Messages

1

General discussions (Q&As) / Re: i-motif: increase the amount of consecutive CYS-CYS+ pairs

« on: February 14, 2014, 07:53:04 am »

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

2

General discussions (Q&As) / i-motif: increase the amount of consecutive CYS-CYS+ pairs

« on: February 13, 2014, 10:13:41 am »

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