Messages

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) / Re: How to bend DNA in a protein-DNA complex

« on: July 12, 2012, 07:13:40 pm »

Hi,

OK

sudipta

3

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

« on: July 12, 2012, 06:40:06 pm »

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

4

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

5

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

« on: July 05, 2012, 07:24:48 pm »

Hi,

Thank you very much for your reply. Yes, I have seen some papers on protein influenced DNA bending.

Thanks again
Sudipta

6

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

« on: July 05, 2012, 05:56:37 pm »

Hi,

Thank you very much for your reply.

Another thing, if I want to perform a molecular dynamics simulation of a bend DNA (crated by 3DNA) using standard AMBER or CHARMM force field then is it possible. Are these force field parametrized for bend DNA? In other way, if I use standard CHARMM or AMBER force field for that then simulation be stable. Do you have any idea for that?

Thanking you
Sudipta

 

7

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

« on: July 05, 2012, 04:10:06 pm »

Hi,
Thank you very much for your reply.

Actually, I was asking about the figure 2 in the documentation file named as, 'x3dna_v1.5.pdf' .

Yes, I have seen the recipe 2 of that paper. But I don't understand what is the relation between roll angles and DNA bending angle. In that paper, I have seen there are four different possibility to obtain the same curvature. So, my question is what is the basis of choosing roll parameters for a specific DNA bending angle?

Thanking you
Sudipta

8

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