Topics

1

General discussions (Q&As) / how to bend a big DNA soomthly?

« on: July 26, 2012, 06:36:33 pm »

Hi,

I want to make a smooth circular bend structure of DNA using 3DNA. The DNA contains 88 base pairs.  I can't able to control the roll parameters that actually produce a smooth circular bend structure of this DNA. How do I choose the roll parameters. Is there any way to choose those parameters? I have followed the same procedure (the roll parameters chosen as sinusoidal) which as proposed in nature protocol paper. However, I have failed to put those parameters in the correct position of bp_step.par file. As a result I get a bend structure but the structure is zigzag type. In this regard if you have any suggestion please let me know.

Looking forward to hear from you soon.

Thanks in advance
Sudipta

2

General discussions (Q&As) / How to bend DNA in a protein-DNA complex

« on: July 12, 2012, 03:40:56 pm »

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

3

General discussions (Q&As) / which parameter shall I change to produce bend DNA

« on: July 05, 2012, 03:33:36 pm »

Hi,
Is it possible to rebuild a  new bend DNA using 3DNA? if so, which parameter should I change? I have seen in the documentation that the changing of  parameter, 'roll' can produce the bend DNA. However, there is no  step by step procedure in the documentation for that. Please explain figure 2 in the documentation. How to obtain that bend DNA with  curvature of 45^o by changing the roll parameter.
Thanks in advance
Sudipta