Example 2-Making an intercalation site.
For clarity, a script is provided.
- Start NAMOT2
- Select "Generate..." from the "File..." menu
- Pick double from the Strand choices.
- Pick form "B"
- Pick "Deoxyribose"
- Enter the sequence "atgc"
- If you are using the Motif interface click on "Apply",
XView users need to simply press return.
- Rotate the molecule on axis three by -90 degrees. (on the XView version
this can be accomplished on the interface, on the motif version use the
- Select the third base by clicking the left, then the middle mouse button
over any atom in the unit. This sets the starting and the ending unit
to that base.
- From the "Parameter" menu select "Dz".
- Leave the "Affect" setting on "Global".
- Input a change of 2.0, this will take affect when you press return. Notice
that the phosphate angles(C5'-O5'-P and O5'-P-O3') will automatically adjust
to compensate for the change in distance.See
- Increase Dz by another 1.4 angstroms. This will break the backbone.
See figure 3.
- To reconnect the back bone, reduce the twist angle by 10 degrees.
See figure 4.