Origin of Replication - I Signals and Systems in Biology Kushal Shah @ EE, IIT Delhi DNA Replication Bacterial DNA Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Some facts I Replication may proceed uni-directionally or bi-directionally I Usually AT-rich region I Bacteria : circular DNA and single origin of replication I Archaea : Circular DNA and multiple origins I Eukaryotes : Linear DNA and multiple origins I Firing time of each Ori may be different I Modeling of this ’firing’ phenomenon is a challenging task Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Cell Cycle I G1 phase : Initiation of major replication regulatory processes I S phase : Actual DNA replication I G2 phase : Correction of replication errors or other damages I M phase : Segregation of parent cell into daughters Prokaryotic cell : ~ 20 mins Eukaryotic cell : ~ 18 to 24 hrs! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Ori : Prokaryotes I Circular DNA and single origin of replication I 9-mer and 13-mer repeats I DnaA box (4 nos.): 5’ - TTATCCACA - 3’ I DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3 I DnaA protein binds to 9-mers & simulates the 13-mers to unwind I DnaC loads the DnaB to each of the two unwound strands I SSB prevents single strands from forming secondary structures I DNA gyrase relieves the stress! Prokaryotic DNA Replication Eukaryotic DNA replication Occurs inside the cytoplasm Occurs inside the nucleus Only one origin of replication Have many origins of replication Ori length about 100-200 nt Each Ori of about 150 nt DnaA and DnaB boxes No conserved consensus sequence (S. cerevisiae : WTTTAYRTTTW) W=A/T, Y=C/T, T=A/G Initiation by DnaA and DnaB Initiation by ORC protein Replication is very rapid Replication is very slow Prokaryotic DNA Replication Eukaryotic DNA replication Occurs inside the cytoplasm Occurs inside the nucleus Only one origin of replication Have many origins of replication Ori length about 100-200 nt Each Ori of about 150 nt DnaA and DnaB boxes No conserved consensus sequence (S. cerevisiae : WTTTAYRTTTW) W=A/T, Y=C/T, T=A/G Initiation by DnaA and DnaB Initiation by ORC protein Replication is very rapid Replication is very slow Prokaryotic DNA Replication Eukaryotic DNA replication Occurs inside the cytoplasm Occurs inside the nucleus Only one origin of replication Have many origins of replication Ori length about 100-200 nt Each Ori of about 150 nt DnaA and DnaB boxes No conserved consensus sequence (S.