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Author Topic: how to analyse a DNA structure which contains isonucleotides  (Read 12333 times)

Offline orangel

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how to analyse a DNA structure which contains isonucleotides
« on: November 12, 2006, 07:23:11 pm »
:?:
My Question is:  If I want to analyse a DNA structure contain iso-nucleotides(for example isoG),what should I do? Maybe I should generate Atomic_isog.pdb file so that the program would recognize my iso-nucleotide,is that right?By the way,this DNA structure is a G-quartet structure,should I analyse it as the quardruplex?
Thanks!

Offline xiangjun

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« Reply #1 on: November 13, 2006, 09:45:13 pm »
Thanks for using 3DNA.

Please refer to  3DNA FAQs on how modified bases are handled in 3DNA, and a working example. Basically, it should be a straightforward process, and the simple scheme works for all the cases we are aware of so far. As far as base-pair parameter goes, the method should also work for the isonucleotide. However, since the base in isonucleotide is not connected to the C1' sugar  atom, the lambda virtual angle and the chi torsion angles will not be what you wanted.

As to the analysis of G-quartet structure, please have a look of the README file in the directory Examples/Triplex in 3DNA distribution. If you follow the directions there and play around a little bit, you would have a better understanding of how 3DNA can be applied in normal nucleotide structures. Again, for the isonucleotide structures, some special handling might be necessay. Could you please send me some sample isonucleitde structures (via email) so I can have a look?

Thanks,

HTH,

Xiangjun

Offline xiangjun

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« Reply #2 on: November 16, 2006, 12:18:24 am »
Hi,

Thanks for sending me the 3 coordinate files via email -- they are helpful in clarifying the issue.

You might be interested to know that in the future, you no longer need to send us email with attachments: I have set up a file upload forum at URL:
http://3dna.rutgers.edu:8080/upload/ so that users can send related information for us to debug and solve their problems. This will also allow for storage and consistent handling of user-cases.

As to your questions, firstly, you can run find_pair on it after adding the following entries to the file baselist.dat, as documented in the FAQs:
Code: [Select]
DG5     G
DG      G
DC      C
MOL     g
DC3     C
Secondly, given the irregularity of the the G-quartet structure, the normal double strand parameters obviously no longer apply. However, you can run the following to get backbone torsion angle etc parameters (of course, watch out the chi torsion related to isoG residue):
Code: [Select]
find_pair -s L1_avstr_min.pdb stdout | analyzeYou can also
Code: [Select]
find_pair -p L1_avstr_min.pdb  multi.infoThe program identifies the two G-quartets. The file multiplets.pdb contained the structures of the multiplets, which you can extract and generate publication quality images, as referred in my previous reply.

Thirdly, with the utility program blocview, run as follows:
Code: [Select]
blocview -i=L1_view.jpg L1_avstr_min.pdb
blocview -i=L1_view_z40.jpg -z=40 L1_avstr_min.pdb

You will get the following two images:


which is the default,  and
,
with a rotation about z-axis by 40 degress to make it "vertical". The color coding the Gs and Cs make them clearly distinguished, and the black minor groove edges of Gs are also obvious, and of course, the stacking ...

The 3 in 3DNA certainly not only stands for 3-dimension, but also the three integrated parts: analysis, rebuilding and visualizaion. Such block view images have been used in the NDB, and PDB. Somehow, it has not been widely adopted by the 3DNA community at large. I am just taking this opportunity to illustrate some of the not-commonly used features.

HTH,

Xiang-Jun

 

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.