).
- Kunkel TA. DNA replication fidelity. J. Biol. Chem.279, 16895–16898 (2004).
- Hogg M, Wallace SS, Doublie S. Bumps in the road: how replicative DNA polymerases see DNA damage. Curr. Opin. Struct. Biol.15, 86–93 (2005).
- Idriss HT, Al-Assar O, Wilson SH. DNA polymerase β. Intl J. Biochem. Cell Biol.34, 321–324 (2002).
- Longley MJ, Graziewicz MA, Bienstock RJ et al. Consequences of mutations in human DNA polymerase γ. Gene354, 125–131 (2005).
- Friedberg EC, Wagner R, Radman M. Molecular biology: specialized DNA polymerases, cellular survival, and the genesis of mutations. Science296, 1627–1630 (2002).
- Kunkel TA. Considering the cancer consequences of altered DNA polymerase function. Cancer Cell3, 105–110 (2003).
- Bignold LP. The cell-type-specificity of inherited predispositions to tumours: review and hypothesis. Cancer Lett.216, 127–146 (2004).
- Cleaver JE. Cancer in xeroderma pigmentosum and related disorders of DNA repair. Nature Rev. Cancer5, 564–573 (2005).
- Srivastava VK, Busbee DL. Replicative enzymes and aging: importance of DNA polymerase α function to the events of cellular aging. Ageing Res. Rev.1, 443–463 (2002).
- Vijg J, Calder RB. Transcripts of aging. Trends Genet.20, 221–224 (2004).
- Cheok CF, Wu L, Garcia PL et al. The Bloom’s syndrome helicase promotes the annealing of complementary single-stranded DNA. Nucleic Acids Res.33, 3932–3941 (2005).
- De Lucia P, Cairns J. Isolation of an E. coli strain with a mutation affecting DNA polymerase. Nature224, 1164–1166 (1969).
- Sutton MD, Smith BT, Godoy VG et al. The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Annu. Rev. Genet.34, 479–497 (2000).
- McHenry CS. Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences. Mol. Microbiol.49, 1157–1165 (2003).
- Kong XP, Onrust R, O’Donnell M et al. Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell69, 425–437 (1992).
- Hamdan S, Carr PD, Brown SE et al. Structural basis for proofreading during replication of the Escherichia coli chromosome. Structure10, 535–546 (2002).
- Jeruzalmi D, O’Donnell M, Kuriyan J. Crystal structure of the processivity clamp loader gamma (γ) complex of E. coli DNA polymerase III. Cell106, 429–441 (2001).
- Gulbis JM, Kazmirski SL, Finkelstein J et al. Crystal structure of the χ:ψ subassembly of the Escherichia coli DNA polymerase clamp-loader complex. Eur. J. Biochem.271, 439–449 (2004).
- Neylon C, Brown SE, Kralicek AV et al. Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance. Biochemistry39, 11989–11999 (2000).
- Loo JA. Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom. Rev.16, 1–23 (1997).
- Fuller RS, Funnell BE, Kornberg A. The DnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell38, 889–900 (1984).
- Messer W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev.26, 355–374 (2002).
- Messer W, Blaesing F, Jakimowicz D et al. Bacterial replication initiator DnaA. Rules for DnaA binding and roles of DnaA in origin unwinding and helicase loading. Biochimie83, 5–12 (2001).
- LeBowitz JH, McMacken R. The Escherichia coli DnaB replication protein is a DNA helicase. J. Biol. Chem.261, 4738–4748 (1986).
- San Martin MC, Stamford NPJ, Dammerova N, Dixon NE, Carazo JM. Three-dimensional structure of the DnaB helicase oligomer from Escherichia coli by electron microscopy and image processing. Proc. Intl Congress on Electron Microscopy, Paris, France 3A, 545–546 (1994).
- San Martin MC, Radermacher M, Wolpensinger B et al. Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC. Structure6, 501–509 (1998).
- Bramhill D, Kornberg A. A model for initiation at origins of DNA replication. Cell54, 915–918 (1988).
- Jiang Y, Yao S, Helinski D et al. Functional analysis of two putative chromosomal replication origins from Pseudomonas aeruginosa. Plasmid (2006) (In Press).
- Davey MJ, Jeruzalmi D, Kuriyan J et al. Motors and switches: AAA+ machines within the replisome. Nature Rev. Mol. Cell Biol.3, 826–835 (2002).
- Davey MJ, Fang L, McInerney P et al. The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J.21, 3148–3159 (2002).
- Mastsumoto T, Morimoto Y, Shibata N et al. Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-ray structure analysis. J. Biochem.127, 329–335 (2000).
