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Questions and answers => General discussions (Q&As) => Topic started by: sgu0752 on June 11, 2019, 03:52:55 pm

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Title: H-bonding information
Post by: sgu0752 on June 11, 2019, 03:52:55 pm
Hi,

I'm analyzing the hydrogen bonding interactions of CC mismatches in DNA, and I came across some interesting hydrogen bonding symbols. While I know that the hyphen '-' between two atoms indicates hydrogen bonding, what does '*' represent? Is it because the hydrogen donor/acceptor roles are vague?

I've attached the summary file below of my results.

Thanks for your time.

Stephanie
Title: Re: H-bonding information
Post by: xiangjun on June 11, 2019, 04:17:39 pm
Hi Stephanie,

Thanks for using 3DNA and for posting your questions on the 3DNA Forum. Your attached file helps illustrate the issue at hand, as shown below for the H-bonding section from the 3DNA output file:

Code: [Select]
Detailed H-bond information: atom-name pair and length [ O N]
   1 T-**+-T  [1]  O2 * O2  3.47
   2 C-**+-C  [3]  O2 - N4  2.82  N3 * N3  2.78  N4 - O2  2.83
   3 C-**+-C  [3]  O2 - N4  2.82  N3 * N3  2.78  N4 - O2  2.85
   4 C-**+-C  [3]  O2 - N4  2.88  N3 * N3  2.82  N4 - O2  2.89
   5 C-**+-C  [3]  O2 - N4  2.84  N3 * N3  2.72  N4 - O2  2.78

For a C+C pair as in the i-motif, the N3...N3 H-bond is between an acceptor (N3) to another acceptor (N3) when C is in its canonical tautomeric form (as in Watson-Crick G--C pairs). The hemi-protonated C cannot be judged from the atomic coordinates. That's what the * symbol is about. Overall 3DNA does not use hydrogen atoms at all in deducing H-bonds.

Have a look of DSSR (http://docs.x3dna.org/dssr-manual.pdf), especially "3.16 The --get-hbond option".

Best regards,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.