How do I stabilize a single base pairing flanked by unpaired bases and a loop?

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  • Updated 9 years ago
I'm routinely having difficulty with configurations where there is a stack, two unpaired bases, a single base pair, then a loop of 3 or more. The single pair I always make a G-C pair but I can't seem to get it to hold and not open up. I've tried all sorts of configurations of the unpaired bases and stack but I've one puzzle that has continued to open up, unpairing that single G-C pair. Suggestions?
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redmountain

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Posted 9 years ago

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Photo of Matt Baumgartner [mpb21]

Matt Baumgartner [mpb21], Alum

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The loops guide may be of interest to you.
http://getsatisfaction.com/eternagame...
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redmountain

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Matt, I had read that. I've tried putting guanines in without success. Actually, I have better luck in general with U's rather than G's in many cases especially in a hexagonal configuration where unpaired bases are flanked by pairs. My rationale is that it is better to have a small unpaired bases rather than large bases so that steric interference is minimized. Loops are another matter and I've not found a strategy that works in all cases. My question is specifically for a small subset of loops where they are held by a single base pair and the general stuff discussed at that link don't necessarily seem to apply to the case that is stumping me at the moment.
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Chris Cunningham [ccccc]

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The easiest way to get an answer would be to post an example puzzle where it comes up. Then people who have solved many, many puzzles would just open up the puzzle, see that they had figured it out, and tell you how they did it.