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General discussions (Q&As) / Determining intercalator roll compared to DNA local helical axis?
« on: September 23, 2014, 12:01:18 am »
Dear Xiang-Jun and other 3DNA users,
I’m studying acridines intercalating between DNA base-pairs using MD and would like to get a value of the intercalator “roll angle” with respect to the DNA base-planes and would appreciate some guidance as to whether my approach is valid.
Can I use the local helical axis vectors produced in 3DNA’s output? I was thinking I take the axis vector corresponding to the base-pair step my drug is intercalated in, and then take cos-1 of the dot product of that axis vector with the intercalator's short-axis to measure the roll angle. Then I can find its difference to the Roll angle given in the .out file.
I would like to compare these simulation values with experiment, we don’t have any atomic resolution data but do have electric dichroism measurements which align the DNA to an electric field and then use UV to polarise the intercalator’s short-axis and hence allow a determination of an average roll angle with respect to the base base-pairs.
To get the intercalator's short-axis vector I’m currently using VMD’s ‘orient’ plug-in to do a principal axis fit. I'm writing a .tcl so the analysis can be done automatically through VMD.
Gratefully,
Keiran
I’m studying acridines intercalating between DNA base-pairs using MD and would like to get a value of the intercalator “roll angle” with respect to the DNA base-planes and would appreciate some guidance as to whether my approach is valid.
Can I use the local helical axis vectors produced in 3DNA’s output? I was thinking I take the axis vector corresponding to the base-pair step my drug is intercalated in, and then take cos-1 of the dot product of that axis vector with the intercalator's short-axis to measure the roll angle. Then I can find its difference to the Roll angle given in the .out file.
I would like to compare these simulation values with experiment, we don’t have any atomic resolution data but do have electric dichroism measurements which align the DNA to an electric field and then use UV to polarise the intercalator’s short-axis and hence allow a determination of an average roll angle with respect to the base base-pairs.
To get the intercalator's short-axis vector I’m currently using VMD’s ‘orient’ plug-in to do a principal axis fit. I'm writing a .tcl so the analysis can be done automatically through VMD.
Gratefully,
Keiran