Plasmids are small, circular DNA molecules that can replicate independently of the host chromosome. They are commonly used in molecular biology to clone and amplify genes. The summarized document describes the key functional elements found in yeast overexpression plasmids, including selection markers like URA3, origins of replication, promoters, and tags. It also summarizes how plasmids are constructed through molecular cloning and purified from bacteria using their unique physical properties like supercoiling and renaturation compared to host chromosomal DNA and proteins. Purification involves alkaline lysis to break open cells, neutralization to allow plasmid renaturation, and multiple wash steps on a silica resin column to isolate pure plasmid DNA.

1. Plasmids
Indispensable tools that allow molecular biologists to obtain
essentially unlimited amounts of a DNA sequence
Definition: Small circular extrachromosomal DNA molecules, that
replicate independently of the host chromosomes

2. How are plasmids constructed?
What functional elements are found in our yeast
overexpression plasmids?
How are plasmids purified?

3. GFP gene
This gene encodes green
fluorescent protein, which
glows in UV light
Kanamycin
resistance
gene
the enzyme
encoded by
this gene
stops the
antibiotic
kanamycin
from working
Origin of
replication
this is needed so
that the plasmid
can be copied,
using the
bacterium’s DNA
copying machinery
The plasmid

4. A Brief History of Plasmids
• Genetic evidence for the existence of plasmids initially
came from studies carried out in the laboratories of J.
Lederberg and W. Hayes in the early 1950s
• 1952:It was Joshua Lederberg who proposed the term
plasmid in 1952 for extranuclear structures that are able
to reproduce in an autonomous state.
• he word 'plasmid' was first coined by Joshua Lederberg
in 1952. He used it to describe 'any extrachromosomal
hereditary element'. Lederberg first used the term in a
paper he published describing some experiments he and
his graduate student Norton Zinder conducted on
Salmonella bacteria and its virus P22.
J. Lederberg, 1952, Physiol. Rev. 32, 403-430

5. • In the late 1950s, a number of laboratories took up the
study of plasmids once the discovery was made that
extrachromosomal antibiotic resistance (R) factors are the
responsible agents for the transmissibility of multiple
antibiotic resistance among the enterobacterial
• The earliest studies on R plasmids, carried out mainly by
scientists in Japan (8), and the pioneering work on
colicinogenic (Col) plasmids by P. Fredericq of Belgium in
the mid-1950s (9) resulted in the identification of a variety
of naturally occurring plasmids that, subsequently, were
analyzed in the 1960s for the plasmid properties of
autonomous replication, mobility, incompatibility, and host
range.

6. • The list of plasmids available for study during this
period was augmented significantly by the
isolation by several laboratories of F-prime
factors from E. coli strains that carried a
chromosomally integrated form of the F factor
(10).
• The detailed genetic analysis of these F-prime
plasmids contributed greatly to our
understanding of the chromosomal state of a
plasmid and the mechanics of chromosomal gene
transfer from donor to recipient bacterium

7. • have no distinct 5’ or 3’ beginning or end.
• double-stranded DNA molecules
• ranging from a few to several hundred
kilobases
• provide one or more benefits to the host
such as resistance to antibiotics,
degradative functions, and virulence.

8. The structure of a plasmid

9. The structure of a plasmid
• Origin of replication (OR),
antibiotic resistance gene
(ARG) and multiple cloning
site (MCS).
• between 1 to more than
1,000 kbp

10. • The final breakthrough came in 1973, when the
first artificial plasmid was constructed by Boyer
and Cohen. By then, scientists had discovered
that special proteins, known as restriction
enzymes, could “cut” DNA by cleaving its
intramolecular bonds. Particularly, Boyer has
isolated a restriction enzyme, EcoRI 1, which
could recognize and cut a particular sequence
of DNA to produce unpaired DNA bases on one
strand, known as “cohesive end” or “sticky end”
(Figure 1) [3].

11. Plasmids used in molecular biology have been constructed in the lab
Molecular cloning
Enzymes are used to insert desired
pieces of foreign DNA into plasmids
Bacterial cells are transformed with
the plasmids. Copies of the
plasmids are purified from bacteria.

12. Shuttle vectors have origins of replication and selectable markers
for propagation in both bacteria and yeast
We are using plasmids that have been termed shuttle vectors,
because they can be propagated in either bacteria or yeast
Plasmids are propagated in
bacteria, which grow quickly
and maintain multiple copies
of the plasmids
non-pathogenic strain
of Escherichia coli
Saccharomyces cerevisiae
deletion strains
Plasmid-encoded genes
are expressed in yeast,
and phenotypes are
analyzed

13. How are plasmids constructed?
What functional elements are found in our yeast
overexpression plasmids?
How are plasmids purified?

