Recombinant DNA

Technology

Needles in Haystacks
How to find one gene in large genome? A gene
might be 1/1,000,000 of the genome. Three
basic approaches:

1. Polymerase chain reaction (PCR). Make

many copies of a specific region of the DNA.

2. cell-based molecular cloning: create and

isolate a bacterial strain that replicates a copy of
your gene.

3. hybridization: make DNA single stranded,

allow double strands to re-form using a labeled
(e.g. radioactive) version of your gene to make it
easy to detect.

Polymerase Chain Reaction

Based on DNA polymerase creating a second strand of DNA.

Needs template DNA and two primers that flank the region to be
amplified. Primers are short (generally 18-30 bases) DNA
oligonucleotides complementary to the ends of the region being
amplified.
DNA polymerase adds new bases to the 3' ends of the primers to create
the new second strand.
go from 1 DNA to 2, then 4, 8, etc: exponential growth of DNA from this
region
A key element in PCR is a special form of DNA polymerase from
Thermus aquaticus, a bacterium that lives in nearly boiling water in the
Yellowstone National Park hot springs. This enzyme, Taq polymerase,
can withstand the temperature cycle of PCR, which would kill DNA
polymerase from E. coli.

advantages:
rapid, sensitive, lots of useful variations, robust (works even with partly
degraded DNA)

disadvantages:
Only short regions (up to 2 kbp) can be amplified.
limited amount of product made

PCR Cycle

PCR is based on a cycle of 3

steps that occur at different
temperatures. Each cycle
doubles the number of DNA
molecules: 25-35 cycles
produces enough DNA to see
on an electrophoresis gel.
Each step takes about 1 minute
to complete.
1. Denaturation: make the
DNA single stranded by
heating to 94oC
2. Annealing: hybridize
the primers to the single
strands. Temperature varies
with primer, around 50oC
3. Extension: build the
second strands with DNA
polymerase and dNTPs: 72oC.

Other PCR Images

DNA Amplification in PCR

original DNA: very long
molecules with neither end
well defined. Number stays
constant in the PCR reaction:
no new ones are made.
initial PCR product made from
original DNA: has one end
defined by the primer, but the
other end is not well defined.
Copy number grows linearly.
all other PCR products have 2
ends defined by the primers,
so they have a constant length
and can be easily detected by
electrophoresis. Copy number
grows exponentially.

Electrophoresis

Separation of charged molecules

in an electric field.
Nucleic acids have 1 charged
phosphate (- charge) per
nucleotide. means constant chare
to mass ratio. Separation based
(mostly) on length: longer
molecules move slower.
Done in a gel matrix to stabilize:
agarose or acrylamide.
average run: 100 Volts across a
10 cm gel, run for 2 hours.
Stain with ethidium bromide:
intercalates between DNA bases
and fluoresces orange.
Run alongside standards of known
sizes to get lengths

PCR Applications
RT-PCR: use reverse
transcriptase to convert
messenger RNA into DNA,
then amplify it with PCR.
Anchor-primed PCR: use one
sequence-specific primer and
use a set of random primers
for the other end. For
example: 3 RACE-PCR
(Rapid Amplification of cDNA
Ends) uses an oligo-dT primer
to bind to the poly A tail of
mRNA and a universal primer
for the internal region.
Adding linkers to the primers
puts them into the amplified
DNA. Useful for cloning or
further PCR.

Allele-Specific PCR
For base change
mutations (single
nucleotide
polymorphisms).
Use a primer
whose 3 base
matches the
mutation. Will
amplify one allele
but not the other
because the 3 end
is not paired with
the template in the
wrong allele.

