1. Electron Microscopy of replicating DNA reveals replicating bubbles. How does one prove bidirectional fork movement?

2. Pulse with radiolabeled nucleotide; chase with cold nucleotide. Then do autoradiography

3. DNA Replication DNA replication is semi-conservative, one strand serves as the template for the second strand. Furthermore, DNA replication only occurs at a specific step in the cell cycle. The following table describes the cell cycle for a hypothetical cell with a 24 hr cycle. Stage Activity Duration G1 Growth and increase in cell size 10 hr S DNA synthesis 8 hr G2 Post-DNA synthesis 5 hr M Mitosis 1 hr DNA replication has two requirements that must be met: 1.DNA template 2.Free 3' -OH group

5. DNA Replication DNA replication is semi-conservative, one strand serves as the template for the second strand. Furthermore, DNA replication only occurs at a specific step in the cell cycle. The following table describes the cell cycle for a hypothetical cell with a 24 hr cycle. Stage Activity Duration G1 Growth and increase in cell size 10 hr S DNA synthesis 8 hr G2 Post-DNA synthesis 5 hr M Mitosis 1 hr DNA replication has two requirements that must be met: 1.DNA template 2.Free 3' -OH group

7. Proteins of DNA Replication DNA exists in the nucleus as a condensed, compact structure. To prepare DNA for replication, a series of proteins aid in the unwinding and separation of the double-stranded DNA molecule. These proteins are required because DNA must be single-stranded before replication can proceed. 1. DNA Helicases - These proteins bind to the double stranded DNA and stimulate the separation of the two strands. 2. DNA single-stranded binding proteins - These proteins bind to the DNA as a tetramer and stabilize the single-stranded structure that is generated by the action of the helicases. Replication is 100 times faster when these proteins are attached to the single- stranded DNA. 3. DNA Topoisomerase - This enzyme catalyzes the formation of negative supercoils that is thought to aid with the unwinding process. In addition to these proteins, several other enzymes are involved in bacterial DNA replication.

8. 4. DNA Polymerase - DNA Polymerase I (Pol I) was the first enzyme discovered with polymerase activity, and it is the best characterized enzyme. Although this was the first enzyme to be discovered that had the required polymerase activities, it is not the primary enzyme involved with bacterial DNA replication. That enzyme is DNA Polymerase III (Pol III). Three activities are associated with DNA polymerase I; *5' to 3' elongation (polymerase activity) *3' to 5' exonuclease (proof-reading activity) *5' to 3' exonuclease (repair activity) The second two activities of DNA Pol I are important for replication, but DNA Polymerase III (Pol III) is the enzyme that performs the 5'-3' polymerase function. 5. Primase - The requirement for a free 3' hydroxyl group is fulfilled by the RNA primers that are synthesized at the initiation sites by these enzymes. 6. DNA Ligase - Nicks occur in the developing molecule because the RNA primer is removed and synthesis proceeds in a discontinuous manner on the lagging strand. The final replication product does not have any nicks because DNA ligase forms a covalent phosphodiester linkage between 3'-hydroxyl and 5'-phosphate groups.

9. A General Model for DNA Replication 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase.

10. RNA primed DNA replication

11. A General Model for DNA Replication 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase.

13. A General Model for DNA Replication 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase.

14. Removal of RNA primers and filling of gaps

15. A General Model for DNA Replication 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand. This is in comparison to the continuous strand that is made off the leading strand. 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase.

17. ATP is an integral part of the ligation reaction

18. The end-replication problem

20. GroupOrganismTelomeric repeat (5' to 3' toward the end) VertebratesHuman, mouse, XenopusTTAGGG Filamentous fungiNeurosporaTTAGGG Slime moldsPhysarum, DidymiumTTAGGG DictyosteliumAG(1-8) Ciliated protozoaTetrahymena, GlaucomaTTGGGG ParameciumTTGGG(T/G) Oxytricha, Stylonychia,TTTTGGGG Euplotes Fission yeastsSchizosaccharomyces pombeTTAC(A)(C)G(1-8) Budding yeastsSaccharomyces cerevisiaeTGTGGGTGTGGTG Telomeres contain arrays of DNA repeats

