Daniel:Notebook/ComboLock/2016-12-9
Lock Oligo Protocol
This protocol covers a new method using ideas taken from Weibrecht et al New Biotechnology 2012 (Landegren lab). The main idea I see is that they almost never use polymerase, but prefer to instead use ligation events as the predominant form. Based on the results from the extended latch experiment, the RCA-based cell test, and the sequencing from the first circularization test, it seems the probes do not circularize correctly. Note the original orientation of the C probes with the 5' end being the genome matching region and the 3' end being the latch/padlock adapter.
When subjected to polymerization, if the latch is not present this yields a product that follows the backbone of the second C probe. See image below for clarification.
Instead, we now introduce the mirror C probes. These C probes have their 3' and 5' ends reversed such that the 3' end is the genome matching region and the 5' end is the adapter region.