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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
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