- Oakley AJ, Loscha KV, Schaeffer PM et al. Crystal and solution structures of the helicase-binding domain of Escherichia coli primase. J. Biol. Chem.280, 11495–11504 (2005).
- Soultanas P. The bacterial helicase–primase interaction: a common structural/functional module. Structure13, 839–844 (2005).
- Benkovic SJ, Valentine AM, Salinas F. Replisome-mediated DNA replication. Annu. Rev. Biochem.70, 181–208 (2001).
- Johnson A, O’Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu. Rev. Biochem.74, 283–315 (2005).
- Schaeffer PM, Headlam MJ, Dixon NE. Protein–protein interactions in the eubacterial replisome. IUBMB Life57, 5–12 (2005).
- Taft-Benz SA, Schaaper RM. The θ subunit of Escherichia coli DNA polymerase III: a role in stabilizing the ε proofreading subunit. J. Bacteriol.186, 2774–2780 (2004).
- Levin DS, Vijayakumar S, Liu X et al. A conserved interaction between the replicative clamp loader and DNA ligase in eukaryotes: implications for Okazaki fragment joining. J. Biol. Chem.279, 55196–55201 (2004).
- Turner J, Hingorani MM, Kelman Z et al. The internal workings of a DNA polymerase clamp-loading machine. EMBO J.18, 771–783 (1999).
- Williams CR, Snyder AK, Kuzmic P et al. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the γ complex. J. Biol. Chem.279, 4376–4385 (2004).
- Snyder AK, Williams CR, Johnson A et al. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the β and DNA binding activities of the γ complex. J. Biol. Chem.279, 4386–4393 (2004).
- Jeruzalmi D, Yurieva O, Zhao Y et al. Mechanism of processivity clamp opening by the δ subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell106, 417–428 (2001).
- Hingorani MM, O’Donnell M. ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme. J. Biol. Chem.273, 24550–24563 (1998).
- Goedken ER, Levitus M, Johnson A et al. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J. Mol. Biol.336, 1047–1059 (2004).
- Bloom LB, Turner J, Kelman Z et al. Dynamics of loading the β sliding clamp of DNA polymerase III onto DNA. J. Biol. Chem.271, 30699–30708 (1996).
- Bertram JG, Bloom LB, Hingorani MM et al. Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when γ complex loads β on DNA. J. Biol. Chem.275, 28413–28420 (2000).
- Ason B, Handayani R, Williams CR et al. Mechanism of loading the Escherichia coli DNA polymerase III β sliding clamp on DNA. Bona fide primer/templates preferentially trigger the γ complex to hydrolyse ATP and load the clamp. J. Biol. Chem.278, 10033–10040 (2003).
- Kamada K, Ohsumi K, Horiuchi T et al. Structure of a replication-terminator protein complexed with DNA. Nature383, 598–603 (1996).
- Neylon C, Kralicek AV, Hill TM et al. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus–Ter complex. Microbiol. Mol. Biol. Rev.69, 501–526 (2005).
- MacAlpine DM, Rodriguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev.18, 3094–3105 (2004).
- Schwob E. Flexibility and governance in eukaryotic DNA replication. Curr. Opin. Microbiol.7, 680–690 (2004).
- Gilbert DM. In search of the holy replicator. Nature Rev. Mol. Cell Biol.5, 848–855 (2004).
- Aladjem MI, Fanning E. The replicon revisited: an old model learns new tricks in metazoan chromosomes. EMBO Rep.5, 686–691 (2004).
- Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu. Rev. Biochem.71, 333–374 (2002).
- Aggarwal BD, Calvi BR. Chromatin regulates origin activity in Drosophila follicle cells. Nature430, 372–376 (2004).
- Bell SP, Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature357, 128–134 (1992).
- Laskey RA, Madine MA. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Rep.4, 26–30 (2003).
- Hyrien O, Marheineke K, Goldar A. Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays25, 116–125 (2003).
- Sclafani RA, Fletcher RJ, Chen XS. Two heads are better than one: regulation of DNA replication by hexameric helicases. Genes Dev.18, 2039–2045 (2004).
- Stillman B. Origin recognition and the chromosome cycle. FEBS Lett.579, 877–884 (2005).
- Adachi Y, Usukura J, Yanagida M. A globular complex formation by Nda1 and the other five members of the MCM protein family in fission yeast. Genes Cells2, 467–479 (1997).
- Robinson NP, Bell SD. Origins of DNA replication in the three domains of life. FEBS J.272, 3757–3766 (2005).
- Iyer LM, Leipe DD, Koonin EV et al. Evolutionary history and higher order classification of AAA+ ATPases. J. Struct. Biol.146, 11–31 (2004).
