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Models of DNA synthesis 
Institute of Lifelong Learning, University of Delhi 
 
 
  
 
 
 
Lesson: Models of DNA synthesis 
Lesson Developer: Dr. Devi Lal 
College/ Department: Department of Zoology, Ramjas College, 
University of Dekhi  
Reviewer: Dr. Neeraj Sood 
college/ Department : Department of Zoology, Dyal Singh College, 
University of Delhi 
 
 
 
 
 
 
 
 
 
Page 2


Models of DNA synthesis 
Institute of Lifelong Learning, University of Delhi 
 
 
  
 
 
 
Lesson: Models of DNA synthesis 
Lesson Developer: Dr. Devi Lal 
College/ Department: Department of Zoology, Ramjas College, 
University of Dekhi  
Reviewer: Dr. Neeraj Sood 
college/ Department : Department of Zoology, Dyal Singh College, 
University of Delhi 
 
 
 
 
 
 
 
 
 
Models of DNA synthesis 
2 
 
 
Table of Contents   
Chapter: Models of DNA synthesis 
 Topic         Page No.                                                       
Introduction……………………………………………………………………………………………………..3 
Initiation of DNA replication ………………………………………………………………………………………………………….3.  
The Replicon Model………….………………………………………………………………………………………………………………………….3 
Regulation of DNA replication  
Regulation of DNA replication in E. coli……………………………………………………..4 
Regulation of DNA replication in eukaryotes……………………………………………4 
Overview of DNA replication  
Overview of DNA replication in prokaryotes…………………………………………….5 
Overview of DNA replication in eukaryotes……………………………………………..8 
End replication problem  
Telomeres and Telomerases…………………………………………………………………….9  
Role of Telomere binding proteins………………………………………………………….11 
Priming protein……………………………………………………………………………………….12 
Replication model for other circular DNAs 
Rolling circle replication………………………………………………………………………….12 
D-loops and mitochondrial DNA replication…………………………………………..13 
Summary………………………………………………………….…………………………………………………….…14 
Exercise/ Practice………………………………………………………….………………………………………….15 
Glossary………………………………………………………….………………………………………………………….19 
References/ Bibliography/ Further Reading…………………………………………….19 
Web links………………………………………………………….……………………………………………………….20 
Answers………………………………………………………….………………………………………………………….20 
 
Page 3


Models of DNA synthesis 
Institute of Lifelong Learning, University of Delhi 
 
 
  
 
 
 
Lesson: Models of DNA synthesis 
Lesson Developer: Dr. Devi Lal 
College/ Department: Department of Zoology, Ramjas College, 
University of Dekhi  
Reviewer: Dr. Neeraj Sood 
college/ Department : Department of Zoology, Dyal Singh College, 
University of Delhi 
 
 
 
 
 
 
 
 
 
Models of DNA synthesis 
2 
 
 
Table of Contents   
Chapter: Models of DNA synthesis 
 Topic         Page No.                                                       
Introduction……………………………………………………………………………………………………..3 
Initiation of DNA replication ………………………………………………………………………………………………………….3.  
The Replicon Model………….………………………………………………………………………………………………………………………….3 
Regulation of DNA replication  
Regulation of DNA replication in E. coli……………………………………………………..4 
Regulation of DNA replication in eukaryotes……………………………………………4 
Overview of DNA replication  
Overview of DNA replication in prokaryotes…………………………………………….5 
Overview of DNA replication in eukaryotes……………………………………………..8 
End replication problem  
Telomeres and Telomerases…………………………………………………………………….9  
Role of Telomere binding proteins………………………………………………………….11 
Priming protein……………………………………………………………………………………….12 
Replication model for other circular DNAs 
Rolling circle replication………………………………………………………………………….12 
D-loops and mitochondrial DNA replication…………………………………………..13 
Summary………………………………………………………….…………………………………………………….…14 
Exercise/ Practice………………………………………………………….………………………………………….15 
Glossary………………………………………………………….………………………………………………………….19 
References/ Bibliography/ Further Reading…………………………………………….19 
Web links………………………………………………………….……………………………………………………….20 
Answers………………………………………………………….………………………………………………………….20 
 
