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1
General discussions (Q&As) / Re: treating abasic site and THF with 3DNA
« Last post by xiangjun 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
2
General discussions (Q&As) / treating abasic site and THF with 3DNA
« Last post by xiaoxia05 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
3
General discussions (Q&As) / Re: mutations to 3-methyladenine
« Last post by meixianghao on January 17, 2019, 02:34:22 am »
Dear Mr Lu,

Thanks for your kindly help! It is indeed fast to create a B-form DNA model using the 3DNA fiber program , and the command mutate_bases is easy but strong!

Best wishes!

Ling-Yan
4
RNA structures (DSSR) / Re: Stems of junction structure have only one base pair
« Last post by xiangjun on January 16, 2019, 01:08:16 pm »
You're welcome. As mentioned on the Forum and in the manual, DSSR contains many undocumented 'features'. User questions on subtle/technical aspects in DSSR are always gladly received.

As a side note, by including isPairs in loops by default, it is possible to filter DSSR output as users see fit. For example, by parsing for the negative index (#-49), or no. of pairs in a stem (1), users can easily remove the 3-way junction.

Quote
1 3-way junction: nts=11; [2,1,2]; linked by [#63,#64,#-49]
     summary: [3] 2 1 2 [i2.1225 i2.1641 i2.1228 i2.1530 i2.1532 i2.1638] 5 3 1

Along the line, it is also feasible to select junction loops with a stem length of e.g. 3 or more canonical pairs.

Best regards,

Xiang-Jun
5
RNA structures (DSSR) / Re: Stems of junction structure have only one base pair
« Last post by lijun on January 16, 2019, 11:43:47 am »
Hi Xiang-Jun,

Thanks for your prompt reply and help.

Jun Li

Hi Jun Li,

Thanks for using DSSR and for posting your questions on the 3DNA Forum.

I understand that the inclusion of isolated canonical pairs (icPairs, those with negative index numbers) in delineating loops may lead to 'spurious' (junction) loops. I am so glad that this issue has been finally brought up on the Forum.

As far as I know, no consensus exists as to whether icPairs should be (always) included in the delineation of loops. Without taking them into consideration, however, the widely documented GUAA tetraloop in PDB entry 1msy (see figure below) cannot be logically identified. That's why DSSR counts icPairs in loops, by default.


While undocumented, DSSR has an option to exclude icPairs from loops, i.e. (--loop-exclude-icpair). Run DSSR with this option on your example PDB entry 5vyc, you'd find that the 3-way junction you reported is gone.


In a similar way, it is also debatable if a non-canonical base pair in an otherwise 'regular' double helix should be taken as part of a stem or as an internal loop. As noted in the 2015 DSSR paper in NAR:
Quote
Following standard conventions (13,35–36), DSSR by default uses only canonical pairs to identify stems and to characterize pseudoknots. Nevertheless, the program contains provisions for including noncanonical pairs in an extended definition of stems

It is my hope that DSSR would help 'standardize' the field, probably in the long run.

Best regards,

Xiang-Jun
6
RNA structures (DSSR) / Re: Stems of junction structure have only one base pair
« Last post by xiangjun on January 15, 2019, 11:40:24 pm »
Hi Jun Li,

Thanks for using DSSR and for posting your questions on the 3DNA Forum.

I understand that the inclusion of isolated canonical pairs (icPairs, those with negative index numbers) in delineating loops may lead to 'spurious' (junction) loops. I am so glad that this issue has been finally brought up on the Forum.

As far as I know, no consensus exists as to whether icPairs should be (always) included in the delineation of loops. Without taking them into consideration, however, the widely documented GUAA tetraloop in PDB entry 1msy (see figure below) cannot be logically identified. That's why DSSR counts icPairs in loops, by default.


While undocumented, DSSR has an option to exclude icPairs from loops, i.e. (--loop-exclude-icpair). Run DSSR with this option on your example PDB entry 5vyc, you'd find that the 3-way junction you reported is gone.