21. Telomerase is a reverse transcriptase together with a template RNA It is active in germ cells, not in somatic cells, and is activated in cancers

22. Finishing school for telomeres

23. * The position on the DNA at which replication start points are found. (4 methods discussed) * A DNA sequence that when added to a non-replicating DNA causes it to replicate. * A DNA sequence whose mutation abolishes replication. * A DNA sequence that in vitro is the binding target for enzyme complexes known to function in initiation of DNA replication. Characteristics used to define Origins of Replication

24. 1) In synchronously replicating cells, density transfer experiments can reveal which sequences replicate earliest. What is the direction of fork movement here?

25. 2) Electron microscopy of bubbles after restriction enzyme digestion

27. 3) Hybridizing lagging strand nascent DNA to strand-specific fragments shows site of switch from leading to lagging strand synthesis

28. 4) 2D Gel electrophoresis of replication intermediates followed by hybridization with a DNA fragment reveals whether a replication bubble originates in the fragment Dimension 1: separates by size; dimension 2: separates by shape

29. Sequence that when added to a non-replicating DNA causes it to replicate; this approach was used to identify Autonomously Replicating Sequences (ARS) in yeast.

30. Sequence that when mutated causes a replicating DNA to fail to replicate; this approach was used to identify essential elements in an (ARS) in yeast

31. Linker scanning mutations in yeast ARS1 % URA+ colonies Examples of mutants A B1B2B3 WT-ARS1

33. OriC in E. coli chromosomal DNA

34. Initiation of DNA replication in E. coli

35. Two primosomes for E. coli chromosomal replication Site of primosome assemblyoriC, A-siten'-pas, D-loop, R-loop RecognitionDnaA proteinPriA protein Auxilliary proteins for(HU for oriC)PriB loading helicase PriC DnaT HelicaseDnaB/DnaC PrimingPrimase DnaA and oriC independent replication initiation in E. coli from hairpins, D-loops and R loops

36. SV40: a polyomavirus that is very useful for studying eukaryotic replication enzymes

37. Early genes : proteins essential for viral DNA replication

38. T antigen binding sites cluster around the ori

39. * 98% nuclear: NLS * origin-specific DNA binding * DNA independent ATPase * ATP dependent DNA helicase * Binds to DNA polymerases, AP2, p53, Rb * Undergoes phosphorylation etc. Properties of SV40 T antigen

40. Li & Kelly SV40 DNA replication In vitro. PNAS (1984) 81:6973 What else could they do to validate their system?

41. Fractionation to homogeneity

42. ELONGATION FACTORS ARE CONSERVED

44. Looping the lagging strand to make both polymerases move in the same direction

45. The discovery of DNA polymerase. Arthur Kornberg and Bob Lehman pursued an enzyme in bacterial extracts that would elongate a chain of deoxyribonucleic acid just like glycogen synthase elongates a chain of glycogen. The enzymatic activity was unusual: 1) Needed a template which dictates what nucleotide was added: substrate was directing enzymatic activity 2) Needed a primer annealed to the template.

49. Wait a minute! John Cairns mutated the gene for DNA polymerase, polA, and the bacteria grew just fine! Either the polymerase hypothesis was all wrong,…… or there were other DNA polymerases in E. coli that carried out DNA synthesis in the polA strains.

52. Which polymerase is processive?

53. POLIII,  subunit PCNA

54. Clamp loaders hydrolyze ATP to load clamp How does one prove that the clamp ring is opened during loading?

57. Structure of a DNA polymerase (gp43 from phage RB69) Side view: Polymerase active site Top view with template-primer: Polymerase site And proofreading site

58. * Topoisomerases II change the linking number in steps of 2 by passing both strands of double-stranded DNA through a break. * Eukaryotic topoisomerases isolated to date only relax supercoiled DNA, while prokaryotic topoisomerases (gyrases) can, given ATP, add supercoils. * TopoII releases catenated daughter molecules at the end of replication. Inhibitors like etoposide are used in chemotherapy. Topoisomerases relax DNA by changing the DNA linking number

59. * Topoisomerases I change the linking number in steps of 1. They pass a single DNA strand through a nick.Topoisomerase I is a protein of the metaphase chromosome scaffold. * In interphase, topoisomerase is bound to the nuclear matrix. * The DNA replication machinery also appears bound to the matrix. * Inhibitor (camptothecin) also used in chemotherapy.

