Single-molecule studies of the replisome.

Replication of DNA is carried out by the replisome, a multiprotein complex responsible for the unwinding of parental DNA and the synthesis of DNA on each of the two DNA strands. The impressive speed and processivity with which the replisome duplicates DNA are a result of a set of tightly regulated interactions between the replication proteins. The transient nature of these protein interactions makes it challenging to study the dynamics of the replisome by ensemble-averaging techniques. This review describes single-molecule methods that allow the study of individual replication proteins and their functioning within the replisome. The ability to mechanically manipulate individual DNA molecules and record the dynamic behavior of the replisome while it duplicates DNA has led to an improved understanding of the molecular mechanisms underlying DNA replication.

[1]  Stephen J Benkovic,et al.  Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. , 2005, Biochemistry.

[2]  M. O’Donnell,et al.  Single-molecule analysis reveals that the lagging strand increases replisome processivity but slows replication fork progression , 2009, Proceedings of the National Academy of Sciences.

[3]  T. Ha,et al.  Coordinating DNA replication by means of priming loop and differential synthesis rate , 2009, Nature.

[4]  R. Dean Astumian,et al.  Tuning and switching a DNA polymerase motor with mechanical tension , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[5]  C. Joo,et al.  Advances in single-molecule fluorescence methods for molecular biology. , 2008, Annual review of biochemistry.

[6]  R. Karpel,et al.  Kinetic regulation of single DNA molecule denaturation by T4 gene 32 protein structural domains. , 2003, Journal of molecular biology.

[7]  S. Benkovic,et al.  The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication. , 2006, Molecular cell.

[8]  M. O’Donnell,et al.  An explanation for lagging strand replication: Polymerase hopping among DNA sliding clamps , 1994, Cell.

[9]  C. Richardson,et al.  The Linker Region between the Helicase and Primase Domains of the Bacteriophage T7 Gene 4 Protein Is Critical for Hexamer Formation* , 1999, The Journal of Biological Chemistry.

[10]  V. Croquette,et al.  Replication by a single DNA polymerase of a stretched single-stranded DNA. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[11]  K. Johnson,et al.  An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. , 1991, Biochemistry.

[12]  O. Saleh,et al.  Single-molecule manipulation measurements of DNA transport proteins. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[13]  Nam Ki Lee,et al.  Single-molecule approach to molecular biology in living bacterial cells. , 2008, Annual review of biophysics.

[14]  J. Drake,et al.  Spontaneous Mutation: Genetic Control of Mutation Rates in Bacteriophage T4 , 1969, Nature.

[15]  K. Schulten,et al.  Fluorescence-Force Spectroscopy Maps Two-Dimensional Reaction Landscape of the Holliday Junction , 2007, Science.

[16]  S. Hamdan,et al.  Primer initiation and extension by T7 DNA primase , 2006, The EMBO journal.

[17]  Antoine M. van Oijen,et al.  Proliferating Cell Nuclear Antigen Uses Two Distinct Modes to Move along DNA* , 2009, The Journal of Biological Chemistry.

[18]  C. Richardson,et al.  DNA recognition by the DNA primase of bacteriophage T7: a structure-function study of the zinc-binding domain. , 2009, Biochemistry.

[19]  J. Drake,et al.  Genetic control of mutation rates in bacteriophageT4. , 1969, Nature.

[20]  Greg L. Hura,et al.  Crosstalk between primase subunits can act to regulate primer synthesis in trans. , 2005, Molecular cell.

[21]  Scott Bailey,et al.  Structure of Hexameric DnaB Helicase and Its Complex with a Domain of DnaG Primase , 2022 .

[22]  C. Dekker,et al.  Single-molecule studies of nucleic acid motors. , 2007, Current opinion in structural biology.

[23]  Michelle D. Wang,et al.  Single-Molecule Studies Reveal Dynamics of DNA Unwinding by the Ring-Shaped T7 Helicase , 2007, Cell.

[24]  J. Griffith,et al.  Coordinated leading and lagging strand DNA synthesis on a minicircular template. , 1998, Molecular cell.

[25]  S. Benkovic,et al.  Interaction between the T4 helicase loading protein (gp59) and the DNA polymerase (gp43): unlocking of the gp59-gp43-DNA complex to initiate assembly of a fully functional replisome. , 2005, Biochemistry.

[26]  T. Strick,et al.  Twisting and stretching single DNA molecules. , 2000, Progress in biophysics and molecular biology.

[27]  Taekjip Ha,et al.  Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy. , 2004, Biochemistry.

[28]  S. Benkovic,et al.  Dynamic protein interactions in the bacteriophage T4 replisome. , 2001, Trends in biochemical sciences.

