Hi amber users,
I am sorry if my question sounds naive but I've been looking through the
literature and could not find a very clear answer.
I did dynamics for a single stranded nucleic acid homopolymer in water
with the initial configuration being helical and the final sort of bulky.
I was thinking that a way to characterize the "distortion" is to follow
during the dynamics the values of the minor/major grooves and also the
helicity.
I have two questions:
1. Between which atoms exactly one should measure the minor/major grooves
2. What is the best way to calculate the helicity of a strand?
Any advice on this matter would be appreciated.
Thanks in advance,
Ioana
Received on Tue Apr 08 2003 - 19:53:00 PDT
