CHAPTER 2

Genomic DNA
vs.
Plasmid DNA

CHAPTER 2: Genomic DNA vs. Plasmid DNA

Introduction
All living organisms possess genomic DNA. Genomic DNA contains genes necessary
for the survival and normal function of each organism. These genes encode proteins such as
enzymes, receptors, and structural proteins. The size of genomic DNA varies, depending on
the species. The more complex the species, the more genomic DNA it usually has. Human
genomic DNA is made of 3 billion base pairs, which are organized into 46 chromosomes. The
genomic DNA of bacterium E. coli has "only" 4.6 million base pairs. Genomic DNA differs
among species not only in size, but also in shape. Most organisms, such as humans, have
linear genomic DNA. Bacterial genomic DNA is circular.
In addition to genomic DNA, most bacteria contain multiple copies of a smaller circular
DNA called plasmid DNA; also known simply as a plasmid or vector. In few bacteria, plasmid
DNA is linear. In this and future chapters, we will concern ourselves with circular plasmids. The
size of plasmids ranges usually from a few thousand to hundreds of thousands of base pairs.
Because plasmids are smaller than genomic DNA, they also contain fewer genes. If all of the
genes required for normal bacterial function and structure are located on genomic DNA, then
what is the role of plasmid DNA?
Sometimes bacteria are exposed to extreme conditions. In nature, microbes often
compete against each other for nutrients. They suppress the growth of other species, including
bacteria, by secreting antibiotics. However, most bacteria have also evolved defense
mechanisms against these same antibiotics. Genes that protect bacteria against antibiotics are
located on plasmids. These genes are called antibiotic-resistance genes, and they encode
enzymes that degrade antibiotics. Plasmids may also carry genes that enable bacteria to
survive in the presence of toxic heavy metals.
Another difference between genomic and plasmid DNA is that plasmids can be
exchanged horizontally from one bacterial cell to another. This transfer occurs between two
individual bacterial cells and does not involve cell division. Some plasmids may even be

CHAPTER 2: Genomic DNA vs. Plasmid DNA

transferred between different bacterial species. Genomic DNA, however, is only passed on
from a mother cell to daughter cells during cell division. This means that a trait carried by
plasmid DNA, such as antibiotic resistance, can quickly be spread within a bacterial population.
Plasmid DNA exists within a bacterial cell in multiple copies, and its replication is
independent of the replication of genomic DNA. High-copy plasmids occur within a single
bacterial cell in over 20 copies. Low-copy plasmids are present within a cell in less than 20
copies. Definitions of high- and low-copy plasmids may vary depending on the source of
information.
Note that both genomic and plasmid DNA are double-stranded.
Commercial plasmids
Plasmids play an important role in recombinant DNA technology. Scientists can put
genes of a species different from the bacteria into plasmid DNA and then introduce the modified
plasmid DNA into bacteria. These bacteria then produce the protein encoded by the foreign
gene in the plasmid. Plasmid DNA that contains a foreign gene (from another species) is called
a recombinant plasmid.
Plasmids that are commercially available from biotechnology companies have been
modified and do not have sequences identical to naturally occurring plasmids. However, all
commercial plasmids have several features in common:
1. A plasmid must have an origin of replication or ori. This is a short stretch of DNA at
which replication of the plasmid is initiated.
2. A commercial plasmid possesses an antibiotic-resistance gene. If this plasmid is
introduced into a bacterium, the bacterium will grow on a solid medium containing an
antibiotic. Any bacteria that didn't take up the plasmid will die in the presence of this

CHAPTER 2: Genomic DNA vs. Plasmid DNA

antibiotic. This allows us to select and propagate only those bacterial cells that contain the
plasmid.
3. A commercial plasmid has a multiple cloning site (MCS). The MCS contains many
different restriction sites. A restriction site is a unique DNA sequence that is
recognized by a specific restriction enzyme. After binding to the restriction site, the
restriction enzyme cuts the plasmid open at the unique restriction site. Both DNA strands
of plasmid are cut by the restriction enzyme, so the plasmid becomes linear. This
process is easily performed in a test tube. Once a plasmid has been opened, a foreign
gene can be "pasted" into the MCS. After this process, a commercial plasmid becomes
a recombinant plasmid.
4. Every commercial plasmid has a promoter, located upstream of the MCS. The promoter
is a short DNA sequence that is recognized by RNA polymerase. Binding of RNA
polymerase to the promoter is the first step in transcription of the foreign gene inside the
MCS.

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CHAPTER 2: Genomic DNA vs. Plasmid DNA

Multiple Cloning Site

promoter
Eco RV
Sal I
Amp

PLASMID

Eco RI
Bgl I
Bam HI
Xba I
Sac I

ori
R

Figure 2.1. Basic features of a plasmid. Amp is the gene that confers resistance to the
antibiotic ampicillin. Note that the MCS is downstream of the promoter. Eco RV through Sac I
are all unique restriction sites. Replication of the plasmid is initiated at the ori.

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