How long should SLiCE homology arms be?

25 bp is the common default and works for most constructs. Arms as short as 15 bp can work; longer arms up to 50 bp improve efficiency for larger fragments.

Do I need to purify the PCR product?

Purification is strongly recommended. Residual primers and template compete with the intended recombination and raise the background.

Is SLiCE the same as Gibson?

The outcome is the same — a seamless join — but the reagent differs. Gibson is a defined three-enzyme mix; SLiCE is a crude cell lysate with recombination activity.

Can SLiCE assemble more than two fragments?

Yes. Multi-fragment assembly works with the same principle, though efficiency drops as fragment count rises; design distinct arms for each junction.

SLiCE Cloning Calculator

Seamless cloning with a cheap bacterial lysate — set the homology arm length and get the recombinant sequence.

Homology arm (bp)Longer arms recombine more efficiently but cost more to synthesise.

Vector (linearised)

0 bp

Insert / PCR product

0 bp

Both a vector and an insert sequence are required.

Description

SLiCE uses a bacterial cell lysate carrying the lambda Red recombination system to join fragments with short homologous ends. Set the arm length, paste vector and insert, and get the product plus the four arm sequences.

How to use

Enter the linearised vector and the insert. Choose the arm length you will add to your primers — 25 bp is the common default; reactions work down to about 15 bp and up to about 50 bp.

Learn more

What it does

SLiCE (Seamless Ligation Cloning Extract) is a laboratory-made reagent: a lysate of E. coli expressing the lambda Red recombination system. It joins DNA fragments with homologous ends in vitro, giving Gibson-like seamless cloning at essentially zero reagent cost.

How it works

The tool takes the last N bases of the vector as its 3′ arm, the first and last N bases of the insert as its 5′ and 3′ arms, and the first N bases of the vector as its 5′ arm. The product is the vector followed by the insert core. Showing all four arms lets you paste them straight into a primer-ordering sheet.

Worked example

With a 25 bp arm setting, a 3.0 kb vector and a 1.2 kb insert produce a 4.2 kb product, and the four 25 bp arm sequences are listed for you to add to the vector primers and the insert primers respectively.

When to use it

Use it when you want Gibson-style seamless cloning without buying a commercial master mix, when assembling several fragments at once, or when teaching molecular cloning on a budget.

FAQ

How long should SLiCE homology arms be?: 25 bp is the common default and works for most constructs. Arms as short as 15 bp can work; longer arms up to 50 bp improve efficiency for larger fragments.
Do I need to purify the PCR product?: Purification is strongly recommended. Residual primers and template compete with the intended recombination and raise the background.
Is SLiCE the same as Gibson?: The outcome is the same — a seamless join — but the reagent differs. Gibson is a defined three-enzyme mix; SLiCE is a crude cell lysate with recombination activity.
Can SLiCE assemble more than two fragments?: Yes. Multi-fragment assembly works with the same principle, though efficiency drops as fragment count rises; design distinct arms for each junction.

Gibson Assembly CalculatorCheck homology arms and assemble multiple DNA fragments into one sequence.In-Fusion Cloning CalculatorDesign 15 bp homology arms and assemble fragments by homologous recombination.TA & TOPO Cloning CalculatorSimulate TA and TOPO cloning of a PCR product into a linear vector.Restriction AnalysisFind restriction sites in a sequence and simulate single or double digests with fragment sizes.

View all Cloning tools