1. Section J Analysis and Uses of Cloned DNA J 1 Characterization of clones J 2 Nucleic Acid Sequencing J 3 Polymerase chain reaction J 4 Organization of cloned genes J 5 Mutagenesis of cloned genes J 6 Applications of cloning
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

2. J 1 Characterization of clones
Restriction mapping
Partial digestion
Labeling nucleic acid
Southern and northern blotting
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

3. Characterization
This process of characterizing a genomic or cDNA clone include: the  size,  restriction map,  transcribed sequence,  position,  polarity and  the sequencing of the insert DNA.
More experiments must be performed to verify that:
Predicted gene is actually transcribed into mRNA in some cells;
A expression gene: a predicted-size protein may be made in vivo;
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

4. Restriction mapping Sal1 19 kb 15 kb 9 kb Sal I Hand III 21 kb 7 kb
Size: The insert can be determined by agarose gel electrophoresis using markers. It is best to digest the DNA with a restriction enzyme
Orientation of the insert: It can be determined by digesting with two restriction enzymes. Fig. la illustrates the process for a EMBL3 genomic clone.
(long arm+insert+short arm)
Sal1
19 kb
15 kb
9 kb
Sal I
HindIII
Hand III
21 kb
7 kb
11 kb
4kb H S
Sal I + Hand III
6kb
2kb
5kb
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

5. Partial digestion
1. End-labeled DNA: Adding a radioactive nucleotide to one end of the DNA fragment producing an end-labeled molecule.
3kb 1k
2kb
4kb E
2. Total digestion of the unlabeled 10kb fragment with EcoRI gives 1, 2, 3 and 4kb pieces.
3. Partial digestion, with low EcoRI concentration, which can generate all possible fragments, shows additional bands of 6, 7 and 10 kb. Note 3, 4 and 6 kb can be generated in more than one way.
Total
Partial
Auto-radio
6kb
3kb
2kb
1kb
10kb
4kb
4. Auto-radiographed: if the partial digestion lane is auto-radiographed to show up only those end-labeled molecules, the pattern is 3, 4, 6 and 10 kb. This allows the map shown (size and orientation).
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

6. Labeling nucleic acid
Classification: DNA and RNA molecules can either be labeled:
End labeling: labeling at their ends
5'-End labeling: using polynucleotide kinase to add a radioactive phosphate to 5’-end of nucleic acids.
3'-End labeling:  using terminal transferase to add one or more nucleotides to the 3’-end of nucleic acids or  using polymerases to “fill in” the 3'-end with [-32P] dCTP.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

7. Labeling nucleic acid Uniform labeling: throughout the fragments
dsDNA is treated with a tiny amount of DNase I, which introduces random nicks along both strands. DNA polymerase I can find these nicks and remove dNTPs, then incorporate radioactive nucleotides.
Strand-specific labeling: one strand of the dsDNA.
Strand-specific DNA probes: for example, using single-stranded DNA obtained after cloning in an M13 phage vector;
Strand-specific RNA probes: using RNA polymerases such as SP6, T7 or T3 phage polymerases (see Topic H1).
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

8. Southern and northern blotting-I
Function and Name: Using labeled probe to hybridize and detect which DNA (or RNA) molecule on an agarose gel. Southern blots is for DNA and Northern blots is for RNA. The former is named after its inventor and the latter was named from the former one.
Procedure:
1. Agarose gel electrophoresis: to separate the nucleic acid molecules;
2. Denatured with alkali: only for DNA;
3. Transfer: then transferred the molecules to a nylon or nitrocellulose membrane. This is done by  capillary action,  electrotransfer,  vacuum transfer;
4. Hybridization: the nucleic acid must be hybridized to labeled probe;
5. Washing and baking: washing extensively and baking
6. Detection: usually by auto-radiography or antibody methods
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

