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Questions and answers => RNA structures (DSSR) => Topic started by: lvelve0901 on January 20, 2020, 05:09:25 pm

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Title: How to detect very distorted base pair?
Post by: lvelve0901 on January 20, 2020, 05:09:25 pm

Dear Xiangjun,

I have a structure of a very distorted G-C base pair (C is modified) see attached. I want to output the base pair parameters like shear, buckle, opening but if I detect the base pair in DSSR it is not in the pair list. Could you please let me know how to analyze such very distorted base pair? Do I need to modify any cutoff?

Thanks.

Best,
Honglue

Title: Re: How to detect very distorted base pair?
Post by: xiangjun on January 20, 2020, 06:55:51 pm

Running DSSR with the default settings on distorted_bp.pdb

Code: [Select]

x3dna-dssr -i=distorted_bp.pdb --more
I got the following:

Code: [Select]

List of 1 base pair
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 K.DOC13        M.DG6          c-G --          n/a       cWW  cW-W
       [-122.8(anti) .... lambda=75.4] [-98.1(anti) .... lambda=84.4]
       d(C1'-C1')=7.91 d(N1-N9)=7.43 d(C6-C8)=9.40 tor(C1'-N1-N9-C1')=-11.8
       H-bonds[1]: "N4(amino)*N1(imino)[3.56]"
       interBase-angle=11  Simple-bpParams: Shear=-0.50 Stretch=0.34 Buckle=0.5 Propeller=-11.4
       bp-pars: [-0.52   0.30    0.26    1.33    -11.32  51.91]

Isn't that what you're looking for?

Xiang-Jun

Title: Re: How to detect very distorted base pair?
Post by: lvelve0901 on January 20, 2020, 07:03:32 pm

I see what is going on!

I was using DSSR version v1.6.5-2017jan22 and it failed to detect such base pair.

By using a new version you gave me before v1.9.4-2019jul08, I am able to detect it. Thanks.

Title: Re: How to detect very distorted base pair?
Post by: lvelve0901 on September 13, 2020, 12:31:45 pm

Dear Xiangjun,

I have two more examples of very distorted base pairs in existing PDB structures that X3DNA-DSSR is not able to detect it. I would like to know the reason and whether there is anyway to adjust the cutoff to be able to detect it?

(1) PDBID: 4NCB nt1: C.DT14 nt2: D.DA6
(2) PDBID: 5LGY nt1: E.DA17 nt2: F.DT5

Thanks.

Best,
Honglue

Title: Re: How to detect very distorted base pair?
Post by: xiangjun on September 13, 2020, 01:34:34 pm

Hi Honglue,

By default, DSSR does not detect these two base pairs because it fails to identify any H-bond between corresponding bases in each pair. These are the cases where users need pay attention to.

For your own understanding and the benefit of other users, it helps that you create an image for each of these base pairs, marking the distances between presumably H-bonded atoms.

Best regards,

Xiang-Jun

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