I’m starting to play with ways to make the relationships between the nucleotides more apparent in the switch labs.
Here is an image with the two shapes for one submission:
And again with related NTs circled with the same color:
With all related groups colored it becomes hard to read. With just a couple of groups, it is easier to follow. For example, here is an image with just the dependencies related to NTs 18-22 colored in:
Another way to denote dependencies is to use lists of paired nodes. For example:
position 44 is fixed at A (pairs with 27),
position 27 is fixed at U (pairs with 44 and 58),
position 58 is assigned A (pairs with 27 and 67),
position 67 is assigned U (pairs with 58 and 18),
position 18 is assigned G (pairs with 67 and 52),
position 52 is assigned C (pairs with 18).
With this notation we can see possibilities for changes:
58 could possibly become G, forming two GU bonds instead of AU bonds;
if it did, 67 could possibly become C forming two GC bonds.
52 could possibly become U forming a GU bond;
if it did, 18 could possibly become A, forming two AU bonds.
Sometimes (especially at loop openings) it is important to note that pairs do NOT form as in:
Here we specify that the fixed A26 should *not* bond with the NT at 59. In this case we used C, but it might be possible to use G instead and invert the rest of the chain, giving:
And, when tested, that also works! So by using an appropriate notation, not only can we see how things are related, but what some other possibilities might be.