The white colonies will all be recombinants, but only one

Lecture 3 – Selection of Recombinants & clone analysis

The white colonies will all be recombinants, but only one of these many colonies will contain the gene you are interested in.

To identify a colony containing a specific cloned gene,you can use:

1) Hybridisation of colonies to specific probe sequences

2) Expression screening where you detect the product of the cloned gene.


Remember that to identify a colony containing a specific gene,you need to know SOMETHING about the gene.

DNA sequence

PROTEIN sequence

Hybridisation screening

Antibody screening

Polymerase Chain Reaction (PCR)


Hybridisation techniques rely on a probe sequence which is complementary to the cloned gene, or to a sequence in the genome.

How do you get the probe???

In order to get a probe, you need to know SOMETHING about the gene you are trying to find.

1) Protein sequence - you might have isolated the protein and sequenced it.

From the protein sequence, you can deduce the DNA sequence: Glu---Asp--Met--Trp--Tyr

GAA-GAT-ATG-AGG-TAT


The DNA sequence can be artificially made in a DNA synthesiser and used as a probe

Applied Biosystems DNA synthesiser


DNA hybridisation is based on the fact that the 2 strands of the double helical DNA are complementary:


The two strands can be separated by heating or alkali – the hydrogen bonds between the bases are broken, making two single stranded DNA molecules:


Complementary (probe) sequences can bind to the single strands:

How do you make DNA radioactive?



If the complementary probe sequences are radioactively tagged, the hybrid formed between the probe and the target will also be radioactive :

You now need to detect this radioactive hybrid, so that you canidentify the clone – this is done using Colony Hybridisation:



An actual colony hybridisation result :

Lecture 3 – Selection of Recombinants & clone analysisB1007 – Identifying and Studying Cloned Genes – Lecture 4

Once a clone has been identified as hybridising to the probe sequence, It has to be further characterised, by isolating plasmid DNA and mapping the insert. This procedure is called Restriction mapping, and identifies restriction enzyme sites.


By analysing the number and size of fragments produced by restriction enzyme cleavage, a “map” of the DNA fragment can be produced.

This map is unique, and defines the sequence which has been cloned.


Within the cloned sequence, there will be a part which contains the gene of interest, and a segment which does not. The easiest way of finding out which segment of the cloned sequence carries a gene is to use a technique called Southern blotting.

Southern Blotting was invented by Prof Ed. Southern of Edinburgh University and is a way of transferring DNA from a gel to a membrane, wherethey can be hybridised to radioactively tagged probe sequences

It allows you to precisely locate the fragment in your cloned sequence which contains the gene you are trying to isolate.

Lecture 3 – Selection of Recombinants & clone analysisSouthern Blotting.


Gel photograph Southern blot

Lecture 3 – Selection of Recombinants & clone analysisSouthern blotting also allows you to detect specific genes in a genome.

It is so sensitive that you can identify one gene out of the whole genome.

Restricted genomic DNA Autorad of genomic blot

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The white colonies will all be recombinants, but only one