9. Southern and northern blotting-II
Definition: The stringency is stability of the hybridized molecules. If the probe and target gene are 100% complementary in sequence, then we say this is a high stringency hybridization.
High stringency: high temperature and low salt is more stringent, as only perfectly matched hybrids will be stable;
Low stringency: If the stringency is too low, then the probe may lose its specialty, and bind to too many sequences.
Washing temperature: Washing step should be carried out at 12C below the theoretical melting temperature (Tm) of the probe and target sequences, using the formula:
Tm = 69.3C [% (G + C)] – 650/L
where L is the length of the probe molecule.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

10. Southern and northern blotting-III
Southern blots:  to find which parts of the genomic clone match a cDNA probe;  If the Southern blot contains genomic DNA fragments from the whole genome, the probe will give information about the size of the fragment;  and how many copies of the gene are present in the genome.
Northern blots:  to find the size of the mRNA and any precursors;  to determine if a cDNA clone used as a probe is full-length;  to determine if it is a family member of related transcripts;  to identify if a genomic clone has regions transcribed;  to find where these transcripts are made (what tissues the RNA is from).
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

11. J 2 Nucleic Acid Sequencing
The two main methods of DNA sequencing are (1) Maxam’s method: the end-labeled DNA is subjected to base-specific cleavage reactions prior to gel separation; (2) Sanger’s method: to uses di-dNTP as chain terminators to produce a ladder of molecules generated by polymerase extension of a primer.
A set of four RNases that cleave 3' to specific nucleotides are used to produce a ladder of fragments from end-labeled RNA. The PAGE analysis allows the sequence to be read.
Newly determined DNA, RNA and protein sequences are entered into databases (EMBL and GenBank).
Special computer software is used to search nucleic acid and protein sequences for the presence of patterns (e.g. restriction mapping).
The entire genome sequences of several organisms have been determined (viruses, bacteria and yeast, some plants and human). Often a genetic map is first produced to aid the project.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

12. J 3 Polymerase chain reaction
PCR
The PCR cycle
Template
Primers
Enzymes
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

13. PCR
Definition: If a pair of oligo-nucleotide primers can be designed to be complementary to a target DNA molecule such that they can be extended by a DNA polymerase towards each other, then the template bounded by the primers can be greatly amplified by carrying out cycles of  denaturation,  primer annealing and  polymerization. This process is known as the polymerase chain reaction (PCR).
The discovery of thermostable DNA polymerases has made the steps in the PCR cycle much more convenient.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

14. The PCR cycle Template Primers Taq polymerase
Denaturation: 95C (60s);
Annealing: 55C (30s)
Polymerization: 72C (60-90s) which will use up dNTPs in the reaction mix and requires Mg2+.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

15. The PCR cycle Molecules with correct length;
At the end of cycle 2, see Fig.1, some newly synthesized molecules with correct length exist. In subsequent cycles, these soon outnumber the original target molecules and increase two-fold with each cycle.
If PCR was 100% efficient, one pair of template,
PCR with 20 cycles are as an example:
 Molecules with non-correct length: 20 ×2 = 40 ssDNA;
 Molecules with correct length: = 2,097,112
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

16. Template
Number of the templates: It has been demonstrated that PCR can sometimes amplify as little as one molecule of starting template.
Source of the template: In principle, any source of DNA that provides one or more target molecules can be used as a template for PCR. This includes DNA prepared:
from blood, sperm or any other tissue;
from older forensic specimens;
from ancient biological samples;
in the laboratory from bacterial colonies or phage plaques as well as purified DNA.
Requirement of the template: Whatever the source of template DNA, PCR can only be applied if some sequence information is known in advance so that primers can be designed.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

17. Primers
Requirements of PCR primers:  They need to be about nt long and  to have similar G+C contents so that they anneal to complementary sequences at similar temperatures.
Length of target sequences:  Short target sequences amplify more easily, so often this distance is less than 500 bp, but, with optimization, PCR can amplify fragments over 10 kb in length.
Primer design:
The region to be amplified should be inspected for two sequences of  about 20 nt with a  similar G+C content;
If the PCR product is used to cloning, the primers had better include the same restriction sites within the 5'-ends.
They are designed to anneal on opposite strands of the target sequence so that they will be extended towards each other by addition of nucleotides to their 3'-ends.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