[29]  N. Tanner,et al.  Dynamic DNA helicase-DNA polymerase interactions assure processive replication fork movement. , 2007, Molecular cell.

[30]  M. O’Donnell,et al.  Cellular DNA replicases: components and dynamics at the replication fork. , 2005, Annual review of biochemistry.

[31]  J. Loparo,et al.  Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis , 2009, Nature.

[32]  M. O’Donnell,et al.  The ring-type polymerase sliding clamp family , 2001, Genome Biology.

[33]  S. Benkovic,et al.  Characterization of bacteriophage T4-coordinated leading- and lagging-strand synthesis on a minicircle substrate. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[34]  S. Benkovic,et al.  Replisome-mediated DNA replication. , 2001, Annual review of biochemistry.

[35]  Kenneth A. Johnson,et al.  Role of Induced Fit in Enzyme Specificity: A Molecular Forward/Reverse Switch* , 2008, Journal of Biological Chemistry.

[36]  C. Bustamante,et al.  Proofreading dynamics of a processive DNA polymerase , 2009, The EMBO journal.

[37]  W. Greenleaf,et al.  High-resolution, single-molecule measurements of biomolecular motion. , 2007, Annual review of biophysics and biomolecular structure.

[38]  S. Kowalczykowski Initiation of genetic recombination and recombination-dependent replication. , 2000, Trends in biochemical sciences.

[39]  J. Griffith,et al.  Formation of a DNA Loop at the Replication Fork Generated by Bacteriophage T7 Replication Proteins* , 1998, The Journal of Biological Chemistry.

[40]  R. Sheaff,et al.  Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination. , 1993, Biochemistry.

[41]  S. Hamdan,et al.  Motors, switches, and contacts in the replisome. , 2009, Annual review of biochemistry.

[42]  Stephen J Benkovic,et al.  Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation. , 2006, Biochemistry.

[43]  J. Griffith,et al.  Architecture of the Bacteriophage T4 Replication Complex Revealed with Nanoscale Biopointers* , 2007, Journal of Biological Chemistry.

[44]  C. Richardson,et al.  Interaction of adjacent primase domains within the hexameric gene 4 helicase-primase of bacteriophage T7 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  K. Marians,et al.  The Interaction between Helicase and Primase Sets the Replication Fork Clock* , 1996, The Journal of Biological Chemistry.

[46]  A. Oijen Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity. , 2007 .

[47]  A. V. van Oijen Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity. , 2007, Biopolymers.

[48]  Boriana Marintcheva,et al.  The C-terminal Residues of Bacteriophage T7 Gene 4 Helicase-Primase Coordinate Helicase and DNA Polymerase Activities* , 2006, Journal of Biological Chemistry.

[49]  C. Bustamante,et al.  Ten years of tension: single-molecule DNA mechanics , 2003, Nature.

[50]  C. McHenry,et al.  Coupling of a Replicative Polymerase and Helicase: A τ–DnaB Interaction Mediates Rapid Replication Fork Movement , 1996, Cell.

[51]  Mike O'Donnell,et al.  Mechanism of the E. coli tau processivity switch during lagging-strand synthesis. , 2003, Molecular cell.

[52]  J. Reems,et al.  Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. V. Primase action regulates the cycle of Okazaki fragment synthesis. , 1992, The Journal of biological chemistry.

[53]  C. Richardson,et al.  Interaction of Ribonucleoside Triphosphates with the Gene 4 Primase of Bacteriophage T7* , 1999, The Journal of Biological Chemistry.

[54]  E. Zechner,et al.  Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. II. Frequency of primer synthesis and efficiency of primer utilization control Okazaki fragment size. , 1992, The Journal of biological chemistry.

[55]  B. Alberts,et al.  The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairpin helix. A model for polymerase release following the termination of each Okazaki fragment. , 1994, The Journal of biological chemistry.

[56]  J. Griffith,et al.  Lagging strand synthesis in coordinated DNA synthesis by bacteriophage t7 replication proteins. , 2002, Journal of molecular biology.

[57]  P. Burgers Polymerase Dynamics at the Eukaryotic DNA Replication Fork* , 2009, Journal of Biological Chemistry.

[58]  M. O’Donnell,et al.  The replication clamp-loading machine at work in the three domains of life , 2006, Nature Reviews Molecular Cell Biology.

[59]  S. Benkovic,et al.  DNA polymerase fidelity: kinetics, structure, and checkpoints , 2004 .

[60]  K. Baradaran,et al.  An N-terminal fragment of the gene 4 helicase/primase of bacteriophage T7 retains primase activity in the absence of helicase activity. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[61]  T. Ellenberger,et al.  Tuning DNA “strings”: Modulating the rate of DNA replication with mechanical tension , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[62]  A. V. van Oijen,et al.  Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion , 2008, Proceedings of the National Academy of Sciences.

