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Would it be possible for short DNA molecules to replicate, for example, if it's heated to the point where the strands separate (as far as I know, that's what happens in PCR?) and freely floating bases could "connect" to their correspondent bases (A/T, C/G)?

I'm assuming that A/T and C/G bases strongly 'attract' each other naturally, perhaps that's where I'm wrong?

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    $\begingroup$ Not what you asked, but note that RNA can do this. (See also Wikipedia.) $\endgroup$
    – Ilmari Karonen
    Sep 9, 2022 at 11:44
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    $\begingroup$ @IlmariKaronen — RNA Can do what? RNA only replicates in certain viruses, where it requires a replicase and NTPs. Speculation about replicative capability of primaeval RNA should be described as “might have been able to” rather than “can”. $\endgroup$
    – David
    Sep 9, 2022 at 18:40
  • $\begingroup$ @David Incorrect, RNA can self-replicate without any other molecule except the nucleic acids it builds itself from. Self replication of RNA was demonstrated over a decade ago. You are confusing Industrial use of RNA replication with what we know the molecule can do. Not only does it replicate it evolves into different linages as well. labroots.com/trending/cell-and-molecular-biology/22442/… and sciencedaily.com/releases/2009/01/090109173205.htm $\endgroup$
    – John
    Sep 11, 2022 at 13:19
  • $\begingroup$ @John - you make it sound like every RNA species is capable of self-replication. What you actually mean is "self-replicating machines can be built from only RNA". These are two very different messages. $\endgroup$
    – markur
    Sep 11, 2022 at 14:42
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    $\begingroup$ @markur I make it sound like no such thing. I'll be crystal clear there are single strands of RNA that fully capable of self-replication, no other machinery needed. No replicase, not even multiple strands of RNA. just water, ONE strand of RNA and some free floating nucleotides. Literally what the OP is asking for but RNA instead of DNA. no speculation. You are just wrong, RNA "can" self replicate without other machinery. I did provide links read them before claiming I "meant" something. $\endgroup$
    – John
    Sep 12, 2022 at 0:04

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Nope. Not happening.

The high temperature (90 °C) needed to separate a DNA strand also makes an association of free floating bases to a template strand much too unstable.

Even if the bases associated with the template strand, they wouldn't spontaneously connect (phosphodiester bond formation) with each other. It needs a catalyst.

Also, it requires not bases, but dNTPs. dNTPs have phosphates (anhydride bonded) that deliver energy to the phosphodiester bond formation connecting each dNTP.

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    $\begingroup$ Only one phosphodiester bond is broken during dNTP utilization for DNA synthesis, so talk of three phosphates delivering energy is misleading, to say the least. The point is thermodynamics — provision of energy for phosphodiester bond formation — which bases cannot provide. $\endgroup$
    – David
    Sep 9, 2022 at 18:48
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    $\begingroup$ The bonds between the three phosphates are of anhydride type, not diester. I removed "three", since it seems to be confusing. $\endgroup$
    – markur
    Sep 9, 2022 at 19:07
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No, replication cannot happen in the absence of polymerase (on the timescales relevant to humans).

You are correct that in PCR, the first step is to separate DNA strands at 98 C. This heating dissociates the strands semi-permanently. So when you cool down the reaction, the strands do not re-associate very quickly.

When you cool down the reaction to 72 C, A/T and C/G can make temporary connections with their opposite bases. However, the free nucleotides cannot quickly form phosphodiester bonds with the growing chain of DNA in the absence of a polymerase. The nucleotide will most likely dissociate from the DNA strand before the correct bond forms. In other words, it is a kinetic problem.

However, at high temperatures, specialized conditions, and on long timescales, such as those present in earth's pre-biotic period, the answer may be different.

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  • $\begingroup$ Is it fair to say that the polymerase is mostly helping the DNA to be put together somewhat "in order" (one nucleotide next to the other) so they can form stronger bonds with each other, becoming stable? $\endgroup$
    – Lem0n
    Sep 11, 2022 at 8:23

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