Models of DNA synthesis 
3 
 
 
Introduction 
The previous unit describes the enzymes and the general principle of DNA replication. The 
enzymes and general machinery for replication is more or less same in both prokaryotes 
and eukaryotes with slight differences. In this unit we will learn about the modes of DNA 
replication in both prokaryotes and eukaryotes. Apart from this we also describe the role of 
telomerase in maintaining the length of linear chromosomes of eukaryotes.  
Initiation of DNA replication 
As already described, for replication to take place both the strands of a double helix unwind 
by the action of helicases and each strand serves as the template for the synthesis of 
complementary strand. These sites from where the unwinding of DNA starts are known as 
origin of replication. In case of prokaryotes, there is generally a single origin of replication 
while eukaryotes have multiple origins of replication. These origins are generally at internal 
regions of the chromosomes. These internal regions bind a number of protein factors that 
direct the initation of DNA replication.  
The Replicon Model 
In order to explain the regulation of DNA replication in bacteria, François Jacob, Sydney 
Brenner and François Cuzin in 1963 proposed the replicon model. A replicon was defined 
as the DNA that is replicated from a particular origin of replication. According to this model, 
two basic elements are required to initiate the DNA replication: replicator and initiator. A 
replicator is defined as a cis-acting genetic element that is required to direct the initiation 
of DNA replication. All known replicators consist of a binding site for the initiator protein and 
AT-rich stretch of DNA. The origin of replication generally is a part of replicator. E. coli has a 
single replicator (OriC) that consisted of two repeated motifs, 9-mer motif that is repeated 
five times and 13-mer motif that is repeated three times (Fig. 1 (A)). The 9-mer motif 
serves as the binding site for the initiator protein and 13-mer motif is the site of unwinding 
DNA. In case of yeast, three sequence motifs are present: A, B1 and B2 (Fig. 1 (B)). While 
A and B1 serve as the binding site for initiator, B2 represents the site from where the 
unwinding of DNA starts. The overall structure of a replicator from different organism is 
found to be same despite sequence diversity.  
 
Page 4


Models of DNA synthesis 
Institute of Lifelong Learning, University of Delhi 
 
 
  
 
 
 
Lesson: Models of DNA synthesis 
Lesson Developer: Dr. Devi Lal 
College/ Department: Department of Zoology, Ramjas College, 
University of Dekhi  
Reviewer: Dr. Neeraj Sood 
college/ Department : Department of Zoology, Dyal Singh College, 
University of Delhi 
 
 
 
 
 
 
 
 
 
Models of DNA synthesis 
2 
 
 
Table of Contents   
Chapter: Models of DNA synthesis 
 Topic         Page No.                                                       
Introduction……………………………………………………………………………………………………..3 
Initiation of DNA replication ………………………………………………………………………………………………………….3.  
The Replicon Model………….………………………………………………………………………………………………………………………….3 
Regulation of DNA replication  
Regulation of DNA replication in E. coli……………………………………………………..4 
Regulation of DNA replication in eukaryotes……………………………………………4 
Overview of DNA replication  
Overview of DNA replication in prokaryotes…………………………………………….5 
Overview of DNA replication in eukaryotes……………………………………………..8 
End replication problem  
Telomeres and Telomerases…………………………………………………………………….9  
Role of Telomere binding proteins………………………………………………………….11 
Priming protein……………………………………………………………………………………….12 
Replication model for other circular DNAs 
Rolling circle replication………………………………………………………………………….12 
D-loops and mitochondrial DNA replication…………………………………………..13 
Summary………………………………………………………….…………………………………………………….…14 
Exercise/ Practice………………………………………………………….………………………………………….15 
Glossary………………………………………………………….………………………………………………………….19 
References/ Bibliography/ Further Reading…………………………………………….19 
Web links………………………………………………………….……………………………………………………….20 
Answers………………………………………………………….………………………………………………………….20 
 
