Tick Diaries… A Midnight Spin.

It is night, and the human form of the AntibioTick- Chandrakant Redican (Chandu), is purifying the DNA of his PCR products.

DNA is the bit in the cells of the body that carries information on what the cell is going to be like, what it is going to do, etc etc. It is made out of four different types of chemicals- A,T,G and C which are arranged in a line in different combinations. It is like a language with four letters. For example- the sequence AAATTGGCTCP does not mean anything at all.

If you really want to know what the sequences say, hunt up your nearest biochemistry professor and ask him. They are usually happy to talk because not many people are interested in what they do.

Chandu had a little DNA, but he needed more of a specific bit of that DNA. To make a lot of copies of DNA, you do a reaction call a PCR.

When a PCR reaction is done in a PCR machine takes a little piece of DNA and turns it into a lot of DNA. And I mean a lot. I mean millions of copies. And It all still fits into the fifth part of a tube that holds only a drop of water.

A PCR reaction without a PCR machine is like The Movie “Tees Maar Khan” without its popular brilliant Item song- “Sheila Ki Jawani”- brainless concept, waste of money and uninteresting.

Another cool thing about PCR is that it makes a lot of copies of any little piece of DNA that you want.

The greatest and most brilliant thing about the PCR though is that the reaction takes three hours in a PCR machine which you turn on and can ignore. Those three hours are bliss because something is going on and you can say you are “Doing a PCR” and feel like you are doing something useful with your life without doing anything at all. While the time should be spent reading research papers or something you actually go have a cup of tea in the Cafe, shout at trainees, bitch about seniors and if it is night-  watch the latest episode of Big Bang Theory downloaded through proxies on the Institute’s servers which you spent the last PCR reaction hunting up.

For more information about PCR, visit this link and be bored, else read on.

Chandu needs these millions of copies of the same bit of DNA to find out what the sequence is.

Because we have a lot DNA, it is a lot of work to sequence all of it. So if you just need to know what type of bug it is you can just take a small piece of DNA and sequence it to find out.
So you are actually treating a sequence like unique identity mark, or a bar code where the order of the DNA sequence is the identity of that bug, bacteria or animal

Some bits of the DNA are really useful if you treat them like identity numbers or barcodes because they do not change much within species and are different between speciesl.

To read the sequence the Chandu needs pure DNA. The DNA in the PCR mix is not pure at all. It has all the stuff that is needed to make many copies of DNA. Large protiens call taq polymerase that read the DNA sequence and make copies. Little molecules call DNTPs which are the building blocks of DNA and some salts because you need a pinch of salt in everything to keep things real.

Actually there is a scientific reason for the salt which the biochemistry professor can tell you. I can tell you too but I don’t want to.

He has a plate containing wells with DNA which has PCR stuff, He puts a thick gooey transparent substance into each well. This thick gooey transparent substance is called PEG (Poly-Ethylene-Glycol), He then puts a rubber seal over the whole plate. He then vibrates his sample plate to mix everything up real nice and puts the plate in the centrifuge

(In the Chandu’s Lab, a centrifuge is an expensive thing that spins other expensive things round and round very fast).

He operates the machine…

Set at- 3800 RPM, thirty minutes.
Start..
Low Rumble…
Whirr…
Speed up
Countdown begins…

As Chandu stares at the machine and hears the whirrs, his vision goes out of focus and the world around him dissolves. Everything goes black.

He opens his eyes. He is the AntibioTIck now. He is lying flat on his back and he feels a bit dizzy. The ceiling is a long way above him where he can see a great round cylinder. He looks to his left and right he sees two steel towers rising up to the cylinder. His hands feel a rubbery floor.

The AntibioTick stands up and looks to his left and right. He sees the towers reaching up to the round steel cylinder above the cylinder he sees bits of a huge plate, very similar to the small one that he just loaded into the centrifuge. He looks below and he sees a rubber floor similar to rubber seal he put on the plate just moments before.

He looks ahead and he understands. He is inside the centrifuge. On the plate which is purifying his PCR products.

The plates are moving round so fast that they are perpendicular to the floor of the centrifuge. He realizes this and is suddenly scared that he will be thrown off and dashed to smithereens. He forgets that centrifugal force will not let him fall.