SSR Genetic Markers

. Microsatellites (Simple Sequence Repeats: SSRs). Used for mapping the human
genome--the main marker system used today.
SSRs are short (2-5 bases) sequences that are repeated several times in tandem:
TGTGTGTGTGTG is 6 tandem repeats of TG.
SSRs are found in and near many genes throughout the genome--they are quite
common and easy to find.
During normal replication of the DNA in the nucleus, DNA polymerase sometimes
slips and creates extra copies or deletes a few copies of the repeat.
This happens rarely enough that most people inherit the same number of repeats that
their parents had (i.e. SSRs are stable genetic markers), but often enough that
numerous variant alleles exist in the population.
Mapping SSRs is a matter of having PCR primers that flank the repeat region, then
examining the PCR products on an electrophoresis gel and counting the number of
repeats.
SSRs are co-dominant markers: both alleles can be detected in a heterozygote.
If an SSR is a 3 base repeat within the coding region of a gene, it will create a
tandem array of some amino acid. Certain genetic diseases, most notably
Huntington's Disease, are caused by an increase in the number of repeats: once the
number gets high enough the protein functions abnormally, causing neural
degeneration. Such SSRs are called "tri-nucleotide repeats" or TNRs.

SSR Example

Cell-Based Molecular Cloning

The original recombinant DNA technique: 1974 by Cohen and
Boyer.
Several key players:

1. restriction enzymes. Cut DNA at specific sequences. e.g.

EcoR1 cuts at GAATTC and BamH1 cuts at GGATCC.
Used by bacteria to destroy invading DNA: their own DNA has been
modified (methylated) at the corresponding sequences by a methylase.

2. Plasmids: independently replicating DNA circles (only circles

replicate in bacteria). Foreign DNA can be inserted into a plasmid
and replicated.
Plasmids for cloning carry drug resistance genes that are used for
selection.
Spread antibiotic resistance genes between bacterial species

3. DNA ligase. Attaches 2 pieces of DNA together.

4. transformation: DNA manipulated in vitro can be put back
into the living cells by a simple process .
The transformed DNA replicates and expresses its genes.

Plasmid Vectors

To replicate, a plasmid must be

circular, and it must contain a replicon,
a DNA sequence that DNA
polymerase will bind to and initiate
replication. Also called ori (origin of
replication).

Replicons are usually species-specific.

Some replicons allow many copies of
the plasmid in a cell, while others limit
the copy number or one or two.

Plasmid cloning vectors must also

carry a selectable marker: drug
resistance. Transformation is
inefficient, so bacteria that arent
transformed must be killed.
Most cloning vectors have a multiple
cloning site, a short region of DNA
containing many restriction sites close
together (also called a polylinker).
This allows many different restriction
enzymes to be used.
Most cloning vectors use a system for
detecting the presence of a
recombinant insert, usually the
blue/white beta-galactosidase system.

Basic Cloning Process

Plasmid is cut open with a restriction
enzyme that leaves an overhang: a
sticky end
Foreign DNA is cut with the same
enzyme.
The two DNAs are mixed. The sticky
ends anneal together, and DNA ligase
joins them into one recombinant
molecule.
The recombinant plasmids are
transformed into E. coli using heat
plus calcium chloride.
Cells carrying the plasmid are
selected by adding an antibiotic: the
plasmid carries a gene for antibiotic
resistance.

DNA Ligase in Action!

I hope

Cloning Vector Types

For different sizes of DNA:
plasmids: up to 5 kb
phage lambda () vectors: up to 50 kb
BAC (bacterial artificial chromosome): 300 kb
YAC (yeast artificial chromosome): 2000 kb

Expression vectors: make RNA and

protein from the inserted DNA
shuttle vectors: can grow in two different
species

Lambda-based vectors

Phage lambda can do 2 different things

when it enters the cell:

Lambda is about 50 kb long, and the central

20 kb is only used for lysogeny; it can be
replaced by foreign DNA.

lytic cycle: it can start reproducing itself

immediately, which produces about 200 new
phage in 15 minutes and kills the cell
lysogenic cycle: the lambda DNA can
integrate into the host chromosome and
remain dormant for many generations. When
given the proper signal, the integrated DNA
(prophage) leaves the chromosome and
enters the lytic cycle.

Ligation of arms with insert using DNA ligase

Packaged into phage particles in vitro using
extracts from cells that have contain pieces of
the phage heads.
Use these phage to infect new E. coli.

Cosmids are similar to phage vectors: use

lambda, but remove all but the ends (cos
sites), ori, and selectable marker. Package
in vitro--becomes a large (50 kb) plasmid in
the E. coli.

