The core technology allows for the assembly of long sequences of DNA units. The elegant approach is simple, inexpensive and robust.

Two fragments (units) of DNA can be joined by an enyzme, DNA ligase, if the units have compatible (sticky) ends (Figure 1). These sticky overhangs can easily be prepared by first attaching a special sequence (called a primer) to either end of the DNA units, performing the amplification of the DNA units, and then applying an enzyme, called a restriction enzyme that cuts out part of the primer sequence at its recognition site, leaving compatible overhangs. Attaching the sequence, applying the restriction enzyme and the DNA ligase are all standard techniques, so what stops anyone from assembling any DNA units in any order they wish?

Unfortunately, it is not possible to perform a complex directed assembly using traditional techniques since at each step, typically, we need to apply the restriction enzyme responsible for preparing the compatible sticky ends, and this cuts the product we are assembling back into its constituent pieces (Figure 2). To progress we would have to use a different restriction enzyme at each step and engineer the corresponding recognition sites. If we needed to join a large number of units this approach would be very complex, but in any case would quickly become impossible as there are not enough viable (unique) restriction enzymes.

The core technology is based on the the Protectable Junction Construct™: protection of the junctions as they are formed, so that once joined, the DNA units are no longer disassembled by the restriction enzyme we are using.

Figure 3 shows how, if the join is protected, a sequence of DNA units can be assembled in a directed fashion.

Figure 1. Restriction Enzymes can cut DNA to leave compatible 'sticky' ends which can then be joined by DNA ligase.

Figure 2. Application of a restriction enzyme to previous joins cuts again.

Figure 3. By protecting ( ) the join we can assemble a long chain of DNA units in any sequence we desire.