Lecture 54: Recombinant DNA and cloning

Office hours: This Thursday (4/15) 2-4 pm LG-126

Monday 4/26 2-4 pm

Note: I will be at a meeting out of town next week

Prep questions and all lecture notes (with additional notations)

will be posted by Friday

Today’s lecture: Text pp. 969-979

Preprinted lecture notes 115-132
Download from
http://biochem.med.ufl.edu/coursetemp.php?cid=44 or
http://www.mbi.ufl.edu/facilities/msg/bch4024-notes.html

Enzymes for DNA analysis and molecular cloning

¾ Restriction endonucleases
fragment the DNA into defined segments
¾ DNA Ligase
joins DNA fragments
¾ DNA polymerase
Synthesizes DNA based on a template
Fills in gaps in DNA
¾ Reverse transcriptase
Copies RNA into DNA Æ “cDNA”
¾ Ribonucleases (endo and exo) Æ Å
5’ 3’
¾ RNA polymerase
¾ Terminal transferase
For radiolabeling
¾ Polynucleotide kinase
For radiolabeling
¾ Alkaline phosphatase
To remove phosphate; 3’ or 5’

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 Restriction endonucleases
¾ Cleave DNA in a sequence-specific manner
¾ Evolved as a defense mechanism against infection by foreign
DNA
¾ Different restriction enzymes in different organisms
¾ Protect host DNA by modification-methylation
¾ Nomenclature: EcoRI

Genus Species Strain Enzyme number

¾ Many restriction enzymes recognize “palindromic” sites

EcoRI cuts: 5’—GAATTC—3’

3’—CTTAAG—5’
To yield:
5’—G-OH and 5’—ATTC—3’
3’—CTTAA—5’ HO-G—5’

¾ EcoRI will not cut at this site if the Adenine is methylated, as

a means of protecting its own DNA from being digested.
5’—GAAmTTC—3’ will not be cut by EcoRI
3’—CTTAmAG—5’

Digestion of DNA
¾ Digestion of a particular DNA gives specific, “invariant”
fragments of characteristic size
¾ Example: 3.2 Kbp DNA
700 bp 2000 bp 500 bp
5’--------ATGAATTCCA--------GCCGAATTCTTT---------3’
3’--------TACTTAAGGT--------GCCGTTAAGAAA--------5’

EcoRI
Restriction fragments of 2.0, 0.7, 0.5 Kbp
1900 bp
0 bp
CTAGAATTCTA
160 GATCTTAAGAT
4.1 Kbp AAAG
Circular DNA C
TTTC TTAAGA
GA
GCTG CT GAAT
TCT
G AC
GCG 600 bp

EcoRI
Restriction fragments of 1.9, 2.2 Kbp (Linear!)

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 Size-separation of DNA molecules and fragments by Electrophoresis

Rate of DNA MIGRATION is inversely proportional to length

¾ Size of DNA
¾ Concentration of Agarose
¾ Conformation of DNA
¾ Applied voltage

(+) (-)
C L

Circular + Linear

Linear λ fragment with insert

Linear 3.2 Kbp λ fragment

λ HinD III Digest

0.5 2.3 4.4 23

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 Restriction Mapping of a 6 Kbp linear DNA fragment
--digested with various restriction enzymes

23.1
9.4
6.0 5.4
6.5
4.4 3.5
3.9
3.5 3.3 3.3 3.3
2.8
2.5 2.5
2.3 2.1 2.1 2.1
1.9 2.0 2.0 2.0
2.0 1.9 1.4
1.4 1.4
0.6 0.6 0.6 0.7 0.7 0.7 0.7
0.5 0.6 0.5
PvuII/PstI

PstI

PstI/EcoRI
PstI/HinDIII
Uncut

PvuII/EcoRI

EcoRI
PvuII/HinDIII

HinDIII

HinDIII/EcoRI
PvuII
HindIII λ DNA
“marker”

Resulting physical map

EcoRI HinDIII PstI EcoRI PvuII
0 6.0
0.7 2.1 3.5 4.0 5.4

Hybridization (probing) of nucleic acids

DNA to DNA hybridization

Southern Blotting

Northern Blot: DNA to RNA hybridization

(p. 123)

mRNA
(Ethidium bromide staining)
Electrophoresis
Denature, blot
Blot

DNA probe

Wash extensively Hybridization

Radioautograph

Labels: 32P, 35S, ELISA, Fluorescent

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 DNA – Protein interactions
“Footprinting”

* *

DNA Sequencing by Sanger Dideoxynucleotide method

1) Single stranded template (M13

vector)
2) Synthetic oligonucleotide primer
3) DNA polymerase; elongation in
presence of dideoxy NTP
synthetic primer

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 Recombinant DNA and cloning
A. Introduction
“Cloning” is a way to isolate a specific DNA fragment (a “gene”) and
produce it in a pure form in large amounts. Cloning makes detailed
analysis possible that would otherwise be difficult or impossible without the
gene in pure form, separated from the rest of the DNA of the organism.