[63]  J. Kuriyan,et al.  Clamp loaders and sliding clamps. , 2002, Current opinion in structural biology.

[64]  S. Doublié,et al.  Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution , 1998, Nature.

[65]  D. Gilbert,et al.  DNA replication and nuclear organization: prospects for a soluble in vitro system. , 1999, Critical reviews in eukaryotic gene expression.

[66]  T. Ha,et al.  A survey of single-molecule techniques in chemical biology. , 2007, ACS chemical biology.

[67]  S. Benkovic,et al.  Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism , 2007, Proceedings of the National Academy of Sciences.

[68]  B. Alberts,et al.  The slow dissociation of the T4 DNA polymerase holoenzyme when stalled by nucleotide omission. An indication of a highly processive enzyme. , 1994, The Journal of biological chemistry.

[69]  M. O’Donnell,et al.  Sliding clamps: A (tail)ored fit , 2000, Current Biology.

[70]  Mark C. Williams,et al.  Optical tweezers experiments resolve distinct modes of DNA-protein binding. , 2009, Biopolymers.

[71]  L. Bloom Loading clamps for DNA replication and repair. , 2009, DNA repair.

[72]  Paul R Selvin,et al.  New fluorescent tools for watching nanometer-scale conformational changes of single molecules. , 2007, Annual review of biophysics and biomolecular structure.

[73]  C. Richardson,et al.  Interactions of the DNA polymerase and gene 4 protein of bacteriophage T7. Protein-protein and protein-DNA interactions involved in RNA-primed DNA synthesis. , 1986, The Journal of biological chemistry.

[74]  Carlos Bustamante,et al.  Grabbing the cat by the tail: manipulating molecules one by one , 2000, Nature Reviews Molecular Cell Biology.

[75]  G. Wagner,et al.  A Molecular Handoff between Bacteriophage T7 DNA Primase and T7 DNA Polymerase Initiates DNA Synthesis* , 2004, Journal of Biological Chemistry.

[76]  C. Richardson,et al.  DNA primases. , 2001, Annual review of biochemistry.

[77]  M. Griep,et al.  Primer synthesis kinetics by Escherichia coli primase on single-stranded DNA templates. , 1995, Biochemistry.

[78]  P. V. von Hippel,et al.  Helicase mechanisms and the coupling of helicases within macromolecular machines Part II: Integration of helicases into cellular processes , 2003, Quarterly Reviews of Biophysics.

[79]  David Keller,et al.  Single-molecule studies of the effect of template tension on T7 DNA polymerase activity , 2000, Nature.

[80]  C. Richardson,et al.  An in Trans Interaction at the Interface of the Helicase and Primase Domains of the Hexameric Gene 4 Protein of Bacteriophage T7 Modulates Their Activities* , 2009, The Journal of Biological Chemistry.

[81]  Stephen D. Bell,et al.  DNA Replication in the Archaea , 2006, Microbiology and Molecular Biology Reviews.

[82]  Gerhard Wagner,et al.  Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. , 2003, Molecular cell.

[83]  K. Bjornson,et al.  Mechanisms of helicase-catalyzed DNA unwinding. , 1996, Annual review of biochemistry.

[84]  Gijs J. L. Wuite,et al.  See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins , 2008, Nucleic acids research.

[85]  R. Karpel,et al.  Mechanical measurement of single-molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 protein. , 2004, Journal of molecular biology.

[86]  L. Bird,et al.  Helicases: a unifying structural theme? , 1998, Current opinion in structural biology.

[87]  J. Kuriyan,et al.  Clamp loaders and replication initiation. , 2006, Current opinion in structural biology.

[88]  Guobin Luo,et al.  Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase , 2007, Proceedings of the National Academy of Sciences.

[89]  M. O’Donnell,et al.  Replisome mechanics: insights into a twin DNA polymerase machine. , 2007, Trends in microbiology.

[90]  E. Greene,et al.  Single molecule studies of homologous recombination. , 2008, Molecular bioSystems.

[91]  Stephen J. Benkovic,et al.  Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome , 2009, Nature chemical biology.

[92]  S. Benkovic,et al.  Repetitive lagging strand DNA synthesis by the bacteriophage T4 replisome. , 2008, Molecular bioSystems.

[93]  Antoine M. van Oijen,et al.  Real-time single-molecule observation of rolling-circle DNA replication , 2009, Nucleic acids research.

[94]  R. Karpel,et al.  Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurements. , 2005, Journal of molecular biology.

