dna primase


Summary: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.

Top Publications

  1. Ito N, Matsui I, Matsui E. Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii. FEBS J. 2007;274:1340-51 pubmed publisher
    ..These findings and a structural comparison with a previously reported PriL(NTD)-PriS complex suggest that the presented alternative conformations of the twisted-strand domain facilitate the heterodimer assembly...
  2. Hamdan S, van Oijen A. Timing, coordination, and rhythm: acrobatics at the DNA replication fork. J Biol Chem. 2010;285:18979-83 pubmed publisher
    ..Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. ..
  3. Sun B, Johnson D, Patel G, Smith B, Pandey M, Patel S, et al. ATP-induced helicase slippage reveals highly coordinated subunits. Nature. 2011;478:132-5 pubmed publisher
    ..Such subunit coordination may be general to many ring-shaped helicases and reveals a potential mechanism for regulation of DNA unwinding during replication. ..
  4. Li Y, Kim H, Zheng C, Chow W, Lim J, Keenan B, et al. Primase-based whole genome amplification. Nucleic Acids Res. 2008;36:e79 pubmed publisher
    ..In vivo, primers are synthesized on-template by DNA primase. The bacteriophage T7 gene 4 protein (gp4) has both primase and helicase activities...
  5. Griffiths D, Liu V, Nurse P, Wang T. Role of fission yeast primase catalytic subunit in the replication checkpoint. Mol Biol Cell. 2001;12:115-28 pubmed
    ..investigate the cell cycle checkpoint response to aberrant S phase-initiation, we analyzed mutations of the two DNA primase subunit genes of Schizosaccharomyces pombe, spp1(+) and spp2(+) (S. pombe primase 1 and 2)...
  6. Muzi Falconi M, Giannattasio M, Foiani M, Plevani P. The DNA polymerase alpha-primase complex: multiple functions and interactions. ScientificWorldJournal. 2003;3:21-33 pubmed
    ..In fact, pol alpha is associated with DNA primase to form a four subunit complex and, as a consequence, is the only enzyme able to start DNA synthesis de novo...
  7. Wanrooij S, Luoma P, Van Goethem G, Van Broeckhoven C, Suomalainen A, Spelbrink J. Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA. Nucleic Acids Res. 2004;32:3053-64 pubmed
    ..Deletion breakpoint analysis showed frequent breakpoints around homopolymeric runs, which could be a signature of replication stalling. Therefore, we propose replication stalling as the principal cause of deletion formation. ..
  8. Soultanas P. Loading mechanisms of ring helicases at replication origins. Mol Microbiol. 2012;84:6-16 pubmed publisher
    ..Current structural and biochemical data reveal a wide range of different helicase-loading mechanisms. Here we review advances in this area and discuss their implications. ..
  9. Lee J, Chastain P, Griffith J, Richardson C. Lagging strand synthesis in coordinated DNA synthesis by bacteriophage t7 replication proteins. J Mol Biol. 2002;316:19-34 pubmed
    ..In the absence of a primase recognition site on the minicircle template no lagging strand synthesis occurs. The size of the Okazaki fragments is not affected by the number of recognition sites on the template. ..

Scientific Experts

More Information


  1. Tanner N, Hamdan S, Jergic S, Loscha K, Schaeffer P, Dixon N, et al. Single-molecule studies of fork dynamics in Escherichia coli DNA replication. Nat Struct Mol Biol. 2008;15:170-6 pubmed publisher
    ..Modulation of DnaB helicase activity through the interaction with DnaG suggests a mechanism that prevents leading-strand synthesis from outpacing lagging-strand synthesis during slow primer synthesis on the lagging strand. ..
  2. Pan H, Wigley D. Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Structure. 2000;8:231-9 pubmed
    ..We present the crystal structure of the zinc-binding domain of DNA primase from Bacillus stearothermophilus, determined at 1.7 A resolution...
  3. Schaeffer P, Headlam M, Dixon N. Protein--protein interactions in the eubacterial replisome. IUBMB Life. 2005;57:5-12 pubmed
    ..coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7. ..
