non paired base interactions

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  • Updated 8 years ago
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what strength are the interactions between base pairs

we know that
AU GU and GC form bonds of various strengths

if those are strength 2, 1 and 3 respectively

please could you let us know what the strength of the (repulsive?) interactions between these base combinations are.

AA
UU
GG
CC
AG
and
CU

or is this already written up somewhere ?
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Edward Lane

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Posted 8 years ago

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Jeehyung Lee, Alum

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Hi Edward,

Yes, there are non paired base interactions in RNA if you fully simulate them..and it depends on how close each bases are to each other, their orientations, the cavity surrounding the bases, etc.

In EteRNA though, those small interactions are not simulated for 2 reasons. 1) Base pair interactions dominate the secondary structure fold of RNAs 2) rendering all the small interactions would make the game unplayable in the real time. However, non paired base interactions will be rendered in some level when we move onto EteRNA 3D in future.