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From 2013.igem.org

MoClo Library Characterization

An Introduction to MoClo

Modular Cloning, or MoClo, is a relatively new assembly method introduced in 2011 by Ernst Weber et al., whereby using Type IIS restriction sites allows the user to ligate up to six DNA parts together in a one-pot reaction. It is a method based on Golden Gate Assembly. Type IIS restriction enzymes cleave outside of their recognition site to one side, thus allowing for removal of those restriction sites when used properly. This helps eliminate excess base pairs, or scars, from forming between DNA Parts. However, in order to ligate together properly, MoClo utilizes a set of 4-bp fusion sites, which remain behind after ligation and thus generate 4-bp scars between DNA parts in the final DNA sequence following ligation of two or more parts.

MoClo Overview

The MoClo system allows directional assembly of DNA parts through using BsaI and BbsI (also called BpiI), two Type IIS restriction enzymes that leave 4bp overhangs after they cut DNA. These four base pair overhangs, or fusion sites, created by either enzyme can be any 4 bases and thus fusion sites can be user-defined. The fusion sites are used to enable directional assembly of DNA Parts. By defining non-palindromic fusion sites that flank each DNA Part, we can ensure proper order of assembly by assigning the same fusion sites between the 3’ and 5’ ends of two DNA Parts that are meant to go next to one another (Fig. 1).







Figure 1: Directional Assembly of DNA Parts. Two basic DNA Parts (DNA Part 1 and 2) are each shown in green vectors to denote the chloramphenicol resistance cassette and each has two 4bp non-palindromic fusion sites flanking the DNA Part. The third vector is the Destination Vector for the final construct, which is orange to denote the kanamycin resistance cassette and contains lacZ for blue-white screening. The BsaI sites (red text) are shown in the DNA Part vectors and Destination Vector with the direction they cut (red arrow). The 4bp fusion sites (blue text) shown in the five top plasmids indicate the fusion sites that will remain with either the DNA Parts or the Destination Vector after the BsaI digestion. By allowing matching fusion sites between the 3’ end of the first part and the 5’ end of the second part and so on, this enables the proper assembly order of the DNA parts to be maintained. The Destination Vector contains the fusion site on the 5’ end of the promoter and the 3’ end of the terminator to allow the properly ordered transcriptional unit to be cloned into a vector containing a different antibiotic resistance from the vectors containing the basic DNA Parts. The DNA parts replaces the lacZ coding sequence, thus allowing for the selection of white colonies on plates containing IPTG and X-Gal. (Figure from BBF RFC 94: The Modular Cloning Assembly: Standardized Assembly of Bacterial Transcriptional Units Using Type IIS Restriction Enzymes BsaI and BpiI, Traci Haddock and Douglas Densmore, 2013).

MoClo Destination Vectors

The MoClo system we're using has three levels of assembly where basic parts (Level 0) are linked together to form transcriptional units (Level 1), which are then linked together to form functional genetic circuits (Level 2). Each MoClo Level also requires Destination Vectors which act as the end carrier for the inserted DNA part(s). In our assembly, we utilize blue/white screening for each level along with different antibiotic resistance markers as a secondary selection method for screening our clones.

We have converted the common BioBrick vectors pSB1C3, pSB1K3, and pSB1A2 into our MoClo Destination Vectors by inserting the alpha fragment of lacZ with flanking MoClo restriction and fusion sites into the cloning site (Fig. 2).







Figure 2: Destination Vector Detail for MoClo Levels 0-2. The BsaI (in red) and BpiI (in purple) sites are interchanged between levels. The green backbone in Level 0 denotes chloramphenicol resistance, the orange for Level 1 is kanamycin, and the blue for Level 2 is ampicillin. The alpha lacZ fragment is in the cloning site for each level and the 4 blue N’s denote the fusion sites, to be designed by the user. (Figure from BBF RFC 94: The Modular Cloning Assembly: Standardized Assembly of Bacterial Transcriptional Units Using Type IIS Restriction Enzymes BsaI and BpiI, Traci Haddock and Douglas Densmore, 2013).

MoClo Parts

As mentioned above, our MoClo system has three levels of assembly.

Level 0: Basic DNA Parts (ex: promoter, gene, etc.) are PCR amplified and cloned into MoClo destination vectors to form Level 0 Parts. During the PCR reaction, the correct fusion sites and BpiI sites are added to either side of the DNA sequence. The orientation of the BpiI sites is crucial, where the 3’ BpiI site is inverted while the 5’ BpiI site is not (Fig. 3). This PCR reaction is mixed with its matching Destination Vector in a MoClo reaction. After a transformed clone has been confirmed, this plasmid is now called a Level 0 Part and has the following order of DNA sequences: BsaI site-Fusion site 1-DNA Part-Fusion site 2-BsaI inverted (Fig. 3). Notice that BpiI is removed from the final product, thus requiring the Destination Vector to contain both BpiI and BsaI flanking the fusion sites (Fig. 3).








Figure 3: Construction of a Level 0 MoClo Part. PCR primers are designed as shown in the top of the figure to include 2bp (NN), then the 6bp BpiI site (in purple), 2bp (NN), then the 4-bp fusion site (in blue), followed by 18-24bp of the DNA part of interest. Once amplified with high fidelity DNA polymerase, the PCR product is mixed with the Level 0 Destination Vector that has matching fusion sites in a MoClo reaction to create the final Level 0 MoClo Part shown in the final plasmid. (Figure from BBF RFC 94: The Modular Cloning Assembly: Standardized Assembly of Bacterial Transcriptional Units Using Type IIS Restriction Enzymes BsaI and BpiI, Traci Haddock and Douglas Densmore, 2013.)