i-motif: increase the amount of consecutive CYS-CYS+ pairs

[vtatsis]

Dear x3dna Developers and Users,

I would like to examine the relation between the stability of the i-motif and the amount of its consecutive CYS-CYS+ pairs, employing computational methods.
Up to now, I have used successfully x3dna  to include defects in i-motif's sequence, while keeping the i-motif's length constant.
As a study molecule, in my computer simulations I used the pdb structure: 1ELN.

I would like to employ x3dna in order to increase the number of consecutive CYS-CYS+ of i-motif  from 3CYS's to 4CYS's and 5CYS's, but keeping the overall conformation of the i-motif structure.
For example, going from 5'-(CCCTAA)₃CCC-3' to 5'-(CCCCTAA)₃CCCC-3'  or 5'-(CCCCCTAA)₃CCCCC-3'


Thanks in advance for your help,

Vassilis

[xiangjun]

Hi Vassilis,

Thanks for using 3DNA and for posting your question on the Forum. I'm glad to see that you found 3DNA useful in your computer simulation studies of the important i-motif formed by semi-protonated C·C(+) pairs.

I would like to employ x3dna in order to increase the number of consecutive CYS-CYS+ of i-motif  from 3CYS's to 4CYS's and 5CYS's, but keeping the overall conformation of the i-motif structure.
For example, going from 5'-(CCCTAA)3CCC-3' to 5'-(CCCCTAA)3CCCC-3'  or 5'-(CCCCCTAA)3CCCCC-3'

3DNA was certainly not designed with such a use-case in mind. So you may well want to try an alternative tool such as NAB (Nucleic Acid Builder). However, 3DNA does provide the necessary 'raw' components to get such jobs done, as illustrated recently on the thread "DNA extending" (see also the thread "build dna bulges and extend dna duplex at both terminals via 3dna" from Users' contributions).

For your particular case, please reproduce (and try to understand) the following steps (assuming the PDB file for 1eln is named '1eln.pdb'):

Code: [Select]

pdb_frag A 1:9 A 13:21 1eln.pdb 1eln-c3taa.pdb
find_pair 1eln-c3taa.pdb 1eln-c3taa.bps
frame_mol -1 ref_frames.dat 1eln-c3taa.pdb 1eln-c3taa-frame1.pdb

pdb_frag A 1:2 A 13:14 A 8:9 A 20:21 1eln.pdb one-unit.pdb
find_pair one-unit.pdb one-unit.bps
frame_mol -3 ref_frames.dat one-unit.pdb one-unit-frame3.pdb

cat 1eln-c3taa-frame1.pdb one-unit-frame3.pdb > c4tta-raw.pdb
I have attached files '1eln-c3taa.pdb', '1eln-c3taa-frame1.pdb', 'one-unit.pdb', 'one-unit-frame3.pdb', and 'c4tta-raw.pdb', and image 'c4tta.png' for your reference and verification. After further clean up of the overlapped nts, you should get 4Cs version. Similar procedures apply to the 5Cs or even longer version.

HTH,

Xiang-Jun

[vtatsis]

Dear Xiang-Jun,

thank you very much for your swift response to my question, your helpful information and for the effort you made to prepare the pdb structures.
This is going to speed-up significantly the preparation of my computer simulations, concerning i-motif.

I tried to repeat the procedure that you mention in your reply, but I cannon include the loop T₁₀A₁₁A₁₂ , which it seems that it is left outside of the molecule.


Best,

Vassilis

[xiangjun]

I tried to repeat the procedure that you mention in your reply, but I cannon include the loop T10A11A12 , which it seems that it is left outside of the molecule.

I was at a meeting over the past week and did not notice your question. In principle, you could use the same idea as outlined in my previous reply to divide and assemble any complicated 3d nucleic acid structures, by using properly aligned reference frames.

Xiang-Jun