Models of DNA synthesis 
3 
 
 
Introduction 
The previous unit describes the enzymes and the general principle of DNA replication. The 
enzymes and general machinery for replication is more or less same in both prokaryotes 
and eukaryotes with slight differences. In this unit we will learn about the modes of DNA 
replication in both prokaryotes and eukaryotes. Apart from this we also describe the role of 
telomerase in maintaining the length of linear chromosomes of eukaryotes.  
Initiation of DNA replication 
As already described, for replication to take place both the strands of a double helix unwind 
by the action of helicases and each strand serves as the template for the synthesis of 
complementary strand. These sites from where the unwinding of DNA starts are known as 
origin of replication. In case of prokaryotes, there is generally a single origin of replication 
while eukaryotes have multiple origins of replication. These origins are generally at internal 
regions of the chromosomes. These internal regions bind a number of protein factors that 
direct the initation of DNA replication.  
The Replicon Model 
In order to explain the regulation of DNA replication in bacteria, François Jacob, Sydney 
Brenner and François Cuzin in 1963 proposed the replicon model. A replicon was defined 
as the DNA that is replicated from a particular origin of replication. According to this model, 
two basic elements are required to initiate the DNA replication: replicator and initiator. A 
replicator is defined as a cis-acting genetic element that is required to direct the initiation 
of DNA replication. All known replicators consist of a binding site for the initiator protein and 
AT-rich stretch of DNA. The origin of replication generally is a part of replicator. E. coli has a 
single replicator (OriC) that consisted of two repeated motifs, 9-mer motif that is repeated 
five times and 13-mer motif that is repeated three times (Fig. 1 (A)). The 9-mer motif 
serves as the binding site for the initiator protein and 13-mer motif is the site of unwinding 
DNA. In case of yeast, three sequence motifs are present: A, B1 and B2 (Fig. 1 (B)). While 
A and B1 serve as the binding site for initiator, B2 represents the site from where the 
unwinding of DNA starts. The overall structure of a replicator from different organism is 
found to be same despite sequence diversity.  
 
Models of DNA synthesis 
4 
 
13-mer  repeated motifs 9-mer  repeated motifs
245 bp
100 bp
A element B1 element B2 element
(A)
(B)
 
Fig. 1. The structure of replicator from (A) E. coli showing 13-mer motif (repeated three 
times) and 9-mer motif (repeated five times) and (B) yeast showing three sequence motifs: 
A, B1 and B2 (Source: Author). 
 
Initiator is defined as a trans-acting protein that recognizes and binds with the initiator 
and recruits other proteins required for replication. Some initiators also function to distort 
DNA that results in initial unwinding of DNA duplex. Initiator proteins are the only sequence-
specific DNA binding proteins involved in replication. All these proteins are ATP binding 
proteins that use energy from ATP hydrolysis. The initiator protein of E. coli is DnaA while 
in case of eukaryotes it is a six-protein complex known as origin recognition complex 
(ORC).   
 
Regulation of DNA replication  
DNA replication should be tightly regulated to ensure that each chromosome is replicated 
only once per cycle. Both prokaryotes and eukaryotes have evolved certain mechanisms 
that keep a check on DNA replication. While prokaryotes like E. coli depend on methylated 
state of their DNA, eukaryotes have tightly regulated cell cycle that ensures that DNA 
replication takes place only in S-phase of cell cycle.  
Regulation of DNA replication in E. coli 
Page 5


Models of DNA synthesis 
Institute of Lifelong Learning, University of Delhi 
 
 
  
 
 
 
Lesson: Models of DNA synthesis 
Lesson Developer: Dr. Devi Lal 
College/ Department: Department of Zoology, Ramjas College, 
University of Dekhi  
Reviewer: Dr. Neeraj Sood 
college/ Department : Department of Zoology, Dyal Singh College, 
University of Delhi 
 
 
 
 
 
 
 
 
 
Models of DNA synthesis 
2 
 
 
Table of Contents   
Chapter: Models of DNA synthesis 
 Topic         Page No.                                                       
Introduction……………………………………………………………………………………………………..3 
Initiation of DNA replication ………………………………………………………………………………………………………….3.  
The Replicon Model………….………………………………………………………………………………………………………………………….3 
Regulation of DNA replication  
Regulation of DNA replication in E. coli……………………………………………………..4 
Regulation of DNA replication in eukaryotes……………………………………………4 
Overview of DNA replication  
Overview of DNA replication in prokaryotes…………………………………………….5 
Overview of DNA replication in eukaryotes……………………………………………..8 
End replication problem  
Telomeres and Telomerases…………………………………………………………………….9  
Role of Telomere binding proteins………………………………………………………….11 
Priming protein……………………………………………………………………………………….12 
Replication model for other circular DNAs 
Rolling circle replication………………………………………………………………………….12 
D-loops and mitochondrial DNA replication…………………………………………..13 
Summary………………………………………………………….…………………………………………………….…14 
Exercise/ Practice………………………………………………………….………………………………………….15 
Glossary………………………………………………………….………………………………………………………….19 
References/ Bibliography/ Further Reading…………………………………………….19 
Web links………………………………………………………….……………………………………………………….20 
Answers………………………………………………………….………………………………………………………….20 
 
