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?
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”