The whole centrifuge seems like a great chamber, it is filled with an eerie light, a type of ether making everything visible. A great steel structure is in the middle going round and round at 3800 revolutions per minute, steel arms swinging around it. The steel arms holding four great white plates with a hundred wells each, there are things shining in those wells.

The AntibioTick looks at the wells, some which are are right below him. Each well seems large enough to hold a grown man. It is filled with a glowing transparent gooey stuff. He remembers what it is called- PEG.

He sees bits of DNA going round and round each other in glowing helixes all through the gooey stuff. The helixes have glowing steps in the middle and the phosphate backbone glowing. The DNA molecules are slowly sinking down. Huge taq polymerase enzymes which do the job of adding base pairs to the DNA are also there. They look like coiled boulders, But they are only floating, too large to be pulled down.

Some stray sequences only a few base pairs long forming different shapes and coils lie here and there. Random stuff that is of no use further. Primer Dimers they are called.Moving to and fro are large molecules of Phosphates that have not been added to any DNA, slowly they are falling apart, randomly colliding.

Life is like a giant centrifuge for the AntibioTick at the moment. He is seeing stuff that he has studied his whole life and thought would never see with his own eyes. All that time he had been doing experiments that you are assuming some invisible substance is there and you find out only at the end if you run it through an experiemental gel and look at it under Ultraviolet Light. Always you deduce what has happened even in the most common experiments, you try to imagine, you know what is going on but you never really see.

But now it  is like Roger Federer playing tennis. He is there, he knows exactly how the ball is turning, what fraction of the ball to hit to send back the way he wants, he is not thinking about the game- he is the game..

And after a very long time in his life, in this standardized and old technique, The AntibioTick has finally found the Zone. Lets hope it lasts.

The long strands of DNA are going deeper and deeper into the well. They are coming together at the bottom to make one large pellet. The large taq enzymes are still suspended. The small strands have also spun down. Just the really small particles still move up and down. Too large to stay up, too small to be pulled down and held there.

When the spin is over, the gooey stuff will be poured out and the pellet should remain. This pellet will be put in water again and the stuff will be check if the DNA is still there. The AntibioTick will follow this procedure, but he is sure that this experiment will work out, he has seen it.

Suddenly there is a slowing down of the spinning, the motors stop the and the plates start spinning slower and slower, finally swinging down and dangling motionless. There is a beeping noise, the AntibioTick feels dizzy and he blacks out.

Chandu wakes with a start. The centrifuge is beeping. His spin has ended.

(Apologies to those doing PCR reactions, I do two hundred a day myself so I am also poking fun at myself. If you think that Sheila ki Jawani is not as good as Munni Badnam hui, I agree- but the thing is the movie Dabbang (The first one) was pretty good so I could not use the analogy in that case. The sequel though is useless primer-dimer waste.)

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About Chandrakant Redican

A researcher and teacher based in Pune, India,
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5 Responses to Tick Diaries… A Midnight Spin.

  1. Shivani says:

    steel towers rising……..hahahahahha reminds me of minas tirith
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    .
    .

    oh wait what is the tower doing in a research lab????
    .>>…
    .
    .
    .
    .
    .hmmmmmm……..
    .
    .yawn!!!.
    .
    .
    .zzzzzzzzzz ( thats what happens to grad students who try to think too hard!)

  2. “A PCR reaction without a PCR machine is like The Movie “Tees Maar Khan” without its popular brilliant Item song- “Sheila Ki Jawani”- brainless concept, waste of money and uninteresting.”

    I completely disagree with the above statement, not the Tees Maar Khan and Sheila ki Jawani part…if you are talking about the modern PCR machine, yes it is indeed a marvel of technology! But I have seen an ingenious “contraption” made of water baths that execute the principle behind the PCR with usable results! Ofcourse this was back in the time when PCR machines were not so common in India 😉 May be its just me but that DIY equipment made me appreciate modern PCR machines is a very different way!

    • I think you misunderstood the statement Bhalachandar… The machine is brilliant- no doubt about that, I was saying that setting up a reaction without a machine is brainless and uninteresting- you can make the mix- but nothing relevant will happen.

      I can imagine though shifting the mix from water bath to water bath. It would be quite a chore! we can just turn it on and forget!

  3. The spider-man mutation was much simpler compared to this. God! Do you do all this to alter a gene and reproduce it.

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