60. Topoisomerase action can be divided into three steps: nicking (1), strand passage (2); resealing (3).

61. 1 3 2 4 Cycle of topoisomerase activity inferred from structure How would you test that the subunits have to open at the lower end to release the T segment?

66. RF-C is a five-subunit complex All subunits are related in sequence and have ATP binding motifs ATP hydrolysis by RF-C is associated with the loading of PCNA RF-C is the functional homolog of the clamp-loader  complex

68. Polymerase switching occurs even on lagging strands; pol  does most of DNA synthesis

70. How do you think the PCNA is removed after ligation?

72. PCNA interacts with RF-C, pol , Fen1, DNA ligase, CAF1 and MCMT Several of these have a common motif used in the interaction: Q-X-X-L/I/M-X-X-F- F/Y p21/CIP1/WAF1, a protein induced by the tumor suppressor p53 uses the same motif to interact with PCNA What effect is p21 expected to have on DNA replication/repair?

73. FEN1 interacts with PCNA

74. DNA Helicase * Helicase binds ss DNA * Hydrolyzes ATP to move along ssDNA and peel of substrate DNA * Can move 5‘ to 3’ or 3‘to 5’ or in both directions on ssDNA and is classified as such * Dimers or hexamers

75. Conserved helicase motifs: Includes the following for ATP binding and hydrolysis I = Walker A motif GxGxGKT II = Walker B motif  DEad Helicases are ATP driven molecular motors

76. Formation of pre-Replicative complex

77. G2 M ORC MCM CDC6 + Cdt1 Replication Machinery “Pre-Replicative Complex” Replication complexes during the cell cycle ORC CDC6+ Cdt1 Slate G1 early G1

78. Eukaryotic initiation complex ORC : A six subunit protein complex which has been implicated as being the eukaryotic DNA replication initiator protein. Subunits are named according to their size, with ORC1 being the largest and ORC6 being the smallest subunit. Yeast ORC specifically binds to replication origins in an ATP dependent manner and has been shown to possess ATPase activity. CDC6/Cdc18 : An essential factor for the assembly of the pre- replicative complexes that co-operates with Cdt1 to load MCM2-7 Proteolyzed in yeasts or exported out of the nucleus in mammalian cells at the G1- S transition. Overexpression of Cdc6 in yeast causes multiple rounds of DNA replication without intervening mitosis, making it a critical regulator of DNA replication. MCM2-7 : A family of six related proteins (MCM2-MCM7) which seem to function together in a large multi-subunit protein complex. The role of MCMís in DNA replication is still speculative, ranging from mediation of protein-DNA interactions to DNA helicase activity.

79. A/TDUEORE Auxiliary elements Auxiliary elements Origin recognition proteins Transcription Factors Transcription Factors Leading str Lagging str Core origin Origins are multi-partite

80. The Structure of ARS1 (S. cerevisiae) B1 ACS B2 B3 ABF1 ORC “Post-RC” protection “Pre-RC” protection 1 3 4 5 6 4 1 2 2

82. ORC uses different strategies for binding DNA in different species

83. Pre-RC formation ORC : A six subunit protein complex which has been implicated as being the eukaryotic DNA replication initiator protein. Subunits are named according to their size, with ORC1 being the largest and ORC6 being the smallest subunit. Yeast ORC specifically binds to replication origins in an ATP dependent manner and has been shown to possess ATPase activity. CDC6/Cdc18 : An essential factor for the assembly of the pre- replicative complexes that co-operates with Cdt1 to load MCM2-7 Proteolyzed in yeasts or exported out of the nucleus in mammalian cells at the G1- S transition. Overexpression of Cdc6 in yeast causes multiple rounds of DNA replication without intervening mitosis, making it a critical regulator of DNA replication. MCM2-7 : A family of six related proteins (MCM2-MCM7) which seem to function together in a large multi-subunit protein complex. The role of MCMís in DNA replication is still speculative, ranging from mediation of protein-DNA interactions to DNA helicase activity.

