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Contents 1 The benefit of vector assembly in yeast 1.1 Introduction 1.2 Design of DNA fragments for gap repair cloning 1.3 Example from our project 1.4 Gap repair cloning for iGEM

The benefit of vector assembly in yeast

Introduction

Gap repair cloning is an elegant method for vector construction. It takes advantage from the homologous recombination system of Sacchaomyces cerevisiae (common yeast) which has a heightened activity. What does this mean in detail? There are many endogenous and exogenous factors (for example reactive oxygen-species, ionizing radiation, chemicals and failing of DNA binding Enzyms (e.g. collapsed replication forks)) which causes DNA double strand breaks. For the cell this is the most dangerous DNA damage because even if it occurs in rather unimportant regions the cell will not survive the next cell circle. That's the reason why yeast possesses enzymes which have the ability to repair a broken double strand by pairing it with a very similiar DNA region (typically on the homologous chromosome). This process is called homologous recombination. Using the gap repair method this natural process can be exploited for the construction of large cloning vectors in yeast.

Design of DNA fragments for gap repair cloning

The idea of the method is to transform a series of linear, successive DNA fragments into one yeast cell. The linear fragments have open blunt ends like they occur after a double strand break. If a homologous sequence is avaiable it will be treated like a genomic double strand break and homologous recombination takes place. When the sucessive DNA fragments are designed in a specific way which includes large sequence overlaps to the respectively following fragment yeast will recombinate them together.

For the formation of a cloning vector (usable in yeast or in other organisms) the first fragment is a yeast shuttle plasmid which is linearized by an appropiate restriction digest. A shuttle plasmid is a plasmid which is stable both in yeast and in Escherichia coli. The first fragment of the insert has to possess an homologous overlap to both the wished insertion site on the plasmid and to the beginning of the second fragment. The end of the second fragment has to possess an overlap to the beginning of the third one and so on. At least the end of the last fragment of the insert again has to possess an overlap homologous to the second insertion site on the plasmid.

At the lab of our instructor up to eighteen single fragments were assembled in a single transformation. Another advantage of the method is that no scars are left between the inserted fragments. Assembly of fragments to joint genes is possible. Restriction enzymes only have to be used once for linearization of the shuttle plasmid.

Example from our project

In our project we have constructed a plasmid for overexpression of three gens of the Mevalonate Pathway. Therefore we used synthesized fragments of the mentioned three gens, two promoters, two terminators (both from yeast) and a yeast expression plasmid which already contained one promotor, one terminator and a gen for Uracil synthesis. Moreover we used a mutant strain where this Uracil Gen is deletion. So we needed the uracil gene on the plasmid as a marker for selection of the transformants. Via PCR we assembled appropriate homologous overlaps to our fragments using primers containing these overlaps. By that we were able to arrange our fragments in the following order:

The DNA of all fragments is transformed together into competent yeast cells. The transformants were selected on synthetic medium lacking from uracil (only transformants should be able to grow). After preparing the plasmid from the transfomed yeast clones it can be transformed into Escherichia coli and gained from there in large ammounts for further use.

Gap repair cloning for iGEM

The cloning standards used in the Parts Registry and in the iGEM competition are based on restriction digest and ligation. One of the advantages of the gap repair method is to avoid this. Restriction digest and religation always leaves scars between the assembled fragments. Another advantage of gap repair cloning is it´s heightened time effiency when a large amount of fragments shall be assembled. Furthermore the expensive use of restriction and ligation enzymes can be reduced significantly. For these reasons we consider gap-repair cloning to be a useful tool for future iGEM Teams. The problem is that the common Biobrick standards are useless by now with regard to gap-repair cloning. Our idea is now to design a new standard based on standardized PCR primers.

Althought the Restriktion sites of the Biobrick Pre- And Suffix are unimportant in our context, the biobricking of gens leads to possiblity to amplify all Biobricks with the same prefix and suffix type with the same PCR primers. There are already some PCR primers in the Registry which anneal at the Pre- or Suffix Sequence. By adding an additional non annealing sequence to the primer an arbitrary overlap can be produced on every Biobrick.

By this system it is possible to create DNA fragments suitable for gap-repair cloning. Any expression plasmid have a similiar ordered insert region. Depending on the number of gens on the plasmid the insert region consists of several repeats of the eneral scheme promotor-gen-terminator. Gap-repair suitable DNA now can simply be created by choosing promotors, terminators and gens from the registry, amplifying the gens with primers which contain overlaps to the end of the promotor and the beginning of the terminator and cotransform everything. Since any Biobrick (from the same standard) can be amplyfied with the same primer it sufficient to construct two standard primers for every promotor and terminator in the registry, one overlaping with the front end and one with the rear end of the promotor. We want to design two standard primers for any of the promotors and terminators we used and for those which can already be found in the registry.