- Shiomi Y, Usukura J, Masamura Y et al. ATP-dependent structural change of the eukaryotic clamp-loader protein, replication factor C. Proc. Natl Acad. Sci. USA97, 14127–14132 (2000).
- Miyachi K, Fritzler MJ, Tan EM. Autoantibody to a nuclear antigen in proliferating cells. J. Immunol.121, 2228–2234 (1978).
- Tan CK, Castillo C, So AG et al. An auxiliary protein for DNA polymerase-δ from fetal calf thymus. J. Biol. Chem.261, 12310–12316 (1986).
- Krishna TS, Kong XP, Gary S et al. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell79, 1233–1243 (1994).
- Yao N, Turner J, Kelman Z et al. Clamp loading, unloading and intrinsic stability of the PCNA, β and gp45 sliding clamps of human, E. coli and T4 replicases. Genes Cells1, 101–113 (1996).
- Conaway RC, Lehman IR. A DNA primase activity associated with DNA polymerase α from Drosophila melanogaster embryos. Proc. Natl Acad. Sci. USA79, 2523–2527 (1982).
- Conaway RC, Lehman IR. Synthesis by the DNA primase of Drosophila melanogaster of a primer with a unique chain length. Proc. Natl Acad. Sci. USA79, 4585–4588 (1982).
- Morrison A, Araki H, Clark AB et al. A third essential DNA polymerase in S. cerevisiae. Cell62, 1143–1151 (1990).
- Hiom K. DNA repair: how to PIKK a partner. Curr. Biol.15, 473–475 (2005).
- Michel B, Grompone G, Flores M-J et al. Multiple pathways process stalled replication forks. Proc. Natl Acad. Sci. USA101, 12783–12788 (2004).
- Bunting KA, Roe SM, Pearl LH. Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the β-clamp. EMBO J.22, 5883–5892 (2003).
- Maga G, Huebscher U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J. Cell Sci.116, 3051–3060 (2003).
- Hoege C, Pfander B, Moldovan G-L et al. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature419, 135–141 (2002).
- Kannouche PL, Wing J, Lehmann AR. Interaction of human DNA polymerase η with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage. Mol. Cell14, 491–500 (2004).
- Haracska L, Johnson RE, Unk I et al. Physical and functional interactions of human DNA polymerase η with PCNA. Mol. Cell Biol.21, 7199–7206 (2001).
- Haracska L, Johnson RE, Unk I et al. Targeting of human DNA polymerase ι to the replication machinery via interaction with PCNA. Proc. Natl Acad. Sci. USA98, 14256–14261 (2001).
- Haracska L, Unk I, Johnson RE et al. Stimulation of DNA synthesis activity of human DNA polymerase κ by PCNA. Mol. Cell Biol.22, 784–791 (2002).
- Nowak MA, Komarova NL, Sengupta A et al. The role of chromosomal instability in tumor initiation. Proc. Natl Acad. Sci. USA99, 16226–16231 (2002).
- Loeb LA, Loeb KR, Anderson JP. Multiple mutations and cancer. Proc. Natl Acad. Sci. USA100, 776–781 (2003).
- Johnson RE, Prakash S, Prakash L. Efficient bypass of a thymine–thymine dimer by yeast DNA polymerase, Polη. Science283, 1001–1004 (1999).
- Lehmann AR, Kirk-Bell S, Arlett CF et al. Xeroderma pigmentosum cells with normal levels of excision repair have a defect in DNA synthesis after UV-irradiation. Proc. Natl Acad. Sci. USA72, 219–223 (1975).
- Masutani C, Kusumoto R, Yamada A et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature399, 700–704 (1999).
- Martin GM, Oshima J, Gray MD et al. What geriatricians should know about the Werner syndrome. J. Am. Geriatr. Soc.47, 1136–1144 (1999).
- Hickson ID. RecQ helicases: caretakers of the genome. Nature Rev. Cancer3, 169–178 (2003).
- Gray MD, Shen J-C, Kamath-Loeb AS et al. The Werner syndrome protein is a DNA helicase. Nature Genet.17, 100–103 (1997).
- Shen J-C, Gray MD, Oshima J et al. Characterization of Werner syndrome protein DNA helicase activity: directionality, substrate dependence and stimulation by replication protein A. Nucleic Acids Res.26, 2879–2885 (1998).
- Huang S, Li B, Gray MD et al. The premature aging syndrome protein, WRN, is a 3´→5´ exonuclease. Nature Genet.20, 114–116 (1998).
