I'm programming an implementation of an algorithm for pattern matching in RNA structures. The algorithm assumes the following types of base pairs:
- Plain: No base pairs (just the primary structure of the RNA)
- Single: Each base can be connected to at most one other base
- Multiple: Each base can be maximally connected to a number of other bases (where 'number' can be constant or infinite)
Although there is no problem with the implementation of the above types of base pairs (apart from the probable high computation complexity), I wonder if all of them were observed in real RNAs?
In particular, I'm interested in the following cases:
- A base pair between two adjacent bases i,j.
- One base (i) which connected to two different bases (j,k) (i is not adjacent to j or/and k).
- One base (i) which connected to more than two different bases, all of them not adjacent to i.
Can these exist? Some of them? If they can, how common is their existence?