I’m finding recent papers explaining double strand breaks in the DNA double helix in terms of the geometry of tetranucleotides. The authors always warn the reader, data on tetranucleotide sequence geometry is lacking. Which brings me to my questions. (1) If I build a tetranucleotide sequence and then apply the bond centric manipulate tool, can I rely on the numerical values for the angles? Is there someway to list your numbers in terms of the standard torsion bond angles for the phosphodiester - sugar linkage? (2) My main interest, changes to the geometry of the helix as a result of the base pair sequence. Would I be better off with a program like Curves+?
I don’t know Curves+ but I’m assuming it’s a more specialized program.
- If you use the bond-centric manipulate tool or edit the torsion angles under Properties -> Torsions, you can rely on the numeric angles. With the bond-centric tool, you can click on atoms in order, so you can certainly be sure to pick out the standard angles you want.
- In this particular case, I’d suggest that more subtle changes may be easier to establish with a specialized program. (Avo2 will make it easier to add some glue to interface with web servers or other programs.)
Hope that helps!