- Ozgenc A, Loeb LA. Current advances in unraveling the function of the Werner syndrome protein. Mutation Res.577, 237–251 (2005).
- Pichierri P, Franchitto A, Rosselli F. BLM and the FANC proteins collaborate in a common pathway in response to stalled replication forks. EMBO J.23, 3154–3163 (2004).
- Macris MA, Lumir K, Bussen W et al. Biochemical characterization of the RECQ4 protein, mutated in Routhmund–Thomson syndrome. DNA Repair5, 172–180 (2006).
- Srivastava VK, Busbee DL. Replicative enzymes, DNA polymerase α (Pol α), and in vitro aging. Exp. Gerontol.38, 1285–1297 (2003).
- Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem.70, 437–473 (2001).
- Shevchenko A, Chernushevich I, Wilm M et al.De novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of-flight instruments. Methods Mol. Biol.146, 1–16 (2000).
- Wilm M, Shevchenko A, Houthaeve T et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature379, 466–469 (1996).
- Shevchenko A, Loboda A, Shevchenko A et al. MALDI quadrupole time-of-flight: a powerful tool for proteomic research. Anal. Chem.72, 2132–2141 (2000).
- Krutchinsky AN, Zhang W, Chait BT. Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification. J. Am. Soc. Mass Spectrom.11, 493–504 (2000).
- Medzihradszky KF, Campbell JM, Baldwin MA et al. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem.72, 552–558 (2000).
- Ito T, Chiba T, Ozawa R et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA98, 4569–4574 (2001).
- Noirot-Gros M-F, Dervyn E, Wu LJ et al. An expanded view of bacterial DNA replication. Proc. Natl Acad. Sci. USA99, 8342–8347 (2002).
- Phizicky EM, Fields S. Protein–protein interactions: methods for detection and analysis. Microbiol. Rev.59, 94–123 (1995).
- Fujise K, Zhang D, Liu J et al. Regulation of apoptosis and cell cycle progression by MCL1. Differential role of proliferating cell nuclear antigen. J. Biol. Chem.275, 39458–39465 (2000).
- Glick BR, Pasternak JJ. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 2nd Ed. ASM Press, Washington DC, USA (1998).
- Loor G, Zhang S-J, Zhang P et al. Identification of DNA replication and cell cycle proteins that interact with PCNA. Nucleic Acids Res.25, 5041–5046 (1997).
- Hughes P, Tratner I, Ducoux M et al. Isolation and identification of the third subunit of mammalian DNA polymerase δ by PCNA-affinity chromatography of mouse FM3A cell extracts. Nucleic Acids Res.27, 2108–2114 (1999).
- Terpe K. Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol.60, 523–533 (2003).
- Gottschalk A, Tang J, Puig O et al. A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins. RNA4, 374–393 (1998).
- Rigaut G, Shevchenko A, Rutz B et al. In the laboratory: a generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol.17, 1030–1032 (1999).
- Puig O, Caspary F, Rigaut G et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods24, 218–229 (2001).
- Gavin A-C, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature415, 141–147 (2002).
- Zeghouf M, Li J, Butland G et al. Sequential peptide affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J. Proteome Res.3, 463–468 (2004).
- Dziembowski A, Seraphin B. Recent developments in the analysis of protein complexes. FEBS Lett.556, 1–6 (2004).
- Tanaka K, Waki H, Ido Y et al. Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom.2, 151–153 (1988).
- Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem.60, 2299–2301 (1988).
- Wong SF, Meng CK, Fenn JB. Multiple charging in electrospray ionization of poly(ethylene glycols). J. Phys. Chem.92, 546–550 (1988).
- Ohta S, Shiomi Y, Sugimoto K et al. A proteomics approach to identify proliferating cell nuclear antigen (PCNA)-binding proteins in human cell lysates. J. Biol. Chem.277, 40362–40367 (2002).
- Niture SK, Doneanu CE, Velu CS et al. Proteomic analysis of human O6-methylguanine-DNA methyltransferase by affinity chromatography and tandem mass spectrometry. Biochem. Biophys. Res. Commun.337, 1176–1184 (2005).
- Shevchenko A, Schaft D, Roguev A et al. Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry analytical perspective. Mol. Cell. Proteomics1, 204–212 (2002).
- Butland G, Peregrin-Alvarez JM, Li J et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature433, 531–537 (2005).
- Maki H, Horiuchi T, Kornberg A. The polymerase subunit of DNA polymerase III of Escherichia coli I. amplification of the dnaE gene product and polymerase activity of the α subunit. J. Biol. Chem.260, 12982–12986 (1985).
