How to bend DNA in a protein-DNA complex

[sudipta]

Hi,

I am working on a homo-dimer DNA complex. My initial aim is to make a  bend protein-DNA complex of that homo-dimer DNA complex. For free DNA molecule, it is easy to make that bend DNA using 3DNA. However, for that protein-DNA complex, it seems difficult because 3DNA only operates on DNA. The 3DNA does not transform the coordinates of the protein. Is there any option or any method  that makes the bend DNA-protein complex? 

Looking forward to hear from you.

Best
Sudipta

[xiangjun]

Could you please make your point specific by using a concreate example? What do your mean "it is easy to make that bend DNA using 3DNA"?

Xiang-Jun

[sudipta]

Hi,
Thank you very much for the reply.

Actually, if I change the roll angle in the bp_step.par file and do rebuild for a free DNA molecule then the DNA undergoes bend. However, for protein-DNA complex, I think it is tedious because  the information for protein does not contain in bp_step.par file. So my point is , is there any way to incorporate protein information in the bp_step.par file such that the whole complex undergoes bend.

Thanks in advance
Sudipta

[xiangjun]

is there any way to incorporate protein information in the bp_step.par file such that the whole complex undergoes bend.

No. The rebuilding process in 3DNA is purely geometric, and it does not handle protein explicitly. If you have a DNA-protein complex to start with, bending DNA will most likely cause steric clashes.

Xiang-Jun

[sudipta]

Hi,

OK

sudipta