In a similar way, it is also debatable if a non-canonical base pair in an otherwise 'regular' double helix should be taken as part of a stem or as an internal loop. As noted in the 2015 DSSR paper in NAR:
Quote
Following standard conventions (13,35–36), DSSR by default uses only canonical pairs to identify stems and to characterize pseudoknots. Nevertheless, the program contains provisions for including noncanonical pairs in an extended definition of stems

It is my hope that DSSR would help 'standardize' the field, probably in the long run.

Best regards,

Xiang-Jun
7
RNA structures (DSSR) / Stems of junction structure have only one base pair
« Last post by lijun on January 15, 2019, 08:27:34 pm »
Hi all,

I am using the newest DSSR to extract the junction structure, but the stems of some junctions have only one base pair. Take 5vyc.cif for an example and one of its 3-way junctions is as follows:

   1 3-way junction: nts=11; [2,1,2]; linked by [#63,#64,#-49]
     summary: [3] 2 1 2 [i2.1225 i2.1641 i2.1228 i2.1530 i2.1532 i2.1638] 5 3 1
     nts=11 UGGAUACGGAA 1..i2.U.1225.,1..i2.G.1226.,1..i2.G.1227.,1..i2.A.1228.,1..i2.U.1530.,1..i2.A.1531.,1..i2.C.1532.,1..i2.G.1638.,1..i2.G.1639.,1..i2.A.1640.,1..i2.A.1641.
       nts=2 GG 1..i2.G.1226.,1..i2.G.1227.
       nts=1 A 1..i2.A.1531.
       nts=2 GA 1..i2.G.1639.,1..i2.A.1640.

The last stem #-49 has only one base pair. There are many cases like this in the output. Is it reasonable to take structure like this as a junction?

Thanks,

Jun Li

8
As a follow-up of the initial request "Mutate_Bases: Option to mutate all residues of the same type to another". In 3DNA v3, I've added a new program named x3dna-mutate which can do this and much more, by incorporating the DSSR annotations. Some examples:

Code: [Select]
x3dna-mutate --mutation='to=A' -i=1ehz.pdb -o=1ehz-allA.pdb
x3dna-mutate --mutation='name=A to=G' -i=1ehz.pdb -o=1ehz-A2G.pdb
x3dna-mutate -m='to=A cond=hairpin' -i=1ehz.pdb -o=1ehz-hairpinsA.pdb
x3dna-mutate --m='name=A negate to=G' -i=1ehz.pdb -o=1ehz-nonA2G.pdb
x3dna-mutate --m='chain=A num=12 to=DT' -i=355d.pdb -o=355d_G12T.pdb
x3dna-mutate --m='num=12 to=DT; num=13 to=DA' -i=355d.pdb -o=355d_TA.pdb

Xiang-Jun
9
Hi Manish,

Thanks for your detailed responses to my follow-up questions. Presumably, such a back-and-forth conversational style should be the norm on an online forum. In practice, as one can see by browsing the 3DNA Forum, that is normally not the case. I sense users may just want a quick and straight answer to their questions, which are frequently not well defined. I then ask for clarifications, but oftentimes receive no responses.

Quote
I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.


I'm aware of the paper "Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians" by Heinz Sklenar et al. which may be relevant to the topic here.

Quote
' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q

I will follow these two links and see what I can get. Since your request in on sugar mutations which is not covered by the 'mutate_bases' program in 3DNA v2.x, please start a new thread for future communications.

Best regards,

Xiang-Jun
10
Hi Xiang-Jun,

First of all, thanks a lot for your earnest response. With regards to your first query, I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.

' Cannot you do it manually? '- I can do it manually but i will have to worry about the dihedral angles and bond length in the case of the mutated sugars and it might be inconsistent with the conformation that i have taken from the fiber model from web x3dna 2.0. So, O2'-C2'-C3'-C4' dihedral is the main cause of my concern.

' How do you consider the sugar conformations (C3'-endo vs C2'-endo) after adding O2' ?'- Ideally, I would like to have the sugar conformations unchanged for the modified bases after addition of O2', if there are no steric clashes. Then, I want to see what changes come up over time to these forcibly retained bases, through MD simulations.

' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q

I would be glad to listen to any of the ideas you have to make these modified sugars. Thanks again for your time and cooperation.

 
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.