  4. Thanbichler M, Shapiro L. MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Cell. 2006;126:147-62 pubmed
    ..The cellular localization of MipZ thus serves the dual function of positioning the FtsZ ring and delaying formation of the cell division apparatus until chromosome segregation has initiated...
  5. Stano N, Jeong Y, Donmez I, Tummalapalli P, Levin M, Patel S. DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase. Nature. 2005;435:370-3 pubmed
    ..The rapid trapping of the ssDNA bases by the DNA synthesis activity of the polymerase in turn drives the helicase to move forward through duplex DNA at speeds similar to those observed along ssDNA...
  6. Sanchez Berrondo J, Mesa P, Ibarra A, Martinez Jimenez M, Blanco L, Mendez J, et al. Molecular architecture of a multifunctional MCM complex. Nucleic Acids Res. 2012;40:1366-80 pubmed publisher
  7. Hamatake R, Bifano M, Hurlburt W, Tenney D. A functional interaction of ICP8, the herpes simplex virus single-stranded DNA-binding protein, and the helicase-primase complex that is dependent on the presence of the UL8 subunit. J Gen Virol. 1997;78 ( Pt 4):857-65 pubmed
    ..These results identify a unique, functional interaction between the ICP8 SSB and the helicase-primase complex, mediated by the UL8 subunit. ..
  8. Chattopadhyay S, Chen Y, Weller S. The two helicases of herpes simplex virus type 1 (HSV-1). Front Biosci. 2006;11:2213-23 pubmed
    ..Functional analyses of UL9 and the helicase-primase complex will be discussed with attention to the roles these proteins play during HSV-1 replication. ..
  9. Lee S, Richardson C. Interaction of adjacent primase domains within the hexameric gene 4 helicase-primase of bacteriophage T7. Proc Natl Acad Sci U S A. 2002;99:12703-8 pubmed
    ..Reconstitution of activity depends on hexamer formation. We propose that the zinc motif of one subunit in the hexamer interacts with the catalytic sites of adjacent subunits. ..
  10. Zenkin N, Severinov K. RNA polymerase -the third class of primases. Cell Mol Life Sci. 2008;65:2280-8 pubmed publisher
    ..Here we discuss the mechanism of primer synthesis by RNA polymerase and compare it to mechanisms used by primases of both types as well as to the mechanisms used by RNA polymerase during transcription. ..
  11. Mizuno T, Yamagishi K, Miyazawa H, Hanaoka F. Molecular architecture of the mouse DNA polymerase alpha-primase complex. Mol Cell Biol. 1999;19:7886-96 pubmed
    ..Taken together, these results allow us to propose the first structural model for the DNA polymerase alpha-primase complex in terms of subunit assembly, domain structure, and stepwise formation at the cellular level. ..
  12. Pandey M, Syed S, Donmez I, Patel G, Ha T, Patel S. Coordinating DNA replication by means of priming loop and differential synthesis rate. Nature. 2009;462:940-3 pubmed publisher
  13. Beck K, Lipps G. Properties of an unusual DNA primase from an archaeal plasmid. Nucleic Acids Res. 2007;35:5635-45 pubmed
    ..Primer synthesis starts outside of the recognition motif, immediately 5' to the recognition motif. The fidelity of the primase synthesis is high, as non-complementary bases are not incorporated into the primer. ..
  14. Nitharwal R, Verma V, Subbarao N, Dasgupta S, Choudhury N, Dhar S. DNA binding activity of Helicobacter pylori DnaB helicase: the role of the N-terminal domain in modulating DNA binding activities. FEBS J. 2012;279:234-50 pubmed publisher
    ..These results provide an insight into the stimulatory and inhibitory effects of different regions of HpDnaB on DNA binding activities that may be central to the loading and translocation functions of DnaB helicases. ..
  15. Weiner B, Huang H, Dattilo B, Nilges M, Fanning E, Chazin W. An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase. J Biol Chem. 2007;282:33444-51 pubmed
    b>DNA primase synthesizes short RNA primers that are required to initiate DNA synthesis on the parental template strands during DNA replication...