Cloning comprises techniques that provide a powerful approach for

1. Understanding eukaryotic genes
2. Providing large scale production of scarce proteins, e.g. peptide
hormones, insulin
3. Controlled alteration of genetic composition of cells

B. Cloning specific DNA fragments

1. Some definitions and concepts
a. Cloning vectors….usually plasmids, DNA molecules capable of
autonomous replication (circular)
b. Foreign DNA…fragment to be studied, that is not originally part of
the cloning vector
c. Recombinant DNA…DNA molecules constructed in vitro, consisting
of DNA from 2 or more sources (i.e. cloning vector with foreign
DNA inserted)

2. Steps in Cloning
a. Cut cloning vectors with a restriction
endonuclease
b. Cut out a piece of foreign DNA with the
same (or compatible) restriction
endonuclease
c. Join the foreign DNA to the vector using
DNA ligase
d. Introduce the recombinant vector into cells
(transfection, transformation) in which they
can replicate
e. Identify and isolate cells that contain the
recombinant vector. From these, other
cells (or clones) may be otained.
3. Cloning vectors
a. Bacterial plasmids: pBR 322, p SP6
b. Bacterial viruses: λ gt 11
c. Animal virsuses: SV40
4. Plasmids
a. Small circular ds DNA molecules
b. Contain genes for antibiotic resistance, to
allow selection by growth on media
containing (lacking) antibiotics
c. Contain several restriction sites
d. Can be replicated (amplified) in bacteria

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 5. Example: pBR322 (4362 bp)

Cut with chosen restriction endonuclease

Incorporation of foreign
DNA inactivates tetR gene

Recombinant plasmid has

1) Foreign DNA
2) 2 HindIII sites
3) Split tetR gene so
plasmid is ampR but tetS

Alternative plasmid (in photocopy book) has

1) Foreign DNA
2) 2 PstI sites
3) Split ampR gene so plasmid is ampS but tetR

6. Introduction of recombinant plasmid into E. coli

4° + Ca2+ Æ 42° Æ 37°

to raise efficiency of transformation (10-6 Æ 10-2)

7. Select bacteria with recombinant plasmid by

growth on media containing both tetracycline and
ampicillan as well as media lacking the antibiotic
for the split gene

8. Obtain clones from single cells (+amp)

1 cell

109 cells (~3 plasmids / cell) (-tet) (+tet)

chloramphenicol (blocks protein synthesis on

bacterial ribosomes)

109 cells (~ 1000 plasmids / cell)

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9. Isolation of cloned fragment
a. Concentrate bacteria with recombinant plasmid
b. Lyse
c. Differential precipitation of plasmid DNA
d. Cut out foreign DNA with Pst I or HindIII
e. Separate plasmid and foreign DNA on agarose gel
(+) (-)

HindIII or PstI

uncut
C. Expression of foreign genes in E. coli
1. Expression vectors
Vectors with a regulated bacterial promotor (eg β Gal) upstream from insertion site

Can construct plasmids that contain sequences causing expressed proteins to be

secreted (to minimize degradation)
Insert

Promoter transcription

2. Limitations of Eukaryotic gene expression in bacteria

a. No splicing. Genes with introns cannot be expressed properly.
Can be circumvented by using cDNA
b. Bacteria cannot process of modify eukaryotic proteins (e.g.
glycosylation, phosphorylation)
c. Codon usage varies
3. Examples of eukaryotic proteins produced in E. coli
a. Somatostatin
b. Human growth hormone
c. Insulin (now mostly produced in yeast cells)
d. Interferons
D. Construction of cDNA (complementary DNA) from mRNA

5’ mRNA 3’
AAAAAAA
Anneal oligo (dT) primer
5’ AAAAAAA
3’ TTTTTTT 5’
Reverse transcriptase
mRNA
5’ AAAAAAA
3’ TTTTTTT
ss cDNA

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 mRNA
5’ AAAAAAA
3’ TTTTTTT
ss cDNA

Remove RNA or degrade with Rnase H

Reverse transcribe to make second strand of DNA
or use DNA Pol. I

ds cDNA

Other tricks
Can add tails (oligo C, G) with terminal transferase or add “linkers”
with ligase to facilitate coupling with vector DNA

Foreign DNA can be inserted behind different promoters which are

responsive to different regulatory signals

Site-directed mutagenesis:
The ability to change individual
codons or groups of codons in
expressed coding sequences.

Primer contains one (or only a few)

mismatched bases

Extend primer with DNA pol., ligate to

generate ds DNA with one (or a few)
mismatches

Replication of primer strand will introduce

mutation at the site of the mismatch.
Variations of this procedure are used to alter
amino acids at active sites of enzymes (one at
a time), to introduce new restriction enzyme
cleavage sites and other directed, specific
alterations

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 Applications of Recombinant DNA technologies
A. Construction of genetic “libraries” to assist in isolation / characterization of specific
genes and gene products:
cDNA libraries / expression libraries
genomic DNA libraries
cosmids
YAC’s (yeast artificial chromosomes)
Human Genome Project (and others…..)
B. Production of scarce proteins using expression vectors
C. Production of vaccines, hormones, blood clotting factors, etc.
D. Diagnostics: antibody and oligonucleotide probes:
cancer cells, detection / imaging
bacterial and viral diseases (Legionnaires, AIDS)
Prenatal diagnoses
Forensics
E. Therapeutics
Human insulin, Human growth hormone, interferons, growth factors, blood clotting
factors, Plasminogen activator, tumor necrosis factor, novel recombinant antibodies,
synthetic peptides as recombinant vaccines (Hep B, malaria, rabies, AIDS)
F. Gene Transfer
Plants---increased yield, improved tolerance, herbicide res., disease res.
Transgenic animals---production of scarce proteins (eg in cow’s milk), studies of
eukaryotic gene regulation
Human gene therapy
p. 150

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