Biotechnology and Recombinant DNA

Introduction

History

Cutting and Splicing

Inserting Recombinant
DNA Into Cells

Selecting Transformants

Applications I
Altering Phenotypes,
Making Products

Applications II
Study and
Characterization of DNA

Ethics

Selecting Transformants

 

Positive Selection

Positive selection is pretty easy to do. Remember from the last chapter on microbial genetics that positive selection is a process that selects the mutant cells and rejects the nonmutant cells.

 

When you build a plasmid vector (or select one from the catalog) you just make sure the plasmid has a gene for at least one antibiotic resistance gene.

 

After you transform the cells, that is, induce the cells to take up the plasmid vector, you grow them on culture media containing the antibiotic that the anitbiotic-resistance gene protects against. Cells that have the vector (the transformants) are resistant to the antibiotic and grow, cells that didn't take the vector up aren't resistant and don't grow.

 

Blue White Screening

 

 

To do blue-white screening, you use a vector that contains the genes for ampicillin resistance (ampR) and the enzyme ß-galactosidase (lacZ). If you put the vector into cells by itself the cells will be resistant to ampicillin and will produce ß-galactosidase (which splits lactose into glucose and galactose).

 

The cloning site, or insertion site, is in the lacZ gene. This site is the sequence of nucleotides recognized by the restriction enzyme used to digest the DNA that contains the gene you want to clone.

 

Remeber that when foreign DNA and the vector are cut with the same restriction enzyme (assuming it produces sticky ends) the restriction fragments can insert into the vector (creating a recombinant vector).

 

Since the insertion site is in the lacZ gene any restriction fragment that manages to recombine with the vector will disrupt the lacZ gene and the plasmid can no longer code for ß-galactosidase. Like a really big insertion mutation.

 

 

So you mix the restriction fragments you got by digesting the foreign DNA with your restriction enzyme with the plasmid vector that you also digested with your restriction enzyme and pray for recombination to occur. And it will, pretty much. You'll have some plasmids that don't recombine with restriction fragments and end up reannealing with themselves but don't worry about that, we've got a way to identify those.

 

Next you mix your plasmid vectors that hopefully carry a restriction fragment with bacterial cells that are competent to take up foreign DNA, maybe zap 'em with some chemicals or electric current to help the process along, and pray for transformation. Of course, like we said earlier, nothing is 100% efficient, so you'll have some cells that don't take up the plasmid (and some cells will take up plasmids that reannealed without recombining with a restriction fragment) but don't worry about that, we've got a way to deal with those.

 

Now here's the screening/selection process: You plate the cells out on culture media that has ampicillin and something called X-gal in it. Cells that didn't take up the plasmid will die from ampicillin poisoning, so you can figure anything that grows has the plasmid.

 

OK, what about cells that took up plasmids that didn't have restriction fragments? Those cells are ampicillin resistant and produce ß-galactosidase. This is where the X-gal comes in.

 

X-gal is a chromogenic analog of lactose (5-bromo-4chloro-3-indoyl-ß –galactopyranoside) which produces a blue color when broken down by ß-galactosidase. If a cell has a plasmid without a restriction fragment the cell makes ß-galactosidase, which breaks down X-gal and causes the colonies to be blue.

 

If a cell has a recombinant plasmid (with a restriction fragment inserted in the middle of the lacZ gene) it can't make ß-galactosidase, so it can't break down X-gal, and colonies are white.

 

So clones containing foreign DNA are identifiable because the colonies they give rise to are white. The individual colonies can be tested for the desired gene product or, if you have a probe, identified by colony hybridization.

 

 

Probes

A probe is a labeled piece of DNA that is complementary to the sequence of DNA you are interested in - say the gene you are trying to put into cells.  The label allows you to visualize the probe (how? - I'll get to that in a minute).

 

If you mix the labeled probe with DNA that has a complementary nucleotide sequence, then denature ("melt") the DNA so that the strands separate, then allow the strands to reanneal (rehybridize, come back together to form double stranded DNA), the probe can bind to (hybridize with) its complementary sequence.

 

So where do you get the probe?  And how does the label work? 

 

You make the probe.  Or you order it from the DNA synthesis lab down the hall (or from a company that sells DNA probes).  A DNA synthesis machine can build short DNA molecules with whatever nucleotide sequence you desire.  There are other ways to make a probe, but let's just go with "order it".

 

 

How does the label work?  Well, you have a couple of options.  The way we always used to do it, back in the day, was to use 32P labeled nucleotides, that is, nucleotides with radioactive phosphorus as part of the sugar phosphate backbone.  Then we had to go through some manipulation to get the DNA on a piece of radiographic film, allow it to incubate long enough for the radioactive phosphorus to expose the film it beneath the labeled DNA, and develop the film.  I'll show you how that works when we talk about colony hybridization and Southern blotting.

 

The other option is to use a probe with fluorescent dyes attached.  Then you need a light source to excite the dye and a detector to pick up the fluorescence emitted when the dye is excited with the appropriate light source.

 

Colony Hybridization

 

 

This is a pretty quick way to look at a plate full of clones directly.  Look at the following figure and it pretty much explains how it works.

 

Your first consideration is that you don't want to destroy your master plate with all your clones, so you need a replica. We don't need a replica plate, like we did when we were talking about negative selection, because we don't need anything to grow to do colony hybridization.  What we really need is a replica map.  Fortunately we can simply transfer some of the cells from each colony on our master plate to a nitrocellulose filter in a way that keeps the original orientation of the colonies intact. 

 

The second thing to think about is being able to line the filter up with the master plate after you identify colonies with the DNA of interest (so you can go back and select the correct colonies from the master plate).  Just be sure to mark the nitrocellulose filter and the master plate in the same spot so you can match the colonies on the master platewith the cells you transferred to the filter after you probe the filter.

 

Of course you have to do the same with the filter and the x-ray film.

 

 

Introduction

History

Cutting and Splicing

Inserting Recombinant
DNA Into Cells

Selecting Transformants

Applications I

Applications II

Ethics