GibsonHomologyArms
in package
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.
Class GibsonHomologyArms
Tags
Table of Contents
Properties
- $downstreamForwardPrimerTail : string
- $upstreamReversePrimerTail : string
Methods
- __construct() : mixed
- GibsonHomologyArms constructor.
- getDownstreamForwardPrimerTail() : string
- getOverlapLength() : int
- getUpstreamReversePrimerTail() : string
Properties
$downstreamForwardPrimerTail
private
string
$downstreamForwardPrimerTail
$upstreamReversePrimerTail
private
string
$upstreamReversePrimerTail
Methods
__construct()
GibsonHomologyArms constructor.
public
__construct(string $sDownstreamForwardPrimerTail, string $sUpstreamReversePrimerTail) : mixed
Parameters
- $sDownstreamForwardPrimerTail : string
-
5' -> 3'
- $sUpstreamReversePrimerTail : string
-
5' -> 3', may be empty, not both tails
getDownstreamForwardPrimerTail()
public
getDownstreamForwardPrimerTail() : string
Return values
stringgetOverlapLength()
public
getOverlapLength() : int
Return values
intgetUpstreamReversePrimerTail()
public
getUpstreamReversePrimerTail() : string