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Author Topic: treating abasic site and THF with 3DNA  (Read 2160 times)

Offline xiaoxia05

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treating abasic site and THF with 3DNA
« on: January 17, 2019, 12:34:02 pm »
Hi Xiao-Jun,

I would like to use 3DNA to get some structural parameters and bending angle of two oligonucleoides: one containing an abasic site in an extrahelical position and without an empty space within the double helix (test_dna_DAP.pdb) , another one containing THF (tetrahydrofuran) in intrahelical position and with the orphan base (test_dna_THF.pdb)

I screened through the forum and I found out that the option --abasic is only applicable for DSSR, can you tell me if the option is also avalaible in 3DNA? If yes, how can I include it in the find_pair and analyze command?

Otherwise, I saw in a post that we can modified manually the find_pair output so that 3DNA can identified these two residues that don't have base atoms. Can you tell me what does the last five columns mean and how can I get these numbers correctly?

Thanks in advance for your help,
Xia

Offline xiangjun

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Re: treating abasic site and THF with 3DNA
« Reply #1 on: January 18, 2019, 10:46:39 am »
Hi Xia,

Thanks for using 3DNA and DSSR, and for posting your questions on the Forum. Your description and the two attached PDB files help clarify the issue. Overall, 3DNA and DSSR are behaving as designed.

Quote
I screened through the forum and I found out that the option --abasic is only applicable for DSSR, can you tell me if the option is also avalaible in 3DNA? If yes, how can I include it in the find_pair and analyze command?

The DSSR --abasic option takes abasic sites in the assignment of loops and the summary output. For example, DAP1030 in your test_dna_DAP.pdb file is classified as a bugle:

Code: [Select]
List of 1 bulge
   1 bulge: nts=5; [0,1]; linked by [#1,#2]
     summary: [2] 0 1 [X.797 X.1031 X.798 X.1029] 7 8
     nts=5 AAT?T X.DA797,X.DA798,X.DT1029,X.DAP1030,X.DT1031
       nts=0
       nts=1 ? X.DAP1030

And MOL885 in test_dna_THF.pdb is part of an internal loop:

Code: [Select]
List of 1 internal loop
   1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2]
     summary: [2] 1 1 [X.884 X.943 X.886 X.941] 8 7
     nts=6 T?TAAA X.DT884,X.MOL885,X.DT886,X.DA941,X.DA942,X.DA943
       nts=1 ? X.MOL885
       nts=1 A X.DA942

Since no base atoms are available, no base-pair parameters can be calculated.

Note that as of v1.7.3-2017dec26, the --abasic option is set by default in DSSR. So users no longer need to specify it explicitly. On the other hand, one can use --abasic=no to see how DSSR behaves by not taking abasic sites into considerations.

Quote
Otherwise, I saw in a post that we can modified manually the find_pair output so that 3DNA can identified these two residues that don't have base atoms. Can you tell me what does the last five columns mean and how can I get these numbers correctly?

There is no --abasic option in 3DNA (v2.x and before). It is not meaningful to manually add an abasic site to the find_pair output and then feed it into analyze. No magic here: without base atoms, the base reference frame cannot be defined, so no base-pair parameters are available.

The last five columns of the find_pair output are some parameters related to the identified pairs. They represent "d, dv, angle, dNN, dsum" -- check the source code for details. Users do not need to manipulate (or care about) them: they are for information only and is ignored by analyze.

HTH,

Xiang-Jun
« Last Edit: January 18, 2019, 10:52:11 am by xiangjun »

 

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.