84. The Xenopus Cdc6 Protein Is Essential for the Initiation of a Single Round of DNA Replication in Cell-Free Extracts Made from Xenopus egg extracts Rxn Time: 0-30 min 30-60 min 60-90 min + 32P labeled DNA replication product Replication initiation required on double-stranded DNA substrate Only elongation required on single-stranded DNA substrate

85. Orc is required to load CDC6; CDC6 is required to load MCM

86. Immunostaining for CDC6 can pick out proliferating cells in Pap smears

87. Pre-RC formation ORC : A six subunit protein complex which has been implicated as being the eukaryotic DNA replication initiator protein. Subunits are named according to their size, with ORC1 being the largest and ORC6 being the smallest subunit. Yeast ORC specifically binds to replication origins in an ATP dependent manner and has been shown to possess ATPase activity. CDC6/Cdc18 : An essential factor for the assembly of the pre- replicative complexes that co-operates with Cdt1 to load MCM2-7 Proteolyzed in yeasts or exported out of the nucleus in mammalian cells at the G1- S transition. Overexpression of Cdc6 in yeast causes multiple rounds of DNA replication without intervening mitosis, making it a critical regulator of DNA replication. MCM2-7 : A family of six related proteins (MCM2-MCM7) which seem to function together in a large multi-subunit protein complex. The role of MCMís in DNA replication is still speculative, ranging from mediation of protein-DNA interactions to DNA helicase activity.

89. Propidium iodide staining No. of cells Fluorescence analysis and cell sorting (FACS) DNA in cells stained with propidium iodide. Intensity of staining in each cell is proportional to amount of DNA in the cell.

90. Chromatin immunoprecipitation (ChIP) tests whether a given DNA sequence is bound by a protein in vivo

92. MCM homolog from M. thermoautotrophicum (an archaebacterium) has helicase activity. What direction?

93. Mt MCM forms double hexamers

94. Pre-RC formation ORC : A six subunit protein complex which has been implicated as being the eukaryotic DNA replication initiator protein. Subunits are named according to their size, with ORC1 being the largest and ORC6 being the smallest subunit. Yeast ORC specifically binds to replication origins in an ATP dependent manner and has been shown to possess ATPase activity. CDC6/Cdc18 : An essential factor for the assembly of the pre- replicative complexes that co-operates with Cdt1 to load MCM2-7 Proteolyzed in yeasts or exported out of the nucleus in mammalian cells at the G1- S transition. Overexpression of Cdc6 in yeast causes multiple rounds of DNA replication without intervening mitosis, making it a critical regulator of DNA replication. MCM2-7 : A family of six related proteins (MCM2-MCM7) which seem to function together in a large multi-subunit protein complex. The role of MCMís in DNA replication is still speculative, ranging from mediation of protein-DNA interactions to DNA helicase activity.

95. Mammalian cells can survive with 0.1x the normal ORC2 level : WT vs  cells

96. oriP EBNA1 EBNA1 protein Replication from an origin in Epstein-Barr virus: a plasmid expressing EBNA1 and containing oriP will replicate and be maintained as an episome in mammalian cells Hygromycin- Resistance gene

97. Establishment of drug-resistant colonies after transfection of EBV-based plasmid

98. Transition to replication: from pre-RC to unwinding

99. MCM10 : essential function in the initiation of DNA replication in yeast. Required in Xenopus after the loading of Mcm2-7, before the loading of CDC45 CDC7/DBF4 : A DBF4 dependent kinase (DDK) which, together with Dbf4, is required for the initiation of DNA replication. Possible substrates of this kinase are the MCMs. How do we know this? Cdk/Cyclin: A protein kinase essential for the initiation of DNA replication. Substrates that are activated by Cdk for replication initiation are unclear. MCM, CDC6 and some ORC subunits are phosphorylated, but this phosphorylation inactivates the proteins and prevents re-replication. CDC45 : it seems to act together with ORC and the MCMs to initiate DNA replication. Has a role in the loading of DNA primase/polymerase complex. It and the MCM proteins appear to move along with the replication fork. How do we know this? Transition to Replication

