3DNA Forum

Questions and answers => MD simulations => Topic started by: tpc2005 on November 19, 2016, 02:33:19 pm

Title: How to fix the phosphate on the DNA backbone
Post by: tpc2005 on November 19, 2016, 02:33:19 pm: Hi,

I have two DNA structures from PDB. I designed a five-base-pair linker to connect these two DNA structures by using BIOVIA Discovery Studio. I've almost done it but found there are two breaking points on the phosphate backbone. Does anyone know how to fix it? Thanks so much!

Best,
Lester
Title: Re: How to fix the phosphate on the DNA backbone
Post by: tpc2005 on November 19, 2016, 03:08:07 pm: Please see the attachment of pdb file.
The two breaks happen on (chain D:position 6, chain D:position 7) and (chain C:position 20, chain M:position 7).

Appreciate!
Title: Re: How to fix the phosphate on the DNA backbone
Post by: xiangjun on November 19, 2016, 04:58:22 pm: From the PDB file you attached, one can see that the distance of O3'(DA6)...P(DT7) on chain D is 7.07 Å, which quite far from the regular ~1.6 Å. On the other hand, DC20 is on chain C, and DT7 is on chain M, which are not supposed to be connected (the actual O3...P distance is 4.61 Å). So it is not a surprise that your DNA structure has two breaking points.

To fix them, you may want to change chain ID to be consistent, and perform some sort of energy minimizations (which is out of the scope of 3DNA per se). See for example, my blogpost titled "Restraint optimization of DNA backbone geometry using PHENIX (http://x3dna.org/highlights/restraint-optimization-of-dna-backbone-geometry-using-phenix)".

Best regards,

Xiang-Jun
Title: Re: How to fix the phosphate on the DNA backbone
Post by: tpc2005 on November 20, 2016, 03:31:26 am: Thanks so much for the quick reply! I will try PHENIX!