  16. Kato M, Ito T, Wagner G, Ellenberger T. A molecular handoff between bacteriophage T7 DNA primase and T7 DNA polymerase initiates DNA synthesis. J Biol Chem. 2004;279:30554-62 pubmed publisher
    The T7 DNA primase synthesizes tetraribonucleotides that prime DNA synthesis by T7 DNA polymerase but only on the condition that the primase stabilizes the primed DNA template in the polymerase active site...
  17. Jing D, Beechem J, Patton W. The utility of a two-color fluorescence electrophoretic mobility shift assay procedure for the analysis of DNA replication complexes. Electrophoresis. 2004;25:2439-46 pubmed
  18. De Falco M, Fusco A, De Felice M, Rossi M, Pisani F. The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity. Nucleic Acids Res. 2004;32:5223-30 pubmed
    ..In this study, we report the purification and biochemical characterization of a DNA primase (Sso DNA primase) from the thermoacidophilic crenarchaeon Sulfolobus solfataricus...
  19. Ricke R, Bielinsky A. Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha. Mol Cell. 2004;16:173-85 pubmed
    ..During elongation, Mcm10 is required for the presence of polalpha at replication forks and may coordinate DNA synthesis with DNA unwinding by the Mcm2-7 complex. ..
  20. Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, et al. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair?. J Mol Biol. 2007;374:1172-85 pubmed publisher
    We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab)...
  21. Lao Sirieix S, Bell S. The heterodimeric primase of the hyperthermophilic archaeon Sulfolobus solfataricus possesses DNA and RNA primase, polymerase and 3'-terminal nucleotidyl transferase activities. J Mol Biol. 2004;344:1251-63 pubmed
    ..In addition to the primase and polymerase activities, we reveal that the primase possesses a template-independent 3'-terminal nucleotidyl transferase activity. ..
  22. Arezi B, Kuchta R. Eukaryotic DNA primase. Trends Biochem Sci. 2000;25:572-6 pubmed
    Eukaryotic DNA primase initiates the synthesis of all new DNA strands by synthesizing short RNA oligomers on single-stranded DNA...
  23. Urban M, Joubert N, Hocek M, Alexander R, Kuchta R. Herpes simplex virus-1 DNA primase: a remarkably inaccurate yet selective polymerase. Biochemistry. 2009;48:10866-81 pubmed publisher
    ..Additionally, we found that herpes primase can misincorporate nucleotides both by misreading the template and by a primer-template slippage mechanism. The mechanistic and biological implications of these results are discussed...
  24. Garcia Gomez S, Reyes A, Martinez Jimenez M, Chocron E, Mouron S, Terrados G, et al. PrimPol, an archaic primase/polymerase operating in human cells. Mol Cell. 2013;52:541-53 pubmed publisher
    ..is proposed to facilitate replication fork progression by acting as a translesion DNA polymerase or as a specific DNA primase reinitiating downstream of lesions that block synthesis during both mitochondrial and nuclear DNA replication.
  25. Kaguni J. Replication initiation at the Escherichia coli chromosomal origin. Curr Opin Chem Biol. 2011;15:606-13 pubmed publisher
  26. Heller R, Marians K. Replication fork reactivation downstream of a blocked nascent leading strand. Nature. 2006;439:557-62 pubmed
  27. Lipps G, Weinzierl A, von Scheven G, Buchen C, Cramer P. Structure of a bifunctional DNA primase-polymerase. Nat Struct Mol Biol. 2004;11:157-62 pubmed publisher
    ..We propose that archaeal and eukaryotic primases and the prim-pol domain have a common evolutionary ancestor, a bifunctional replicase for small DNA genomes...
  28. Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis. J Biol Chem. 2012;287:16209-19 pubmed publisher
    ..In this study, we describe the isolation and biochemical characterization of the DNA primase complex and its subunits from the archaeon Thermococcus kodakaraensis. The T...
