My strategy is for unpaired bases in loops:
Adenine gets 1 point
Uracil and Cytosine get 0 points
Stipulations (for the following):
- Applies to unpaired bases adjacent to stacks and paired bases only
- Applies to loops with only 2 stacks “coming out of it” (for loops with 3+ stacks Guanine gets 0 points)
If Guanine reduces Free Energy it gets 2 points else 0 points; the number of Guanine in the unpaired bases of a loop can not exceed 2.
Note:
I tried to express my system in the most basic terms above for programming but I have some specific situations that seem to hold true most of the time, though I think these lean toward “design strategies” (so don’t feel compelled to include these):
1-1 loops get 2 Guanine bases (2 points)
1-2 " get 2 Guanine bases (in 1-1 locations) (2 points)
1-3 " gets 1 Guanine base (in 1 location) (2 points)
1-4 " get 2 Guanine bases (in lowest FE combo) (2 points)
2-2 " get 2 Guanine bases (kitty corner) (2 points)
The following seem to hold true less often:
2-3 loops get 2 Guanine bases (kitty corner) (1.5 points)
end loops (any size) get 1 Guanine at lowest Free Energy (1.5 points)