18. Enzymes
Source: Thermo-stable DNA polymerases which have been isolated and cloned from a number of thermo-philic bacteria are used for PCR.
Taq polymerase: The most common is Taq polymerase from Thermus aquaticus.
Feature: It survives during the denaturation step at 95 C for 1-2 min, having a half-life of more than 2 h at this temperature.
Disadvantages: Because it lacks 3' to 5' proofreading exonuclease activity (see Topics F1 and G1, Table1), Taq polymerase is known to introduce errors when it copies DNA roughly one per 250 nt polymerized. For this reason, other thermostable DNA polymerases with greater accuracy are used for certain applications.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

19. J 4 Organization of cloned genes
Mapping cDNA on genomic DNA
Primer extension
DNase I footprinting
Reporter gene
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

20. cDNA Organization
Organization: cDNA clones have a defined organization, especially those synthesized using oligo (dT) as primer.
Start codon: If the cDNA clone is complete, it must have an ATG start codon;
ORF: Open reading frame (ORF);
A residues: Usually a run of A residues is present at cDNA 3'-end;
Stop codon for transcription;
Regulate sequences of transcription.
Absent Sequences of the cDNA organization:
Introns;
Sequences upstream of the transcription start site;
Sequences downstream of the 3‘-processing site.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

21. Mapping cDNA on genomic DNA
Southern blotting: If restriction maps are available for both the genomic and its cDNA clones, an important experiment is to run a Southern blot using all or part of the cDNA as a probe.
Using all cDNA as probe: will show  which genomic restriction fragments contain sequences also present in the cDNA.
 These cDNAs may not be adjacent fragments in the restriction map if large introns are present.
Using one end of a cDNA as a probe: will indicate
 The polarity of the gene in the genomic clone.
 Some restriction sites are common in both clones but may be different distances apart. These can often help to determine the organization of the genomic clone.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

22. Primer extension
Purpose: This technique can determine the length of the 5'- and 3'-end of RNA transcripts.
Procedure: (p156 Fig. 2)
1. RNA-DNA hybridization: The probe is an antisense DNA. Annealing DNA primer, to form the RNA-DNA hybrids.
2. Primer extension: Using reverse transcriptase to extend the DNA primer in the 5' to 3' direction, from the site where it base-pairs on the target to where the polymerase dissociates at the end of the template.
3. PAGE analysis: The primer extension product is run on a gel next to size markers and/or a sequence ladder from which its length can be established.
RNA preparation 5’
Polymerase
+ dNTP
DNA primer
PAGE analysis
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

23. DNase I footprinting
Problem and solution:  Although gel analysis shows that a protein is binding to a DNA, it does not provide the sequence information of the binding site.  DNase footprinting shows the actual region of sequence with which the protein bends.
1. End-labeled DNA
2. Protein binding
3. DNase I partial
digestion
4. PAGE Analysis
5. Auto-radiography
- DNA binding Protein
+ DNA binding Protein
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

24. Reporter gene
Purpose: This technique can test if the promoter works or not.
Mechanism: When the promoter has been identified by sequencing, Sl mapping and/ or DNA-protein binding experiments, it is common to attach the promoter region to a reporter gene, to study its action and verify that the promoter has the properties being ascribed to it.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

25. J 5 Mutagenesis of cloned genes
Deletion mutagenesis
Site-directed mutagenesis
PCR mutanenesis
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

26. Deletion mutagenesis
Progressively deleting DNA from one end is very useful for finding the function of particular sequences.
EcoRI SacI KpnI BamHI XbaI SalI PstI SphI HindIII
XmaI
GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTT
CTTAAGCTCGAGCCATGGGCCCCTAGGAGATCTCAGCTGGACGTCCGTACGTTCGAA
MCS
insertion
SacI and bamH1
GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTT
CTTAAGCTCGAGCCATGGGCCCCTAGGAGATCTCAGCTGGACGTCCGTACGTTCGAA
GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTT
CTTAAGCTCGAGCCATGGGCCCCTAGGAGATCTCAGCTGGACGTCCGTACGTTCGAA
GAATTCG
CTTAAGC
Transcription and expression
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