  29. Pellegrini L. The Pol ?-primase complex. Subcell Biochem. 2012;62:157-69 pubmed publisher
  30. Arezi B, Kirk B, Copeland W, Kuchta R. Interactions of DNA with human DNA primase monitored with photoactivatable cross-linking agents: implications for the role of the p58 subunit. Biochemistry. 1999;38:12899-907 pubmed
    ..Additionally, the ability of p58 to interact with primer-template species suggests that p58 mediates the transfer of primers from the primase active site to pol alpha. ..
  31. Yotov W, Hamel H, Rivard G, Champagne M, Russo P, Leclerc J, et al. Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma. Genes Chromosomes Cancer. 1999;26:62-9 pubmed
    ..PRIM1 is therefore a new candidate for the role of a major target gene of 12q13 amplifications in human cancers. Genes Chromosomes Cancer 26:62-69, 1999. ..
  32. Tyynismaa H, Sembongi H, Bokori Brown M, Granycome C, Ashley N, Poulton J, et al. Twinkle helicase is essential for mtDNA maintenance and regulates mtDNA copy number. Hum Mol Genet. 2004;13:3219-27 pubmed
    ..These data demonstrate that Twinkle helicase is essential for mtDNA maintenance, and that it may be a key regulator of mtDNA copy number in mammals. ..
  33. Mitkova A, Khopde S, Biswas S. Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis. J Biol Chem. 2003;278:52253-61 pubmed
    ..the lagging strand of the replication fork in Escherichia coli requires the replicative DnaB helicase and the DNA primase, the DnaG gene product...
  34. Zerbe L, Kuchta R. The p58 subunit of human DNA primase is important for primer initiation, elongation, and counting. Biochemistry. 2002;41:4891-900 pubmed
    The p58 subunit of human DNA primase contains a region, M288-K344, that is homologous to part of the 8 kDa domain of DNA polymerase beta...
  35. Zhang H, Lee S, Richardson C. The roles of tryptophans in primer synthesis by the DNA primase of bacteriophage T7. J Biol Chem. 2012;287:23644-56 pubmed publisher
    ..Therefore, Trp-42 is important in maintaining the conformation of the ZBD for template binding; Trp-97 contributes to NTP binding and the catalysis step; and Trp-147 maintains the catalysis step...
  36. Godson G, Schoenich J, Sun W, Mustaev A. Identification of the magnesium ion binding site in the catalytic center of Escherichia coli primase by iron cleavage. Biochemistry. 2000;39:332-9 pubmed
    ..Cleavage data suggested that binding to D345 is significantly stronger than to D347 and somewhat stronger than to D269. ..
  37. Prato S, Vitale R, Contursi P, Lipps G, Saviano M, Rossi M, et al. Molecular modeling and functional characterization of the monomeric primase-polymerase domain from the Sulfolobus solfataricus plasmid pIT3. FEBS J. 2008;275:4389-402 pubmed publisher
    ..To the best of our knowledge, Rep245 typifies the shortest functional domain from a crenarchaeal plasmid endowed with DNA and RNA synthesis and terminal transferase activity. ..
  38. Hines J, Ray D. A mitochondrial DNA primase is essential for cell growth and kinetoplast DNA replication in Trypanosoma brucei. Mol Cell Biol. 2010;30:1319-28 pubmed publisher
    ..and proteins have been identified, in vitro replication of these DNAs has not been possible since a kinetoplast DNA primase has not been available...
  39. Vaithiyalingam S, Warren E, Eichman B, Chazin W. Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase. Proc Natl Acad Sci U S A. 2010;107:13684-9 pubmed publisher
    DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large ..
  40. Schumacher M, Funnell B. Structures of ParB bound to DNA reveal mechanism of partition complex formation. Nature. 2005;438:516-9 pubmed
    ..These unique structural features of ParB explain how this protein can bind complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site. ..
  41. Samuels M, Gulati G, Shin J, Opara R, McSweeney E, Sekedat M, et al. A biochemically active MCM-like helicase in Bacillus cereus. Nucleic Acids Res. 2009;37:4441-52 pubmed publisher
    ..A divergent amino terminus makes BcMCM a useful model for typical MCM-helicases since it accomplishes the same function using an apparently unrelated structure. ..
