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General discussions (Q&As) / DNA Triple Helix Generation

« on: October 20, 2011, 04:31:49 am »

Hello everyone,

I want to generate the DNA Triple Helix. So I docked Double Helix DNA with Single Stranded DNA.
But, the ssDNA show intramolecular bonding(backbone and nitrogen bases) which is un-usual.
Most of the softwares are based on the energy functions.

Can we ignore those bonds ?
Why DNA-DNA docking is not possible for larger size DNA(ligand)?
Is there any rotational bond limitations for DNA-DNA docking?

Any help or suggestions would be greatly appreciated.

Thanks
Himanshu