14. 1 URA3
2 β-lactamase gene
3 pBR322 ori
4 yeast 2 µm origin
5 GAL1 promoter
6 C-terminal tags
1
2
3
4
5 6
ORF goes
here
*Plasmid names begin with a lower case “p”
The pBG1805*-derived plasmids are complex vectors designed
to express S. cerevisiae ORFs

15. pYES2.1-based plasmids used for S. pombe ORFs have many
elements in common with pBG1805-based plasmids
pYES2.1 (5886 bp)
used for S. pombe ORFs
1
2
3
4
5
7
2
1 3
4
5
6
URA3
β-lactamase gene
pBR322 ori
yeast 2 µm origin
GAL1 promoter
C-terminal tags
7
pBG1805 (6573 bp)
used for S. cerevisiae ORFs
1
2
3
4
5 6
ORF goes
here ORF goes
here

16. How are plasmids constructed?
What functional elements are found in our yeast
overexpression plasmids?
How are plasmids purified?

17. Plasmids are much smaller than bacterial
chromosomes
Plasmids are supercoiled in their native form
Supercoiling allows plasmids to renature quickly
after they are denatured
Plasmid purification is based on their distinctive
physical properties
Plasmids used in molecular biology are highly engineered and
contain elements of use to researchers

18. Plasmid purification from bacteria relies on their unique
physical properties
Bacterial cell with
plasmids
contains
MANY different,
well-folded proteins
1-2 copies of large
(>Mbp) , circular
bacterial DNA
complexed with
proteins
Multiple copies of small
(5-15 kbp) plasmids
Purification involves sequential denaturation and renaturation steps

19. Cells are first treated with base and a detergent
breaks open membrane
and denatures both DNA
and proteins
Proteins denature
irreversibly
Chromosomal DNA
denatures—will have
difficulty renaturing
because of its length
and many proteins
complexed to it
Plasmids denature, but
strands stay together
because of supercoiling

20. Extract is neutralized to allow DNA molecules to renature
Plasmids
renature and are
suspended in the
SUPERNATANT
following
centrifugation
Proteins and
chromosomal DNA form
aggregate irreversibly,
forming a PRECIPITATE
that can be collected by
centrifugation
When purifying plasmids, use a micropipette to remove the
supernatant for further processing steps

21. Zyppy purification kit use multiple steps to purify plasmids
Alkaline lysis
Neutralization
Purification of plasmid DNA on a silica resin
Elution of purified DNA from he silica resin
Let's look at the individual steps……………..

22. 1 Transformed E. coli cultures are
concentrated by centrifugation
2. The cell pellet is resuspended
in 600 µL TE buffer by vortexing
3. 100 µL of 7X Blue Zyppy lysis buffer
is added
0.1 N NaOH in buffer lyses the cells
GENTLY mix the contents by inverting the tube 4-6 times
Solution changes from cloudy to clear when cells are lysed
Warning: too much mechanical agitation can shear chromosomal DNA
Alkaline lysis

23. Neutralization
4. Add 350 µL yellow Zyppy
Neutralization buffer
Mix by inverting several times
A heavy precipitate will begin to form immediately!
The initial “glop” will become more granular when
neutralization is complete—but don’t overdo it!
The precipitate contains denatured proteins and
the denatured chromosomal DNA.
5. Spin down the denatured molecules
for 3 minutes at top speed. CAREFULLY
remove the supernatant containing the
plasmid – Don't be greedy! Purity is
preferred to yield!

24. Purification on
Zyppy silica resin
6. Apply the supernatant to the spin
column. Place the column in the
collection tube. Centrifuge the column
for ~15 seconds at top speed.
7. Discard the flow through in the
collection tube. Add 200 µL Zyppy
EndoWash. Centrifuge ~15 sec.
EndoWash contains guanidine
hydrochloride and
isopropanol. It removes
contaminating proteins that
are bound to the resin.
8. Discard the flow through in the
collection tube. Add 400 µL Column
Wash. Centrifuge 1 min.

25. Plasmid Elution
9. Transfer the column to a clean,
LABELED microcentrifuge tube
10. Add 50 µL TE buffer directly on
top of the column. Allow the column to
stand upright in the test tube for ~10
min. (Plasmid is being eluted.)
11. Spin the column for 30 seconds.
Plasmid DNA will be collected in the
microcentrifuge tube. Pure plasmid DNA
collects here!