[95]  M. O’Donnell,et al.  Replicative helicase loaders: ring breakers and ring makers , 2003, Current Biology.

[96]  C. McHenry,et al.  τCouples the Leading- and Lagging-strand Polymerases at the Escherichia coli DNA Replication Fork* , 1996, The Journal of Biological Chemistry.

[97]  B. Alberts,et al.  The bacteriophage T4 DNA replication fork. Only DNA helicase is required for leading strand DNA synthesis by the DNA polymerase holoenzyme. , 1989, The Journal of biological chemistry.

[98]  K J Marians,et al.  The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate. , 1987, The Journal of biological chemistry.

[99]  M. Chandler,et al.  The replication time of the Escherichia coli K12 chromosome as a function of cell doubling time. , 1975, Journal of molecular biology.

[100]  Leila Shokri,et al.  Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA , 2008, Nucleic acids research.

[101]  M. O’Donnell Replisome Architecture and Dynamics in Escherichia coli* , 2006, Journal of Biological Chemistry.

[102]  Smita S. Patel,et al.  Mechanisms of Helicases* , 2006, Journal of Biological Chemistry.

[103]  I. Konieczny Strategies for helicase recruitment and loading in bacteria , 2003, EMBO reports.

[104]  B. Alberts,et al.  Studies on DNA replication in the bacteriophage T4 in vitro system. , 1983, Cold Spring Harbor symposia on quantitative biology.

[105]  S. Patel,et al.  Structure and function of hexameric helicases. , 2000, Annual review of biochemistry.

[106]  X. Zhuang Single-molecule RNA science. , 2005, Annual review of biophysics and biomolecular structure.

[107]  Charles C. Richardson,et al.  University of Groningen Single-Molecule Kinetics of λ Exonuclease Reveal Base Dependence and Dynamic Disorder , 2018 .

[108]  B. Alberts,et al.  Effects of the bacteriophage T4 gene 41 and gene 32 proteins on RNA primer synthesis: coupling of leading- and lagging-strand DNA synthesis at a replication fork. , 1990, Biochemistry.

[109]  W. Greenleaf,et al.  Single-molecule studies of RNA polymerase: motoring along. , 2008, Annual review of biochemistry.

[110]  Colin Echeverría Aitken,et al.  Translation at the single-molecule level. , 2008, Annual review of biochemistry.

[111]  N. Ribeck,et al.  Multiplexed single-molecule measurements with magnetic tweezers. , 2008, The Review of scientific instruments.

[112]  X. Xie,et al.  DNA primase acts as a molecular brake in DNA replication , 2006, Nature.

[113]  N. Tanner,et al.  Single-molecule studies of fork dynamics in Escherichia coli DNA replication , 2008, Nature Structural &Molecular Biology.

[114]  M. Betterton,et al.  Opening of nucleic-acid double strands by helicases: active versus passive opening. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[115]  Carlos Bustamante,et al.  Recent advances in optical tweezers. , 2008, Annual review of biochemistry.

[116]  A. Brunger,et al.  Single-molecule studies of the neuronal SNARE fusion machinery. , 2009, Annual review of biochemistry.

[117]  C. Richardson,et al.  Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. , 1987, The Journal of biological chemistry.

[118]  M. O’Donnell,et al.  DNA Polymerase δ Is Highly Processive with Proliferating Cell Nuclear Antigen and Undergoes Collision Release upon Completing DNA* , 2008, Journal of Biological Chemistry.

[119]  E. Egelman,et al.  The primase active site is on the outside of the hexameric bacteriophage T7 gene 4 helicase-primase ring. , 2001, Journal of molecular biology.

[120]  S. Benkovic,et al.  Assembly of the bacteriophage T4 primosome: single-molecule and ensemble studies. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[121]  Z. Debyser,et al.  Coordination of leading and lagging strand DNA synthesis at the replication fork of bacteriophage T7 , 1994, Cell.

[122]  J. Walter,et al.  Chromosomal DNA replication in a soluble cell-free system derived from Xenopus eggs. , 2006, Methods in molecular biology.

[123]  X. Xie,et al.  Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. , 2003, Science.

[124]  Guobin Luo,et al.  Fluctuating enzymes: lessons from single-molecule studies. , 2005, Accounts of chemical research.

[125]  J. Berger,et al.  Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions , 2006, Nucleic acids research.

[126]  J. Griffith,et al.  Architecture of the Replication Complex and DNA Loops at the Fork Generated by the Bacteriophage T4 Proteins* , 2003, Journal of Biological Chemistry.

[127]  Z. Kelman,et al.  Trading Places on DNA—A Three-Point Switch Underlies Primer Handoff from Primase to the Replicative DNA Polymerase , 1999, Cell.