Bacterial Artificial Chromosomes

Based on the F plasmid that

confers the ability to conjugate.
Low copy number plasmids
(usually 1 per cell), which prevents
crossing over between repeated
sequences in the insert DNA
But, low copy number also means
low DNA yield.
Transformed into E. coli using
electroporation, subjecting the
bacteria to a high voltage
electrical field.
BACs are currently the most
common vector for large inserts
such as eukaryotic genome
projects.

Yeast Artificial Chromosomes

A linear chromosome, has
centromere, telomeres, ARS
(autonomously replicating
sequence), selectable marker
for yeast (uracil or tryptophan
biosynthesis genes usually).
Also has E. coli ori and
selectable marker: you can
grow the vector itself in E. coli
Then purify it, ligate in foreign
DNA, transform into yeast.

Expression Vectors
Various types:
RNA only: use a vector that has a phage T7 promoter in front of
the cloning site, and an inducible T& polymerase gene.
Induction by the lac operon repressor gene and the synthetic
inducer IPTG (isopropyl thiogalactoside).
polypeptide or fragments of polypeptides: can be produced in E.
coli using a ribosome binding site in addition to the promoter.
Need to use the correct reading frame.
can also be done as a fusion protein (your protein fused to a marker
protein) for easy detection or purification

post-translationally modified or intron-spliced protein: needs to

be expressed in eukaryotic cells. Needs eukaryotic promoter and
polyadenylation (poly-A addition) signals, plus a selectable
marker that works in eukaryotes (since most antibiotics are
specific for prokaryotes).

Example Expression Vector

For eukaryotic expression, this vector (from

Invitrogen) has a cauliflower mosaic virus
promoter (PCMV), a bovine growth hormone
polyadenlyation site (BGHpA).
The DNA inserted at hORF gets fused to a
short peptide called an epitope, for which
very specific anitbodies exist. It also gets
fused to 6 histidines, which allow easy
purification on a column that has nickel ions
bound to it (an affinity tag).
For growth in mammalian cells, it has an
SV40 viral origin of replication (SV40ori),
and a zeocin resistance gene (Zeocin, with
SV40 promoter/enhancer and SV40 poly A
site).
For growth in E. coli it has the ColE1
replicon. Zeocin works as a selectable
marker in baceria as well as in eukaryotic
cells.
There is also a T7 promoter for making RNA
from the inserted gene, and an f1 origin of
replication for making single stranded DNA
(useful for sequencing).

Sources of DNA to Clone

Genomic DNA: cut up whole genome and clone small pieces.

Advantage is, you get everything. Disadvantage is, a lot of it is junk.
Two general methods:
1. randomly shear DNA into small pieces, then ligate linkers to the ends:
oligonucleotides that contain a useful restriction site.
2. partially digest the DNA with a restriction enzyme that has a 4 base
recognition site. These sites will appear at random every 256 (44) base
pairs. Take long pieces.

cDNA: DNA copy of mRNA, made with reverse transcriptase.

Advantage: you just get the expressed genes. Disadvantages: you
don't get control sequences or introns, and frequency depends on
level of expression.

Synthetic DNA: synthesized de novo (for example multiple cloning

sites or linkers), or made by PCR

cDNA Synthesis
use oligo-dT primer,
which binds to poly-A
tail.
make the first DNA
strand from the RNA
using reverse
transcriptase

More cDNA Synthesis

Remove the RNA with
heat or alkali.
The 3 end
spontaneously forms a
small hairpin.
Extend the hairpin with
DNA polymerase
Cut eh loop with S1
nuclease (which cuts at
unpaired bases)
Attach synthetic
linkers with DNA ligase
and clone into a vector.

Libraries
A large number of clones, often pooled together (so you
have to fish out the one you want), but sometimes
ordered.
Genomic library vs. cDNA.
Genomic uses enough input DNA to cover the genome 5-10x, so
chance fluctuations don't prevent all sequences from being
cloned. Repeat sequence DNA is a problem.
cDNA libraries are usually made from single tissues: expression
varies between tissues. Large difference in expression levels,
often compensated for by normalizing the library: trying to
equalize copy number of different sequences.

detection of clones containing specific genes is generally

by hybridization with labeled probes. It can also be done
using antibodies if the genes in the library are being
expressed.

