GibsonHomologyArms.php
Immutable value object describing the primer tails needed to create a Gibson junction Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 7 October 2026
Table of Contents
Classes
- GibsonHomologyArms
- Both tails are given 5' -> 3', ready to be prepended to the primer's own annealing portion (this class only designs the homology arm, not the annealing portion itself, which needs its own melting temperature calculation). downstreamForwardPrimerTail goes on the forward primer that amplifies the downstream fragment ; upstreamReversePrimerTail goes on the reverse primer that amplifies the upstream fragment. Each tail carries one share of the overlap : after PCR, the two products share the downstream forward tail followed by the reverse complement of the upstream reverse tail, which is what lets Gibson assembly's exonuclease chew-back and annealing join them. A 1-base overlap leaves the upstream reverse tail empty.