Models of DNA synthesis 
3 
 
 
Introduction 
The previous unit describes the enzymes and the general principle of DNA replication. The 
enzymes and general machinery for replication is more or less same in both prokaryotes 
and eukaryotes with slight differences. In this unit we will learn about the modes of DNA 
replication in both prokaryotes and eukaryotes. Apart from this we also describe the role of 
telomerase in maintaining the length of linear chromosomes of eukaryotes.  
Initiation of DNA replication 
As already described, for replication to take place both the strands of a double helix unwind 
by the action of helicases and each strand serves as the template for the synthesis of 
complementary strand. These sites from where the unwinding of DNA starts are known as 
origin of replication. In case of prokaryotes, there is generally a single origin of replication 
while eukaryotes have multiple origins of replication. These origins are generally at internal 
regions of the chromosomes. These internal regions bind a number of protein factors that 
direct the initation of DNA replication.  
The Replicon Model 
In order to explain the regulation of DNA replication in bacteria, François Jacob, Sydney 
Brenner and François Cuzin in 1963 proposed the replicon model. A replicon was defined 
as the DNA that is replicated from a particular origin of replication. According to this model, 
two basic elements are required to initiate the DNA replication: replicator and initiator. A 
replicator is defined as a cis-acting genetic element that is required to direct the initiation 
of DNA replication. All known replicators consist of a binding site for the initiator protein and 
AT-rich stretch of DNA. The origin of replication generally is a part of replicator. E. coli has a 
single replicator (OriC) that consisted of two repeated motifs, 9-mer motif that is repeated 
five times and 13-mer motif that is repeated three times (Fig. 1 (A)). The 9-mer motif 
serves as the binding site for the initiator protein and 13-mer motif is the site of unwinding 
DNA. In case of yeast, three sequence motifs are present: A, B1 and B2 (Fig. 1 (B)). While 
A and B1 serve as the binding site for initiator, B2 represents the site from where the 
unwinding of DNA starts. The overall structure of a replicator from different organism is 
found to be same despite sequence diversity.  
 
Models of DNA synthesis 
4 
 
13-mer  repeated motifs 9-mer  repeated motifs
245 bp
100 bp
A element B1 element B2 element
(A)
(B)
 
Fig. 1. The structure of replicator from (A) E. coli showing 13-mer motif (repeated three 
times) and 9-mer motif (repeated five times) and (B) yeast showing three sequence motifs: 
A, B1 and B2 (Source: Author). 
 
Initiator is defined as a trans-acting protein that recognizes and binds with the initiator 
and recruits other proteins required for replication. Some initiators also function to distort 
DNA that results in initial unwinding of DNA duplex. Initiator proteins are the only sequence-
specific DNA binding proteins involved in replication. All these proteins are ATP binding 
proteins that use energy from ATP hydrolysis. The initiator protein of E. coli is DnaA while 
in case of eukaryotes it is a six-protein complex known as origin recognition complex 
(ORC).   
 
Regulation of DNA replication  
DNA replication should be tightly regulated to ensure that each chromosome is replicated 
only once per cycle. Both prokaryotes and eukaryotes have evolved certain mechanisms 
that keep a check on DNA replication. While prokaryotes like E. coli depend on methylated 
state of their DNA, eukaryotes have tightly regulated cell cycle that ensures that DNA 
replication takes place only in S-phase of cell cycle.  
Regulation of DNA replication in E. coli 
Models of DNA synthesis 
5 
 
In E. coli DNA replication is tightly controlled by two proteins: the initiator DnaA; and 
SeqA. Just before DNA replication, the A within every GATC sequence throughout the E. coli 
genome are methylated by Dam methytransferase. The initiator, DnaA with ATP bound to 
it, binds with these methylated sites and recruits other proteins required for replication 
initiation. The bound ATP is hydrolyzed to ADP after the initiation process, inactivating 
DnaA, so that it cannot initiate fresh round of DNA replication. Moreover, the rate of 
exchange of ATP with ADP is slow, further delaying the activation of DnaA.  
Once DNA replication takes place, the methylated sites are converted to hemi-methylated 
state (methyl group on only one DNA strand). This state of hemi-methylation is detected by 
a protein SeqA which binds to GATC sequences present near the OriC. This binding prevents 
the methylation by Dam methytransferase and also prevents the binding of the initiator 
DnaA, thus inhibiting the initiation of DNA replication. So, the two mechanisms exists in E. 
coli that prevent the unnecessary DNA replication making it a controlled phenomenon.  
 
