martes, 9 de abril de 2013

Taq polymerase, or why basic research is not a waste of money

Sometimes the people don't understand what in the world we, the scientists, are doing. We send stuff to Mars or to the very bottom of the ocean; we take samples from sulfur ponds (o from the Tinto river) and we try to unveil the secrets of the moth's virus. The first-and more stupid-explanation, supported by the ones that know nothing about science, is that we deeply love useless things, so we spend the money of the government in that (and earning a huge income by the way).
Not long ago, Fabra (a Spanish politician) said that the government must only invest in the research with direct application. And many other people ask why don't we focus only in cancer or Alzheimer, instead of Tasmania's sea phytoplankton? I constantly hear "we have to research only in practical science".

A very clear example of why that point is wrong is exposed on my previous post about GFP (sorry, not in English yet). And now behold another example of the power of basic research.

Basic research is just to try to answer the questions that appear when we observe the universe: ¿how do the spiders make silk?, ¿why do the stars shine? ¿how do the living beings obtain their energy?, ¿why did the dinosaurs disappear?.... Without any other purpose than just know the answer, because we want to know the secrets of life, the universe and everything. Applied science, on the other hand, is looking for solutions to mankind problems, with the knowledge that provides the basic science. But, the process since the basic science starts to research something, until that thing can be applied in our technology, can take decades. So, cuts in basic science won't show consequences immediately, but within a decade our technology will stop moving forward: we didn't build the base.

To make this clear, I will tell you a story very well know in the scientific world, Taq polimerase.

Everything started with a question, as always, ¿which are the limits of life? Or, in other questions ¿what is the maximum pressure that can life stand?, ¿what is the maximum temperature that can life stand?... These questions led the scientist to seek all over the world: into the poles, volcanoes under water, sulfur springs...

Until the 60's we thought that 55ºC was the upper limit of life. But in National Yellowstone Park (among other places) were founded bacteria living in 80ºC water. In other places, another organisms were found and our knowledge about the limits of life was expanded. These new organisms were called "extremophiles", and the most awesome about this it is that the extremoplhiles can actually make all their biological functions (energy obtaining, reproduction...) in such extreme conditions.

But... ¿For what do we need that knowledge? extremophiles would be very interesting and so, but they won't be useful for our problems.

Well, scientists had a problem that prevents them to work as fast as they would like to. And that problem was DNA. As you may know, the DNA contains all information that makes cells and organisms operatives. So if we want to deeply study any aspect of a living being (and this include cancer, SARS, drug resistance...), we can't ignore this molecule. Is critical to know the sequence of DNA and we must be able to work with DNA.
We can obtain DNA directly from bacteria, tissues... but the amount of DNA is very, very small, and there we have de secuence of DNA we want (of an oncogenic protein, for example) mixed with other sequences we don't want. 

And for working at full capacity we must obtain more copies of our interest sequence of DNA. But there isn't any chemical method that allows us to copy DNA. First, the scientists used bacteria to make them copy the DNA sequence of interest, using plasmids (a molecule of circle DNA). You insert your sequence of interest in a plasmid (that have another sequences needed if we want the bacteria to copy it). Then you insert the plasmids in the bacteria and feed them. Every time the bacteria reproduces, make a copy of the plasmid. When you had enough bacteria, you just make them explode and extract the plasmids with the copies of your sequence.

¿And the problem is...? well is a very slow method and you depend on your bacteria, if they lose the plasmid or they die, all your work is lost. But it was widely used, because it was the only method, if we had to work with DNA.

The alternative was to copy the DNA without cells, using the proteins, nano-machines of the living cells, but for understanding that, we must know someting about the replication of DNA.

Every chain of DNA of a living being consists in two strands connected, one in front of the other. The strands are made with units called nucleotides. There are 4 nucleotides: adenine (A), thymine (T), cytosine (C) and guanine (G), they are complementary. In one chain, the nucleotides of one strand bind to the ones of the other strand, but this binding is specific: A only binds to the T; and C only binds to the G. So to copy a chain, one must separate the strands an build another ones using the originals as a template.

This is the way nature copy de DNA, but the problem for us is how to create the new strands from a template, because nucleotides don´t place themselves alone. We need an enzyme, the DNA polymerase,which creates new strands using templates. It only needs a double strand place to start copying.


Well and then, why don't we use polymerase with our DNA to make a lot of copies?

There are two main problems. First, as I said, the DNA polymerase needs a place with double strand to start copying. Buy this is easy to solve, we can use short sequences of nucleotides (oligos) made with organic chemistry, that will bind spontaneously to any sequence complementary. For example if the start of the template says A-T-G, we can use a sequence that says T-A-C and the binding between them will happen spontaneously.
But the most important problem is how to separate the two strands in order to allow the copy process. Cells use a very complex system that recognize specific sequences and open the chain of DNA, but is too delicate and complicated to use in vitro. The other way is the heat, at certain temperature (70ºC-90ºC) the DNA strands unbind and break free. But at that temperature, the polymerase is destroyed. It seems that we are in a dead end.

But we are lucky, because of someone took the task of study microbes that had, aparently, no practical interest, and we know that they can live above 70ºC, so they must have a polymerase that can copy DNA at that temperature without be destroyed. And, because of somenoe studied them deeply we know the secuence of DNA of that heat-resistent polymerase, and now, we can introduce it into a bacteria that growth a lot in order to produce it and make millions of heat-resistent polymerase that can be used in all laboratories all over the world, to copy the all the DNA they want.

The process is called PCR (polymerase chain reaction) and goes as the picture below.

The great about this technique is that not only copy DNA, but also that it only copy the sequence between the oligos, so we can select the gene that we want to copy.

Indeed, this invention allowed the accomplishment of the Human Genome Project. The applications are many, not only to copy DNA, also to diagnose genetic diseases very fast. It was a huge discovery, like the wheel or the telegraph. So the money we spent researching things that didn't care to anyone, except some crazy scientists, has become in tons of economic a social benefits, and lots of knew knowledge.

So now you know, if someone says that basic science research is nonsense, he just don't understand the way that science moves forward. If basic science stops, we will be losing an incredible opportunity.

Thanks for reading, and sorry for the orthography.

1 comentario:

  1. Hi there! glad to drop by your page and found these very interesting and informative stuff. Thanks for sharing about taq polymerase, keep it up!


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