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Author Topic: How to analyze helical parameters of DNA with unnatural bases  (Read 28839 times)

Offline shengxiehuang

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How to analyze helical parameters of DNA with unnatural bases
« on: September 18, 2017, 09:31:20 am »
Dear Mr Lu,
  Recently, we are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, base pairs DX:DA / DY:DA / DZ:DA can’t be recoganized when I used “find_pair”. Notably, the unrecoganized base-pair (named DX, DY, DZ, DA) are not typical purine or pyrimidine. How can I analysis the conformation parameters with 3DNA in a such case. 
  The pdb files of DX, DY, DZ, DA and a frame of MD simulations are given in the attachment . Thank you very much!

Best wishes!

Xiehuang Sheng

Offline xiangjun

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Re: How to analyze helical parameters of DNA with unnatural bases
« Reply #1 on: September 18, 2017, 10:38:50 pm »
Hi Xiehuang,

I've had a look of your attached PDB files. DX/DY/DZ deviate too much from normal purines in terms of base orientation and atoms nomenclature, as shown in the attached image for DX. They are no longer recognized as nucleotides so "find_pair" cannot identify any pairs associated with them. This is clearly a limitation of 3DNA.

Xiang-Jun
« Last Edit: September 19, 2017, 02:51:22 pm by xiangjun »

 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University