helical Parameters of a Modified nucleic acids

[Mathew]

Hi,
I am trying to calculate the helical parameters of a modified nucleic acid xDNA, which contains 4 modified bases and the normal bases.
Each modified base contains an additional bezene ring. I ahve tried the suggestion for adding the entry for additional bases in baselist.dat file. Atomic_X.pdb files for each new entry were added in the BASEPAIRS directory. Modified adenines and Guanines were identified by the program, but the modified Thymine and Cytosine were not identified.Modified ADE and GUA have same connection atom with the sugar, but the connection atom name is different for CYT and THY. I have also tried by modified ADE as A, GUA as G etc. Here also the purines were identified and pyrimidines were not.How can I make the program identify the new residues?

 
Thanking You for your help,

Mathew

[xiangjun]

Hi Mathew,

Thanks for using 3DNA. As suggested, could you provide us a minimal reproducible example (using attachment) so others see clearly what's going wrong? I understand your description of the problem, but need more details to provide you a solution.

Xiang-Jun

[Mathew]

Hi,

I am sending my pdb file of the modified nuclic acid, baselist.dat, and input file created with find_pair.
I have given names W, X, Y, and Z for the modified bases and added Atomic_X.pdb, Atomic_Y.pdb etc. in the BASEPAIRS directory.
Thes files were extracted from the pdb file of the molecle, by taking just the coordinates of the corresponding bases.


I have edited the cent.inp file to include the missing basepairs and tried to run analyse. Here I got an error message that an unknown residue in the chain 1
------------------------------------------------------------------------
......Processing structure #1: <cent02.inp>......

 ...... /usr/people/X3DNA/BASEPARS/ ......
 ...... reading file: misc_3dna.par ......

 ...... /usr/people/X3DNA/BASEPARS/ ......
 ...... reading file: baselist.dat ......
Non-base: residue XT5    1  on chain   [#1]
-----------------------------------------------------------------------

Looking forward to your help,

Thanking you,

Mahew

[xiangjun]

Thanks for adding the attachments -- now the problem becomes quite clear.

Your modified bases, with an additional benzene ring, are so different from the normal cases where the modifications are on the exocyclic atoms, or some of the base ring atoms,  that the mechanism provided with 3DNA (baselist.dat") is no longer applicable.

For example, for residue #3 (XTY, a modified pyrimidine) there is no "N1" atom but a "N" atom. Moreover, it is the C8 atom on the benzene ring that connects to the sugar, not the normal "N1" atom.

If you attach all of the modified Atomic_?.pdb files, I would like to look further: maybe I could make some modifications to the code to incorporate these dramatic changes.

Hope this clarifies the issue.

Xiang-Jun

[Mathew]

Hi Xiangjun,

Thanks for your detailed reply.
I am attaching herewith the Atomic_?.pdb, which are taken from the xDNA by just taking the coordiantes of the modified bases. (I have added xae,xga,xcs and xty with the files to distingish them. In baselist.dat the name is only Atomic_X.pdb etc.)
In some of the xDNA papers, The authors   used 3dna and curves for calculating the the helical parameters. In the case of curves, the atom which is connected to the   C1' is just converted to nitrogen and renamed it to N1. Is this a valid thing to do?  

Thanks for you help.

Mathew

[xiangjun]

Hi Mathew,

Thanks for your cooperation. I am aware of the xDNA story, and actually helped a 3DNA user on a modified purine a while ago. I need to dig it out -- it is buried in somewhere... Now you see the importance of this forum!

I am pretty occupied right now, but I will get back to you about your modified bases when I get time. Please check back in a week or so.

Xiang-Jun

[Mathew]

Dear Dr.Lu,

Thanks for your reply.
Hope that you will look into the XDNA parameters calculation

Thanks in advace

Mathew

[xiangjun]

Hi Mathew,

I have checked the files you uploaded. There are a few issues that are needed to be clarified to run 3DNA against your XDNA structure:

• Each Atomic_?.pdb file must be set with regard to the standard base reference frame, not just taken directly from a PDB file, as in your four attachments. Have a look (e.g., using RasMol of Atomic_A.pdb with the 3DNA distribution to see an example).
  
• For 3DNA to take a residue as a nucleotide, it must contain at least a six-membered ring with standard atom names common to A/C/G/T/U etc, including the " N1 " atom. In you modified Y bases (Atomic_Y-xty.pdb, Atomic_Z-xcs.pdb and Atomic_W-xae.pdb), you have atom " N  " in place of " N1 ". In your cent02.pdb file, you also have atom " ND " in stead of " N1 " in residue XCS. That's why thay are not recognized by 3DNA. The modified R base, Atomic_X-xga.pdb, is fine.
  
• So to get to the bottom of it, you need to manually edit your cent02.pdb file to change " N  " and "  ND " to " N1 ", which I have done and attached as cent02_N1.pdb. Your Atomic_X-xga.pdb does not conform to PDB format (check Chain ID column), and you need to manually change atom name " N  " to " N1 " in the other 3 Atomic_?-???.pdb files. I have modified "std_base" with option "-fit" to set a nucleotide with regard to the standard base reference frame to be used with 3DNA, and I have attached the re-oriented bases as Atomic_r.pdb and Atomic_y.pdb. You could also use Atomic_R.pdb and Atomi_Y.pdb, but the small case letter would lead 3DNA print out diagnostic message.
  
• You do not need to have a separate Atomic_?.pdb file for each modified base. In your case, two should be enough, and the updated baselist.dat is as follows:
  
  Code: [Select]
  # for XDNA residues from Mathew
XTY     y
XCS     y
XT5     y
XAE     r
XGA     r
XA5     r
DT3     t
DA3     a
• I have also attached the 3DNA 'analyze' output file cent02_N1.out (renamed cent02_N1.txt so it can be attached) for your reference.
  
• As I said in my previous email, I helped another 3DNA user on XDNA a while ago, and here is the URL for some of the info I provided: http://rutchem.rutgers.edu/~xiangjun/3D ... /xdna.html. Please download the updated 'std_base' program (Linux version) there. In the coming new release of 3DNA v2.0 (no specific date yet!), the "-fit" option comes as built in.

HTH,

Xiang-Jun

[Mathew]

Dear Dr. Lu,

With your help I have calculated the helical parameters of the xdna.


Thank you verymuch for your help.


Mathew