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If we denature dsDNA by heating it and then rapidly cooling it then what would happen? I read this question, where it was written that if we were given dsDNA sample which was completely denatured and then if we rapidly cool it. What would the result be? Would it anneal rapidly too or the annealing will be slow?

  1. If we see PCR the annealing time varies but is around 45 sec min with temperature range from 55-65 °C ( depending on Tm value). So my first doubt is that is it called rapid cooling?
  2. In case of preserving the RNA or DNA- cooling on ice pack preserves its structure and prevents any further changes in structure also.
  3. I tried to read papers and I read somewhere thatif we completely denature it then it anneals slowly. That takes place in two steps- first, it will try to find its completely match by collision process. Second, it will zipper up. That takes around 55 mins. So that states that it will be rapid annealing.
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  • $\begingroup$ “I read this question” Where? Is it some sort of homework or test question. Are you sure this has anything to do with PCR? Could it be a basic question that has been used for the last 50 years and merely relates to the effect of temperature — low, medium and high on the hybridization interactions? $\endgroup$ – David Aug 5 '20 at 16:19
  • $\begingroup$ How long of a DNA molecule are we considering? For short fragments like in routine PCR, the collision process and annealing will occur much quicker than 55 min. What temperature is it annealing at? Think of it like molecule kinematics.... $\endgroup$ – A. Radek Martinez Aug 5 '20 at 21:33
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To denature something can have different meanings:

In context of dsDNA it means separation of the 2 stands, while the individual strands themselves are fragmented.

I assume your question addresses PCR. In this context, rapid cooling to very low temperatures would prevent annealing of the two separated strands.

Other than that I want to point out a common misconception, that rapid cooling somehow has 'destructive' effects, which is not true. The more rapid something is frozen, the better it's structure is preserved.

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  • $\begingroup$ But in PCR the primers are of short length, that means it would anneal rapidly as, annealing in that case is primer attachment. If I consider a complete ds DNA which would again anneal. That might be a long strand, so that would probably take more time? $\endgroup$ – Gargi Aug 5 '20 at 14:43
  • $\begingroup$ A long strand takes more time. Also lower temperatures don't automatically mean faster annealing. There is an optimal temperature around 50C, where far below that the reduced molecular movement actually reduces the annealing speed. $\endgroup$ – KaPy3141 Aug 6 '20 at 15:18
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It really depends on a variety of factors. (1) the nature of the dsDNA, is it a plasmid or chromosomal DNA? Plasmids more easily renature than chromosomes, so rapid cooling and heating my not affect renaturing of plasmids, but affect DNA.

Cooling it slowly in some PCR-based experiment may be done if you want to annealing DNA fragments but are not sure about the optimal annealing temperature. Commonly done if you want to anneal two primers together for example. You need to be more specific so we can help you out.

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  • $\begingroup$ I have edited my question. Can you check again? $\endgroup$ – Gargi Aug 5 '20 at 14:41

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