Restriction Digest and Cloning
Before you cut anything at the bench, cut it here. Restriction Digest picks the enzymes, shows the fragments they produce, and runs the gel you would run, so you can tell a clean single cutter from a mess of comigrating bands while the plasmid is still on screen. Construct Assembly goes the other way and joins parts from your library into a new sequence.
Both live under Assembly & Cloning in a sequence's sidebar, which starts collapsed, and both work on DNA.
Running a Digest
Restriction Digest opens on Select Enzymes. The list starts with the common enzymes, and every row carries its recognition sequence and how it behaves on this sequence: 1 cut, 6 cuts, or no sites. Single cutters sort to the top, since they are usually what you came for. EcoRI is ticked when you arrive, as a starting point rather than a recommendation.
Searching reaches the whole catalog rather than the common set, by name or by recognition sequence, so an enzyme you already have in the freezer is one search away even when it is not in the short list.
Single cutters only narrows the list to enzymes that cut exactly once here. Anything you have already ticked stays visible, so the filter never hides a choice you made. When nothing cuts once, the list says so rather than going blank.
Tick your enzymes and the Fragments list fills in underneath, each fragment with its length and both of its ends, either blunt or the overhang and the enzyme that left it. View Gel takes you to the picture.
Reading the Gel
The gel draws a ladder in the first lane, then your uncut sequence, then the digest.
Tip: The uncut lane draws what you would actually load. A circular plasmid runs as a bright supercoiled band ahead of its length and a faint nicked band behind it, both labelled with the real number of base pairs, which is why an uncut plasmid never sits where the ladder says it should.
Gel %: offers 0.8, 1.0, 1.5, 2.0, 2.5, and 3.0, and the one that suits your fragment sizes is marked (suits these sizes). That suggestion follows the average fragment length, so a digest of one large piece is offered a loose gel and a fistful of small ones a tight gel.
Hover a band to read it. A fragment gives you its size, the supercoiled and nicked bands name themselves and say which way they run, and a band carrying more than one fragment says how many.
Two fragments within five percent of each other in size run as one band, and Conspecta says so under the gel and marks the band in Expected bands: with the count, such as 1,234 bp ×2. That is the number that decides whether this digest can actually tell you what you want to know.
Save image downloads the gel as a PNG you can put beside the real photograph. Send to notebook adds it to the end of a page you pick, as a caption naming the enzymes and the percentage followed by the picture, and the confirmation carries an Open link straight to it.
Building a Construct
Construct Assembly joins sequences end to end into a new one. Name it first, in Assembly name, since the name is what the saved sequence is called.
Add parts opens the Part Library, which searches your project by name, description, or registry identifier, and filters by registry type. Tick everything you want and Add to assembly drops it on the canvas.
Each part on the canvas has Move up, Move down, and Remove fragment, and a toggle reading Fwd or RC that flips it to its reverse complement. A reversed part draws in a different colour with an RC tag, so the orientation of every piece is readable at a glance. Reorder them into the order you want, because the order on the canvas is the order they are joined in.
The running total underneath tells you how long the construct will be and how many fragments it holds, and mixing sequence types is called out rather than quietly concatenated.
Save Assembly writes the result as a new DNA sequence, recording the sequence you started from as its parent. The parts you picked are not written into the record, so name the assembly for what it contains if that matters later.