Protocols

SLiCE Ex vivo DNA assembly

Introduction

We developed a DNA assembly system purely based on parts homology, which only uses E. coli lysate to carry out the reaction. Our work builds on the previous research on lysate based assembly methods, in the particular SLiCE. and Ex vivo. The concept is very similar to that of a Gibson method: the parts to be assembled contain an overlapping homology region, which allows homologous recombination to occur. While the Gibson assembly utilises an expensive piece of kit, containing a 3' to 5' exonuclease, a DNA polymerase to fill the gaps and a ligase to seal the nick. The Ex vivo, as we like to call it "E.G., or E. coli gratiae" only uses E. coli lysate to carry out this reaction. The lysate in fact does contain all the cellular machinery necessary to recognise a homology and to repair DNA. This process if facilitated when the lysate contains three lambda proteins, which can be easily expressed in the strains used to produce it. In addition to normal lysate, this system was tested using a lysate of cells expressing lamda proteins. These are the same protein that allow Lambda Red Recombineering Knock-Outs, i.e. Gam, Exo and Beta, which respectively protect linear DNA from RecBCD nuclease activity, cleave DNA 3' to 5' and promote annealing of complementary single strands.

We decided to test the efficacy of SLiCE for the assembly of parts only based on a short flanking homology. This homology is roughly equivalent to that of the biobrick prefix and suffix. This means that a two part assembly, of the insert - such as a gblock - into the standard pSB1C3 vector would only require one Seamless Ligation step. This avoids the standard (and costly!) digestion/ligation steps that usually are required for the biobrick assembly.
We tested this approach by ligating the standard J04450 RFP generator to pSB1C3 using 22bp and 21bp of homology (biobrick prefix and suffix :) ) and successfully achieved pink, ligated colonies.

Materials and methods

These are the Standard SLiCE reaction
- 50–200 ng linear vector
- Appropriate amount of insert DNA in a 1 : 1 to 10 : 1 molar ratio of insert to vector,
- 1 ul 10X SLiCE buffer (500mMTris–HCl (pH 7.5 at 25?C), 100mM MgCl2, 10mM ATP, 10mM DTT)

Quick Reaction
- 50–200 ng linear vector
- Appropriate amount of insert DNA in a 7:1 molar ratio of insert to vector - 25ul of 2X T4 ligase buffer (66mM Tris-HCL. 10mM MgCl2, 1mM Dithiothreitol, 1mM ATP, 7.5% Polyethylene glycol (PEG6000), pH 7.6 @ 25°C)
Preparing the lysate Amplifying the parts

Results

Initial reaction, SPLiCE

Discussion

Reaction conditions, improved "quick ex vivo", prefix suffix homology and homology length. control to exclude background