Cloning
Ligation
Join cut DNA and see what comes out before you set the reaction up. Give the tool molecules and their enzymes and it lists every fragment each digest would produce with its real end structure and its span on the plasmid, then joins the ones you pick and reports the products with the junction each one was built on. Because the ends are modelled as structure rather than text, an incompatible pair is an answer the tool gives you rather than a plate you throw away.
Arrives loaded: pUC19 and its own polylinker as an annealed adapter — run it, every junction comes back nicked, add T4 PNK and they close
What it does
- 01Ligate fragments you have already cut, picking which fragment of each digest goes in the pot
- 02Cut and ligate in one pot from a shared enzyme set
- 03Per-molecule fragment inventory with each fragment real end structure, 5′GATC, 3′TGCA or blunt, and its span on the plasmid
- 04Clicking a fragment highlights it on the circular and linear map, including the origin-spanning one
- 05Products with their junctions, which fragment met which and on what overhang, read from the assembly graph
- 065′-phosphate chemistry: how the ends were made, and CIP, rSAP, Quick CIP or T4 PNK treatment per molecule
- 07Nicked products reported rather than hidden, because a one-sided phosphate still transforms
- 08Measured T4 ligase fidelity for the junction set, which refuses a meaningless number on palindromic overhangs
- 09Vector to insert mass for a target molar ratio, weighed on the picked band rather than the whole plasmid
- 10Products sent to the virtual gel bench as circular and linear lanes
What it runs on
Both reactions are the pydna assembly ports in packages/ports, golden-validated byte-for-byte against real pydna. End chemistry is sourced from the ligation literature rather than ported, because no upstream models it, and is validated behaviourally. The panel runs on @ports/goldengate, @ports/ligation.
Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.
Questions
- Why does my ligation return no products?
- Most often because every fragment you supply has to be used: the underlying engine requires all of them, so offering every band of two digests at once usually yields nothing while picking one from each yields the construct. The panel says which inputs were dropped and why rather than showing an empty list.
- Does it model a dephosphorylated vector?
- Yes. A phosphatase is applied after the digest, which is the bench order, so a treated vector can no longer self-close while a phosphorylated insert still goes in. The resulting join is reported as nicked, which is a real product that transforms and is repaired in vivo.
- Can it tell me a PCR product will not blunt-ligate?
- Yes. A PCR product carries the primer 5′ terminus, which ships unphosphorylated, so choosing that origin makes the reaction refuse the self-circularisation the same way the bench does until the product is treated with T4 PNK.
- What is the difference between the two tabs?
- Ligate fragments takes molecules that are already cut, each with its own enzymes, and lets you choose which fragment takes part. Cut and ligate does the digestion and the joining in one pot from a shared enzyme set, which is what a Golden Gate reaction is.
Also searched as
DNA ligation simulator · sticky end ligation tool · blunt end ligation online · vector insert ligation calculator · insert to vector molar ratio calculator · T4 DNA ligase simulation · restriction ligation cloning · cut and ligate one pot · annealed oligo adapter design · dephosphorylated vector self-ligation · CIP rSAP vector treatment · ligation product predictor · compatible overhang checker