Re: AMBER: Question about NAB (Nucleic Acid Builder)

From: David A. Case <>
Date: Wed, 11 Jul 2007 16:23:05 -0700

On Wed, Jul 11, 2007, Cenk Andac wrote:
> I have an RNA hairpin system whose crystal structure is available. I would
> like to throw in a single-stranded anti-sense d(CCG) DNA into the system and
> base-pair it with a complemetary sequence (with three nicely stacking bases)
> in the loop region of the RNA hairpin without disturbing much of the crystal
> structure coordinates in the system. Is this doable by the NAB (Nucleic Acid
> Builder ) program?

Sounds very tough. If you have an idea of how to go about the model building,
NAB can help you turn ideas into a real program. But it doesn't arbitrarily
solve problems by itself.

You might want to just put in H-bonds you want to form as "NMR" constraints,
then run some annealing protocol with the two molecules to get them to come
together, perhaps also restraining the RNA hairpin to not move far from its
starting position. But that's just one idea.

...good luck...dac

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Received on Sun Jul 15 2007 - 06:07:13 PDT
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