Friday, 16 May 2014

SBOL for gene design? - postscript

There's an added complication to my previous post on using SBOL for gene design.

The system that I am designing has two phases. The first is the assembly phase, involving arrangement of short single-stranded oligomers as shown in Figure 1:

Figure 1: Synthetic gene assembly from short single-stranded oligomers. See full interactive results.

After this has been fully assembled into double stranded DNA through PCR, the double stranded DNA is inserted into a plasmid for expression (let's call this the ligation phase).

At this point, the system resembles the following (figure 2), and my guess is that this is more typical of systems that have been considered by SBOL so far:

Figure 2: Double-stranded DNA system, consisting of a single coding sequence bookended by overhanging sequences for ligation into an expression plasmid.

The two steps / figures are clearly related, but how would such a system be represented in SBOL? Or should we even try?