  42. Donmez I, Rajagopal V, Jeong Y, Patel S. Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability. J Biol Chem. 2007;282:21116-23 pubmed
    ..Modeling of the dependence provided the degree of the active involvement of helicase in base pair destabilization during the unwinding process and distinguished between passive and active mechanisms of unwinding. ..
  43. Lee J, Hite R, Hamdan S, Xie X, Richardson C, van Oijen A. DNA primase acts as a molecular brake in DNA replication. Nature. 2006;439:621-4 pubmed
    ..This observation suggests a mechanism that prevents leading-strand synthesis from outpacing lagging-strand synthesis during the slow enzymatic steps on the lagging strand. ..
  44. Chu M, Mierzwa R, Xu L, He L, Terracciano J, Patel M, et al. Isolation and structure elucidation of Sch 642305, a novel bacterial DNA primase inhibitor produced by Penicillium verrucosum. J Nat Prod. 2003;66:1527-30 pubmed
    ..Compound 1 exhibited inhibitory activity against bacterial DNA primase enzyme with an EC(50) of 70 microM.
  45. Ramirez Aguilar K, Low Nam N, Kuchta R. Key role of template sequence for primer synthesis by the herpes simplex virus 1 helicase-primase. Biochemistry. 2002;41:14569-79 pubmed
    ..In addition to hydrolyzing NTPs the NTPase could also hydrolyze the 5'-terminal phosphate from newly synthesized primers. ..
  46. Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F. Crystallization and preliminary X-ray analysis of a DNA primase from hyperthermophilic archaeon Pyrococcus horikoshii. J Biochem. 2001;130:727-30 pubmed
    ..understand the structural basis for the primer synthesis by archaeal/eukaryotic-type primases, the gene of the DNA primase from hyperthermophilic archaeon Pyrococcus horikoshii was cloned and overexpressed in Escherichia coli as a ..
  47. Yuzhakov A, Kelman Z, O Donnell M. Trading places on DNA--a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell. 1999;96:153-63 pubmed
    ..The conservation of this three-point switch, in which two proteins exchange places on DNA via mutually exclusive interaction with a third protein, is discussed. ..
  48. Beck K, Vannini A, Cramer P, Lipps G. The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis. Nucleic Acids Res. 2010;38:6707-18 pubmed publisher
    ..Furthermore, we identified mutants of the C-terminal domain, which are defective in template binding, dinucleotide formation and conformation change prior to DNA extension. ..
  49. Agarkar V, Babayeva N, Pavlov Y, Tahirov T. Crystal structure of the C-terminal domain of human DNA primase large subunit: implications for the mechanism of the primase-polymerase ? switch. Cell Cycle. 2011;10:926-31 pubmed
    DNA polymerases cannot synthesize DNA without a primer, and DNA primase is the only specialized enzyme capable of de novo synthesis of short RNA primers...
  50. Liao J, Jeong Y, Kim D, Patel S, Oster G. Mechanochemistry of t7 DNA helicase. J Mol Biol. 2005;350:452-75 pubmed
    ..Our analysis methods provide a systematic procedure to study kinetic pathways of multi-subunit, multi-state cooperative enzymes...
  51. Della M, Palmbos P, Tseng H, Tonkin L, Daley J, Topper L, et al. Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine. Science. 2004;306:683-5 pubmed
    ..These results demonstrate that prokaryotic Ku and ligase form a bona fide NHEJ system that encodes all the recognition, processing, and ligation activities required for DSB repair. ..
  52. Kleymann G, Fischer R, Betz U, Hendrix M, Bender W, Schneider U, et al. New helicase-primase inhibitors as drug candidates for the treatment of herpes simplex disease. Nat Med. 2002;8:392-8 pubmed
    ..Thus, this class of drugs has significant potential for the treatment of HSV disease in humans, including those resistant to current medications. ..
  53. Bocquier A, Liu L, Cann I, Komori K, Kohda D, Ishino Y. Archaeal primase: bridging the gap between RNA and DNA polymerases. Curr Biol. 2001;11:452-6 pubmed
    ..In Escherichia coli, the DNA primase (DnaG) exists as a monomer and synthesizes a short RNA primer...