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===Lock Oligos (Ligation-Based Templates)=== I have also had a second idea based off the Landegren (Weibrecht) paper. The idea is to add a ligation event that will connect together the two C probes (via the latch). This will provide a stable template for the padlock probe that becomes latch independent. First, we look at just the latch binding. Now I introduce the "Lock oligo", which is reverse complement to the latch oligo. Rather than incubating the latch and padlock at the same time, we incubate the lock and latch at the same time which ligate the C probes together. It then no longer matters if the latch remains bound to the adapter regions, the padlock has a contiguous template to work off. <gallery perrow=2 heights=300px widths=400px caption="Modified latch-padlock system integrating the lock oligo. Lock/Latch binding is ligase based-only creating a solid block to read for polymerization. C probe in red, mirror C probe in blue, latch in dashed green, polymerization-added bases in magenta, lock oligo in brown, and template in black."> File:Latch_Binding.png|Latch binding event File:LockBinding.png|Lock binding event; the lock is RC to the region between adapters (in v1 latches, the barcode+UMI) File:LockBridge.png|Lock-C probe ligation produces a "bridge" for padlock circularization File:LockPadlockCircularization.png|Padlock now binds with a complete template and can circularize/ligate for further amplification </gallery>
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