Regulation of DNA replication in eukaryotes 
Like E. coli, mechanism also exists in eukaryotes that make sure that DNA is replicated once 
per cell cycle. These mechanisms prevent the entry into mitosis with incompletely replicated 
chromosomes or with extra chromosomes. However, the situation in eukaryotes is more 
complex as compared to prokaryotes because of the presence of many origin of replication. 
So tightly regulating the replication initiation from these origins is a challenge. In case of 
eukaryotes the process of replication initiation takes place in two phases: replicator 
selection and origin activation. The replication selection involves the identification of DNA 
sequences that will direct initiation. Replication selection occurs in G1 phase and involves 
the formation of pre-replicative complexes (pre-RCs). The assembly of pre-RCs involves 
four different proteins. The first protein is the initiator, ORC (origin recognition complex) 
which recognizes and binds with the replicator and recruits Cdc6 and Cdt1, helicase 
loading proteins. These three proteins then recruit the helicase Mcm2-7 complex. Pre-
RCs assemble in inactivated form and therefore no unwinding of DNA takes place until the 
cell reaches the S-phase of cell cycle.  
The activation of pre-RCs is mediated by two protein kinases: cyclin dependent kinase 
(Cdk) and Dbf4-dependent kinase (Ddk). These kinases are inactivated in G1 phase 
and therefore no activation of pre-RCs takes place during this phase. The kinases get
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FAQs on Lecture 3 - Models of DNA synthesis - Molecular Biology (DNA) by ILLL, DU - Biotechnology Engineering (BT)

1. What are the different models of DNA synthesis in biotechnology engineering?
Ans. There are three main models of DNA synthesis in biotechnology engineering: the conservative model, the semiconservative model, and the dispersive model. In the conservative model, the original DNA molecule serves as a template for the synthesis of a completely new DNA molecule, while the original remains intact. In the semiconservative model, the original DNA molecule is split into two strands, and each strand serves as a template for the synthesis of a new complementary strand. In the dispersive model, the original DNA molecule is also split into two strands, but the newly synthesized DNA strands contain a mixture of original and newly synthesized DNA segments.
2. How does the conservative model of DNA synthesis work?
Ans. In the conservative model of DNA synthesis, the original DNA molecule remains intact while a completely new DNA molecule is synthesized. The process begins with the separation of the two strands of the original DNA molecule. Each strand then serves as a template for the synthesis of a new complementary strand. Once the new strands are synthesized, they recombine with each other to form two complete DNA molecules, one consisting of the original strands and the other consisting of the newly synthesized strands.
3. Explain the process of DNA synthesis in the semiconservative model.
Ans. In the semiconservative model of DNA synthesis, the original DNA molecule is split into two strands, and each strand serves as a template for the synthesis of a new complementary strand. The process begins with the separation of the two strands of the original DNA molecule. Each separated strand then attracts the appropriate nucleotides to form a new complementary strand. This results in the formation of two DNA molecules, each consisting of one original strand and one newly synthesized strand.
4. How is DNA synthesized in the dispersive model?
Ans. In the dispersive model of DNA synthesis, the original DNA molecule is also split into two strands, but the newly synthesized DNA strands contain a mixture of original and newly synthesized DNA segments. The process begins with the separation of the two strands of the original DNA molecule. As the DNA strands separate, new nucleotides are attracted to each strand, resulting in the synthesis of new DNA segments. These newly synthesized segments contain both original and newly synthesized DNA. The final DNA molecules formed have a mixture of segments from the original DNA and newly synthesized segments.
5. Which model of DNA synthesis is widely accepted in biotechnology engineering?
Ans. The semiconservative model of DNA synthesis is widely accepted in biotechnology engineering. This model, proposed by Watson and Crick in 1953, has been extensively supported by experimental evidence. It accurately explains the process of DNA replication and is the basis for many molecular biology techniques, such as PCR (polymerase chain reaction) and DNA sequencing. The semiconservative model suggests that each new DNA molecule consists of one original strand and one newly synthesized strand, allowing for accurate replication and inheritance of genetic information.
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