- Nakayama H. RecQ family helicases: roles as tumor suppressor proteins. Oncogene21, 9008–9021 (2002).
- Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol.17, 994–999 (1999).
- Ranish JA, Yi EC, Leslie DM et al. The study of macromolecular complexes by quantitative proteomics. Nature Genet.33, 349–355 (2003).
- Tackett AJ, DeGrasse JA, Sekedat MD et al. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Proteome Res.4, 1752–1756 (2005).
- Magdalena Coman M, Jin M, Ceapa R et al. Dual functions, clamp opening and primer-template recognition, define a key clamp loader subunit. J. Mol. Biol.342, 1457–1469 (2004).
- Alekseev OM, Richardson RT, Pope MR et al. Mass spectrometry identification of NASP binding partners in HeLa cells. Proteins61, 1–5 (2005).
- Xi J, Zhuang Z, Zhang Z et al. Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. Biochemistry44, 2305–2318 (2005).
- Steen H, Jensen ON. Analysis of protein–nucleic acid interactions by photochemical crosslinking and mass spectrometry. Mass Spectrom. Rev.21, 163–182 (2002).
- Deterding LJ, Prasad R, Mullen GP et al. Mapping of the 5´-2-deoxyribose-5-phosphate lyase active site in DNA polymerase β by mass spectrometry. J. Biol. Chem.275, 10463–10471 (2000).
- Lavrik OI, Khlimankov DY, Khodyreva SN. The eukaryotic replication complex and its affinity modification analysis. Mol. Biol.37, 477–485 (2003).
- Khodyreva SN, Lavrik OI. Photoaffinity labeling technique for studying DNA replication and DNA repair. Curr. Med. Chem.12, 641–655 (2005).
- Dezhurov SV, Khodyreva SN, Plekhanova ES et al. A new highly efficient photoreactive analogue of dCTP. Synthesis, characterization, and application in photoaffinity modification of DNA binding proteins. Bioconjug. Chem.16, 215–222 (2005).
- Lavrik OI, Prasad R, Sobol RW et al. Photoaffinity labeling of mouse fibroblast enzymes by a base excision repair intermediate: evidence for the role of poly(ADP-ribose) polymerase-1 in DNA repair. J. Biol. Chem.276, 25541–25548 (2001).
- Wan KX, Shibue T, Gross ML. Non-covalent complexes between DNA-binding drugs and double-stranded oligonucleotides: a study by ESI ion-trap mass spectrometry. J. Am. Chem. Soc.122, 300–307 (2000).
- Ding J, Anderegg RJ. Specific and nonspecific dimer formation in the electrospray ionization mass spectrometry of oligonucleotides. J. Am. Soc. Mass Spectrom.6, 159–164 (1995).
- Potier N, Donald LJ, Chernushevich I et al. Study of a noncovalent Trp repressor: DNA operator complex by electrospray ionization time-of-flight mass spectrometry. Protein Sci.7, 1388–1395 (1998).
- Kapur A, Beck JL, Brown SE et al. Use of electrospray ionization mass spectrometry to study binding interactions between a replication terminator protein and DNA. Protein Sci.11, 147–157 (2002).
- Heck AJR, van den Heuvel RHH. Investigation of intact protein complexes by mass spectrometry. Mass Spectrom. Rev23, 368–389 (2004).
- Kennaway CK, Benesch JLP, Gohlke U et al. Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis. J. Biol. Chem.280, 33419–33425 (2005).
- Yu X, VanLoock MS, Poplawski A et al. The Methanobacterium thermoautotrophicum MCM protein can form heptameric rings. EMBO Rep.3, 792–797 (2002).
- Kelman LM, Kelman Z. Archea: an archetype for replication initiation studies? Microbiology48, 605–615 (2003).
- Sobott F, Hernandez H, McCammon MG et al. A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal. Chem.74, 1402–1407 (2002).
- Robinson CV. Characterization of multiprotein complexes by mass spectrometry. In Protein–protein Interactions. Golemis EA, Adams PD (Eds), Cold Spring Habor Laboratory Press, NY, USA, 317–327 (2005).
- Sopher BL, McCammon MG, Hernandez H et al. The flight of macromolecular complexes in a mass spectrometer. Phil. Trans. Royal Soc. London, Series A: Mathematical Phys. Eng. Sci.363, 379–391 (2005).
- Videler H, Ilag LL, McKay ARC et al. Mass spectrometry of intact ribosomes. FEBS Lett.579, 943–947 (2005).
- Ruotolo BT, Giles K, Campuzano I et al. Evidence for macromolecular protein rings in the absence of bulk water. Science310, 1658–1661 (2005).