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81

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on March 14, 2025, 08:12:34 am »

Thanks for your follow-up questions and the details you provided. It is always helpful to to be specific when discussing research topics.

Yes, "rebuild -atomic" would have issues with backbone connectivity, since in Z-DNA, nucleotide G is in syn conformation instead of anti (for C). The building block must be adjusted accordingly. I'll look into this further to see what we can get.

Another approach is to take the whole Z-DNA structure as a unit, and perform some transformations to extend it. See the PyMOL thread a few years ago on "create a 26 bp RNA from a 13 bp system" (https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg16190.html). The idea is applicable to Z-DNA as well. Note that the features are now available in the free DSSR Academic license (previously in DSSR Pro Academic only). Check if that method makes sense to you.

Best regards,

Xiang-Jun

82

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by shr on March 14, 2025, 06:05:18 am »

Thank you for your quick responses!
My input structure is the PDB structure 1QBJ. It is a 6nt DNA. I have attached a picture. Without using the x3dna_utils, even without extending, the backbone cannot  be modelled due to the distance of O3' and P being over 4.5 and throws the following error. However, I also tested with the fiber model of Z-DNA to understand how it works with Z-DNA. I found that besides the backbone not being modelled which is because of the PDB dataset not being since I'm not using x3dna_utils, rebuild could model the bases as separate molecules. So, this is possibly the issue with my Z-DNA crystal structure model.

Another observation was, previously, for the crystal structure of BDNA complexed with the protein, I tried to manually extend the DNA in pymol but due to the terminal base positions, I could not properly build the double helix. But after analyze and rebuild, I could. So I assume it is due to standardization of the structure after rebuild. However, there is a problem with this method for Z-DNA. Even if I manage to standardize the structure, pymol does not offer building Z-DNA. So, I was wondering if I could add the extended DNA before rebuild. As you suggested, I modified the bp_step.par file since that is the file used as input for rebuild. Is that the correct way? I apologize if I am asking too many questions.   

83

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on March 13, 2025, 03:56:04 pm »

Thanks for your quick follow-up.

As noted in the x3dna_utils cp_std -h help message, the utility covers the most common use cases:

Select the standard data files to be used with "analyze" and "rebuild".
Available sets include BDNA, ADNA, NDB96 and RNA, which have exactly
the same base geometry and orientation (in the standard base reference
frame) but different backbone conformations.

Z-DNA is different from the standard right-handed DNA/RNA double helix in that it has not only a left-handed twist but also a base flip, and it has a di-nucleotide (most commonly CpG) as a the building block. So the x3dna_utils cp_std does not cover Z-DNA. However, you can run analyze, modify the output parameters (and extend as needed), and then rebuild a Z-DNA structure according to the modified parameters.

What specific Z-DNA structure you’d like to extend? If you do not want share details, please use a sample Z-DNA structure that helps illustrate your point. Reproducibility is important.

Best regards,

Xiang-Jun

84

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by shr on March 13, 2025, 02:23:03 pm »

I have a PDB structure of Z-DNA-protein complex that I wanted to simulate. Before simulation, I wanted to make the DNA longer to avoid the issue of the protein interacting with any of the terminal bases. I can use the following commands to achieve this in case of B-DNA:

find_pair 1MNN.pdb 1mnn.bps
x3dna_utils cp_std bdna
rebuild -atomic bp_step.par extended_dna.pdb

But x3dna_utils does not take zdna as an argument so I was wondering how I can do it?

85

General discussions (Q&As) / Re: Rebuilding Z-DNA

« Last post by xiangjun on March 13, 2025, 02:14:06 pm »

Hi,

Thanks for using 3DNA and for posting your questions on the Forum. 3DNA rebuild should be able to build Z-DNA structures given a set of parameters. Please be specific with what you are trying to achieve, and we can start from there.

Best regards,

Xiang-Jun

86

General discussions (Q&As) / Rebuilding Z-DNA

« Last post by shr on March 13, 2025, 02:10:17 pm »

I was wondering if there is a way to rebuild Z-DNA with rebuild module in the local installation of x3DNA. I know it works for B-DNA and A-DNA and I can make a Z-DNA fiber model as well but I couldn't find a direct way to extend an existing Z-DNA structure. Is there a workaround which I can try? Thank you in advance.

87

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by xiangjun on February 28, 2025, 08:47:06 am »

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun

88

General discussions (Q&As) / Re: Generation of ssDNA PDB with m3C modification using 3DNA webserver

« Last post by Sunera on February 27, 2025, 11:24:32 pm »

Hi Dr. Jun,

Sorry for the late reply. Yes, I definitely think the idea in the FAQ is relevant. But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

89

MD simulations / Re: Update of do_x3dna package

« Last post by xiangjun on February 22, 2025, 11:23:27 pm »

Hi Rajendra,

Thanks for the update to do_x3dna for GROMACS-2025. It is great that the "binary package can be used with files generated by any version of GROMACS". Over the years, I've received emails about applying 3DNA to MD simulations, and I know that your do_x3dna package is well received by the community.

Best regards,

Xiang-Jun

90

MD simulations / Update of do_x3dna package

« Last post by rkumar on February 22, 2025, 11:12:53 pm »

Dear All,

I have updated the do_x3dna package for GROMACS-2025. I have built binary executable of do_x3dna that can be downloaded and used without any compilation. Most importantly, this binary package can be used with files generated by any version of GROMACS.

Thanks,
Dr. Rajendra Kumar
Associate Professor
NIPER, Mohali, India