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I have recently read an article which explains that, in the RNA World hypothesis, an RNA molecule gets 'scanned' by nucleic acid, catalysed by a different specifically-folded RNA molecule, to arrange itself complimentarily to the original molecule. However, what causes the new, complementary molecule to detach from the original molecule? I always hear people say that this complementary base pairing allows the RNA molecule to reproduce, but I never quite understood: how? If complementary bases tend to bind together, shouldn't the newly formed structure then be stable? What causes the actual reproduction?

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  • $\begingroup$ Both complementary binding of RNA & DNA is dependent on temperature and salt concentrations (among other things), so if these factors change so does the stability of a double-strand complex $\endgroup$ – Nicolai May 19 '18 at 10:57
  • $\begingroup$ @Nicolai so both of those have to exactly spot on, or the bondings deform? Why, then, does an RNA copy itself completely most of the time? Why does it first have to scan itself completely and then detach (i.e. why can't some bases pair while the others will not due to a different temperature?) $\endgroup$ – Max May 19 '18 at 11:01
  • $\begingroup$ There are many single-stranded RNA viruses in which the daughter strand must be released from the template. I imagine that this strand displacement is a feature of the action of the RNA-dependent RNA polymerase. How it works I have not been able to find from a brief search (hence comment, rather than answer), but it obviously does. So this is not a particular problem of the RNA world. I'd check the virology literature if you want more info. $\endgroup$ – David May 21 '18 at 12:41
  • $\begingroup$ @David I know it's not an issue with the hypotheses - it's my lack of understanding. So the RNA copy disentangles itself from the parent RNA because of a virus/polymerase? That seems logical, but then again, same problem: why can't it infect the RNA while it's being copied? Wouldn't it then create an incomplete copy, thus perhaps causing the whole system to malfunction? Or are these events rare because the copying stage is too quick? $\endgroup$ – Max May 21 '18 at 12:49
  • $\begingroup$ The polymerase somehow starts synthesis at one end, the complementary NTP binds and the enzyme catalyses a phosphodiester bond, goes along the template strand one base so as to be able to catalyse the bond between the growing chain and the next NTP to bind, etc. etc. Your valid question is why the growing chain is released from the template rather than staying H-bonded to it. I assume that as the polymerase moves along it somehow destablizes the interaction (rather than just dissociating randomly). However I am unaware of the molecular mechanism. $\endgroup$ – David May 21 '18 at 13:44
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First, I want to point out that the RNA world hypothesis is just that - an hypothesis. While it has been shown that it's possible for certain RNA molecules to make copies of itself, this is not a 'normal' function of any RNA.

Edit - to give a clearer answer to the question itself:

After replication of an RNA molecule it may form a stable structure together with its template or it may dissociate. Due to the various possibilities and complexity of RNA structures its almost impossible to predict this, since both the (exact) sequence itself and environmental conditions especially temperature are very important.

More background from the unedited answer:

Whether two complementary strands or RNA (or DNA) bind together is not something that can always be easily answered. For DNA of a given length (in a given environment / buffer) one can more or less predict the temperature at which complementary strands will separate (often called melting temperature), because DNA forms relatively stable helices. RNA, however, often forms complicated 3-dimensional structures, often involving self-complementary and is not restricted to the typical helices seen in DNA. Trying to predict the resulting 3D structure of RNA molecules is still an ongoing field of research. Some of these structure are quite stable (e.g. in tRNA) but in other cases they can also be very dynamic and change quickly. In the end it always depends on the RNA sequence, temperature and many other environmental factors.

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  • $\begingroup$ So I assume this melting temperature is quite low, then? Seeing as (okay, I will switch to DNAs for now for simplicity) a DNA unwinds itself so often? $\endgroup$ – Max May 19 '18 at 12:12
  • $\begingroup$ You mention various factors affecting base-pairing in RNA but you do not answer the poster's question, which is if the bases anneal to the template to allow polymerization in the first place, why does the product dissociate? Talking about RNA “liking to form complicated structures” won't do. It may have the potential to do so, but dsRNA viruses show that it has the potential to form duplexes. $\endgroup$ – David May 20 '18 at 16:42
  • $\begingroup$ @David I don't think it's possible to give another answer to the question than my last sentence (maybe I should make that clearer), because it will always depend on the RNA sequence and environment whether it dissociates after replication or not (even in the first place) - the fact that dsRNA viruses are possible is just another example to the ones I listed $\endgroup$ – Nicolai May 20 '18 at 20:53
  • $\begingroup$ I also remove the 'RNA likes to ...' which was indeed a bad way to describe this. $\endgroup$ – Nicolai May 20 '18 at 20:57

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