Restriction enzymes cut a strand of DNA at a specific location, the binding site, typically separating the DNA strand into two pieces. In the real chemical process a strand can be split into several pieces at multiple binding sites, we’ll simulate this by repeatedly dividing a strand.
Given a strand of DNA aatccgaattcgtatc and a restriction enzyme like EcoRI gaattc, the restriction enzyme locates each occurrence of its pattern in the DNA strand and divides the strand into two pieces at that point, leaving either blunt or sticky ends as described below. In the simulation there’s no difference between a blunt and sticky end, and we’ll use a single strand of DNA in the simulation rather than the double-helix/double-strand that’s found in the physical/real process.
Restriction enzymes have two properties or features: the pattern of DNA that marks a site at which separation occurs and a number/index that indicates how many characters/nucleotides of the pattern attach to the left-part of the split strand. For example, the adjacent diagram shows a strand split by EcoRI. The pattern for EcoRI is gaattc and the index of the split is one indicating that the first nucleotide/character of the restriction enzyme adheres to the left part of the split.
In some experiments, and in the simulation you’ll run, another strand of DNA will be spliced into the separated strand. The strand spliced in matches the separated strand at each end as shown in the diagram below where the spliced-in strand matches with G on the left and AATTC on the right as you view the strands.
Your code will be a software simulation of this recombinant process: the restriction enzyme will cut a strand of DNA and new DNA will be spliced-in to create a recombinant strand of DNA. In the simulation the code simply replaces every occurrence of the restriction enzyme with new genetic material/DNA — your code models the process with what is essentially string replacement.