LECTURE: STUDYING DNA

Study programme Bioinformatics, 2021

Student (name & family name):

Source: GENOMES4, AT BROWN

CHAPTER 2: STUDYING DNA
pages: 27-50.

2.1 Enzymes for DNA manipulation, their function

Notes/summary:

Explain figure:
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Describe the function of enzymes:

• DNA polymerases:

• Nucleases:

• Ligases:

• End-modification enzymes:

The mode of action of a template-dependent DNA polymerase

Explain figures:

a)
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

b)

c)

d)
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

The types of DNA polymerase used in research

Describe the function of polymerases:

• Kornberg polymerase:

• Klenow polymerase:

• Reverse transcriptase:

• Taq polymerase:

Restriction endonucleases enable DNA molecules to be cut at defined

positions

Notes/summary:
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Explain figure:

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LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Ligases join DNA fragments together

Notes/summary:

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LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

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End-modification enzymes

Notes/summary:

(Role of alkaline phosphatase and T4 polynucleotide kinase)

LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Explain figure:

2.2 The polymerase chain reaction

Notes/summary:

LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

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2.3 DNA cloning

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LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

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LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

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QUESTIONS

1. Describe how a DNA fragment containing a single gene of interest would be obtained
by (A) PCR or (B) gene cloning.
2. How can a researcher identify a single restriction enzyme fragment containing a gene
of interest in a digest of genomic DNA that contains thousands of different restriction
fragments?
3. Describe a useful and quick method for increasing the ligation efficiency of blunt-
ended DNA molecules.
4. How do the primers determine the specificity of a PCR?
5. Explain why bacterial plasmids are popular cloning vectors.
6. Distinguish between the ways in which antibiotic resistance and Lac selection are
used in identification of recombinant cloning vectors.
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Source: INTRODUCTION TO GENETIC ANALYSIS, GRIFFITHS ET AL.

CHAPTER 10: GENE ISOLATION AND MANIPULATION, different pages

DNA copies of mRNA can be synthesized, pages 358-359

(Construction of cDNA-complementary DNA)

Notes/summary:
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Explain figure:

Amplification of donor DNA inside a bacterial cell (pages 362-365)

Notes/summary:
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Explain figure:

Choice of clonning vectors (pages 363-365)

Notes/summary:

Describe (brief presentation):

• Plasmid vectors
• Bacteriophage vectors
• Vectors for larger DNA inserts (fosmids, BAC)
LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Making genomic and cDNA libraries (pages 366-367)

Notes/summary:

Using molecular probes to find ana analyze a cpecific clone of interest

(pages 367-370)

Notes/summary:

(Probes for finding DNA, Probes for finding proteins)

LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

Explain figure:

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LECTURE: STUDYING DNA
Study programme Bioinformatics, 2021

QUESTIONS:

1) Why was cDNA and not genomic DNA used in the commercial cloning of the human
insulin gene?
2) After Drosophila DNA has been treated with a restriction enzyme, the fragments are
inserted into plasmids and selected as clones in E. coli.

How would you identify a clone that contains DNA encoding the protein actin, whose
amino acid sequence is known?