27. Site-directed mutagenesis
Function: It is very useful to be able to change just one, or a few specific nucleotides in a sequence to test a hypothesis. Suspected amino acids in a protein could be changed by altering the cDNA sequence so that by a one nucleotide change an amino acid, the effect is examined by testing the function of the mutant protein.
Methods:
 Single-stranded template: Originally, site-directed mutagenesis used this method (it was created by subcloning in M13) and a primer oligonucleotide with the desired mutation in it. The primer was annealed to the template and then extended using a DNA polymerase, ligated using DNA ligase to seal the nick and the mismatched duplex transformed into bacteria.
 PCR mutanenesis: Because single-stranded template method is not very efficient and because subcloning in M13 to prepare single-stranded DNA is time consuming, much site-directed mutagenesis is now carried out using the polymerase chain reaction (PCR),
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

28. J 6 Applications of cloning
Recombinant protein
Genetically modified organisms
DNA fingerprinting
Medical diagnosis
Gene therapy
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

29. Applications
Importance of gene cloning: The gene cloning has made a great impact on the speed of biological research and it is increasing its presence in several areas of everyday life.
Applications: These include:
recombinant protein production;
genetically modified organisms;
DNA fingerprinting;
diagnostic kits
gene therapy
This topic describes some of these applications.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

30. Recombinant protein production
Purpose: Some proteins that are known to be missing or defective in various disorders. These include growth hormone, insulin, interferon, blood clotting factor VIII and so on. Production of protein from a cloned gene can solve these problems.
Main methods:
In bacteria:  Initially, production in bacteria was the only way available. cDNAs had to be linked to prokaryotic transcription and translation signals and inserted into multi-copy plasmids.  However, often the overproduced proteins were lacked eukaryotic post-translational modifications.
In eukaryotic cells:  Production in yeast or mammalian cell lines has helped greatly.  For example, the human factor VIII protein, which is administered to hemophiliacs (血友病), is produced in a hamster cell line which has been transfected with a 186 kb human genomic DNA fragment.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

31. Genetically modified organisms
Definition: Genetically modified organisms (GMO) are created when cloned genes are introduced into germ cells. In eukaryotes, if the introduced genes are from another organism, the transgenic plants or animals can be propagated by normal breeding.
Examples:
Transgenic plants: One example is a tomato that has had a gene of a ripening enzyme inactivated. The strain of tomato takes longer to soften.
Transgenic sheep: They produce valuable proteins in their milk. The desired gene requires a sheep promoter to be attached to ensure expression in the mammary gland.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

32. DNA fingerprinting
Definition: The Southern blots of genomic DNA with probes that recognize simple nucleotide repeats gives a pattern that is unique to an individual and can be used as a fingerprint.
Applications: For example
Maternity and paternity testing in humans;
To show pedigree in animals bred commercially.
Analysis:
Some of these bands will be in common with those of the mother and some with those of the father. The different patterns in individuals at each of these kinds of simple repeat.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

33. Medical diagnosis
Background: A great variety of diseases arise from mutation. In genetic disorders, individuals are born with faulty genes that cause the symptoms of the disorder. Many cancers arise due to spontaneous mutations in somatic cells in genes whose normal role is the regulation of cell growth.
Diagnostic kits: By using sequence information to design PCR primers and probes, many diagnostic kits have been developed to screen patients for these clinically important mutations.
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

34. Gene therapy
Definition: Attempts have been made to treat some genetic disorders by delivering a normal copy of the defective gene to patients. This is known as gene therapy.
Examples of the methods:
Defective virus: The gene can be cloned into a defective virus used as a vector that can replicate but not cause infection.
Bone marrow transplant: For treating some disorders, the bone marrow must be destroyed and is replaced with treated cells that have had a normal gene, or a protective gene, introduced.
Perspective: Gene therapy is in its infancy, but it seems to have great potential.
P53 gene
therapy
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences

35. That’s all for Section J
Section J: Analysis and uses of cloned genes
Yang Xu, College of Life Sciences