Hybridization
The idea is that if DNA is made single stranded
(melted), it will pair up with another DNA (or
RNA) with the complementary sequence. If one
of the DNA molecules is labeled, you can detect
the hybridization.
Basic applications:
Southern blot: DNA digested by a restriction enzyme
then separated on an electrophoresis gel
Northern blot: uses RNA on the gel instead of DNA
in situ hybridization: probing a tissue
colony hybridization: detection of clones
microarrays

Labeling
Several methods. One is
random primers labeling:
use 32P-labeled dNTPs
short random oligonucleotides
as primers (made
synthetically)
single stranded DNA template
(made by melting double
stranded DNA by boiling it)
DNA polymerase copies the
DNA template, making a new
strand that incorporates the
label.

Can also label RNA

(sometimes called riboprobes),
use non-radioactive labels
(often a small molecule that
labeled antibodies bind to, or a
fluorescent tag), use other
labeling methods.

Hybridization Process

All the DNA must be single stranded

(melt at high temp or with NaOH).
Occurs in a high salt solution at say
60oC. Complementary DNAs find each
other and stick. Need to wash off nonspecific binding.
Stringency: how perfectly do the DNA
strands have to match in order to stick
together? Less than perfect matches will
occur at lower stringency (e.g. between
species). Increase stringency by
increasing temp and decreasing salt
concentration.
Rate of hybridization depends on DNA
concentration and time (Cot), as well as
GC content and DNA strand length.
Autoradiography. Put the labeled DNA
next to X-ray film; the radiation fogs the
film.

Southern Blot

Used to detect a specific DNA

sequence in a complex mixture,
such as genomic DNA
Cut DNA with restriction enzyme,
then run on an electrophoresis
gel.
Suck buffer through the gel into a
nitrocellulose membrane. The
buffer goes through but the DNA
sticks to the membrane.
Fix the DNA to the membrane
permanently with UV or heat
Hybridize membrane to a
radioactive probe, then detect
specific bands with
autoradiography.
Northern blot uses RNA instead.
RNA must be denatured so the
distance it migrates on the gel is
proportional to its length: put
formaldehyde in the gel.

Restriction Fragment Length

Polymorphisms

RFLPs: the first DNA-based genetic

mapping technique. Advantage:
every individual has many variations
in their DNA, so you dont need a
special set of marker mutations.
Also, the markers are co-dominant so
you can accurately determine the
genotype.
Probe is a fragment of a cloned gene
(labeled).
Genomic DNA is cut with a restriction
enzyme.
Polymorphic sites: the restriction site
is present in some individuals but not
in others (due to mutation). But,
even if one site is missing, there will
be another restriction site a little
further away (a restriction enzyme
with a 6 base site cuts on the
average every 46 = 4096 bp).
Then do a Southern blot and
autoradiography.

Colony Hybridization
Bacterial colonies (or
phage plaques)
containing recombinant
DNA are grown on agar,
then blotted to
nitrocellulose and
hybridized as with
Southern blots.
The colonies on the agar
plates stay alive, and
once the correct colony
has been detected, it can
be picked and grown up
for further work.

In Situ Hybridization
Using tissues or tissue
sections.
Often done with nonradioactive probes
because the high energy
of 32P emission gives an
imprecise view of where
the hybridization is.
Counterstain the tissue
so non-hybridizing parts
are visible.

Microarrays

Place probes from many different genes

on a glass microscope slide, then
hybridize to cDNA made from messenger
RNA isolated from a tissue. You see
which genes are active in that tissue.
Mostly done with 60mers: 60 bases long,
synthetic oligonucleotides, made using
sequence information from the genes.
cDNA is fluorescently labeled
Often 2 conditions are compared (control
and experimental), using red and green
fluorescent tags.
Semi-quantitative
Can also be used to screen for DNA
mutations.