100. S phase: Chromosome duplication Mitosis: Chromosome segregation Problems for the cell: (1) Alternation of S and M (2) Completion of S before M and vice versa

101. With their multiple origins, how does the eukaryotic cell know which origins have been already replicated and which still await replication? Two observations: When a cell in G1of the cell cycle is fused with a cell in S phase, the DNA of the G1 nucleus begins replicating early. Thus S phase cells have a positive factor for DNA replication that G1 cells lack. When a cell in G2 of the cell cycle is fused with a cell in S phase, the DNA of the G2 nucleus does not begin replicating again even though replication is proceeding normally in the S-phase nucleus. Not until mitosis is completed, can freshly- synthesized DNA be replicated again. Thus cells in G2 have a negative factor that disappears in mitosis and/or lack a positive replication licensing factor until they pass through mitosis. Control of Replication through the cell cycle

102. Cyclin/cdk protein kinase (i) yeast with temperature sensitive mutation in CDC28 (a cdk) arrest in G1 (ii) addition of a cdk inhibitor (e.g. p21) to Xenopus egg extracts in G1 inhibits replication DBF4/CDC7 protein kinase (i) ts mutation of CDC7 in yeast blocks cell cycle in G1 (by- passed by a mutation in MCM5) (ii) antibody mediated depletion in Xenopus egg extracts Positive factor present in S phase cells

103. CDC6 (i) degraded in yeasts after G1/S (ii) displaced out of the nucleus after G1/S in mammalian cells MCM2-7 (i) displaced out of the nucleus after G1/S in yeast (ii) loses tight association with chromatin after G1/S in mammalian cells CDC45 (i) loses tight association with chromatin after G1/S in mammalian cells Cdt1 (i) degraded in mammalian cells during S phase. (ii) inactivated by interaction with a protein called geminin. ORC: may be inactivated by phosphorylation Mcm10: ? Positive factor (replication licensing factor) absent in G2 cells, but present in G1 cells

104. HsCDC6G1S H 2 NCOOH Cy SS Wild-type H 2 NCOOH Cy SS  H 2 NCOOH Cy DD H 2 NCOOH Cy AA Ser  Ala Ser  Asp Proper Subcellular Localization of HsCDC6 is Dependent on Both IntactPhosphorylation Sites and a Functional Cy Motif CDC6 in mammalian cells is exported out of the nucleus In S phase due to phosphorylation by cyclin/cdk G1 S

105. GFP-MCM4 localization through the cell cycle in yeast Movie: http://users.ox.ac.uk/~kearsey/mcm4.html

106. Highly active cyclin/cdk protein kinase (i) inactivated in mitosis due to degradation of cyclins. (ii) artificial inactivation in G2 yeast with ts mutations in the cdk or by induction of a cdk inhibitor results in re-replication of DNA without mitosis. (iii) the nuclear export (in mammalian cells) or proteolysis (in yeast) of CDC6 is due to phosphorylation by cyclin/cdk. Therefore the negative factor present in G2 cells may also be responsible for the absence of a positive replication licensing factor in G2 nuclei! Geminin (i) elevated in G2 cells and degraded in mitosis (ii) addition of a stable form of the protein to Xenopus egg extract inhibits the loading of MCM2-7 on chromatin and prevents DNA replication (iii) interacts with Cdt1. Negative factor present in G2 cells, but absent in G1 cells

107. Low cyclin/cdk activity is required at G1/S to initiate DNA replication Low cyclin/cdk activity in G1/S is inadequate to initiate mitosis High cyclin/cdk activity in G2 inhibits DNA replication High cyclin/cdk activity in G2 is required for mitosis Solution to the alternation problem Solution to the completion problem For mitosis to be completed, cyclin-cdk has to be inactivated. Thus S phase cannot occur before mitosis is completed. Why doesn’t mitosis occur before S phase is completed? Checkpoint pathways that are still being worked out.