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I know helicase breaks the hydrogen bonds between the strands of a DNA, but how is this done?

Does it put an ion between the strands of the nucleic acid so that the bond breaks apart itself or is there some other mechanism?

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    $\begingroup$ Welcome to SE Biology. I have edited your question for two reasons. We discourage extraneous material and chat in questions — keep to the facts. If you want to add personal information, the most relevant is what level your knowledge of the subject is already. This is not my field, but I found a 2006 mini-review of the topic which indicates that there are many different helicases and their mechanisms of action are not simple to summarize. Someone may be able to do it for you, however. $\endgroup$ – David Sep 17 at 22:32
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    $\begingroup$ This is indeed a broad question. For a detailed mechanism you should read a structural biology paper on this topic. This subject is complicated to explain in a site like this (also requires good knowledge of biochemistry and biophysics). A very short answer would be that helicases use energy of ATP hydrolysis to separate the DNA strands. $\endgroup$ – WYSIWYG Sep 18 at 7:28
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Im not sure if there is a decided helicase mechanism but the ‘backbone stepping motor’ model has been proposed for helicase translocation and unwinding. Helicases contain two domains that are analogous to a set of ‘pincers’ (motor domain), when ATP is present, there is only a distance of two nucleotides between the pincers and so they are closed, whereas when ATP is absent, there is a distance of three nucleotides between the pincers and so they are open. The motor domains interact with the nucleic acid through contacts between threonine residues on the pincer terminus and phosphoryl oxygen on the nucleic acid. ATP binding weakens these interactions, allowing a pincer to move one nucleotide closer to the second pincer. A third domain (D3), that is part of the helicase but not involved in the binding of ATP, also interacts with the nucleic acid using a threonine residue. As the motor domains move along, tension builds up between the motor domain and D3 and after the motor domain has moved three base pairs, the protein contracts like a spring, pulling D3 toward the motor domains, disrupting the DNA in between. The structures responsible for prying apart the DNA are called “pins” or wedges”, which act as a physical barrier between the two strands of nucleic acid, prying apart its structure. The single stranded regions are stabilised by helicases as well as other proteins such as single stranded DNA binding proteins, which prevent the reformation of the double stranded nucleic acid.

For more information and good images see: “Translocation and unwinding mechanisms of RNA and DNA helicase

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    $\begingroup$ It's good to have more people answering questions in this area, but as you are a new member of this list, allow me to point out an important feature of answering questions on SE. This is that answers should be supported by external sources — reputable scientific articles, either in print or online (preferably with links). The reason for this is two-fold. 1. Without it it is difficult for the poster or others with the same question to know whether the answer is correct. 2. It is helpful for anyone wishing to learn more about the topic. Could you add references to your answer, please. $\endgroup$ – David Sep 19 at 8:55
  • $\begingroup$ Sorry I put the name of the paper at the end which is in my opinion a really good article but I'll add the doi $\endgroup$ – pepsiandsoda Sep 19 at 12:12

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