method of choice to identify DNA bending, kinking or any other deformation?

[Richard Koepsel]

Dear Ji Hyun,
I'm not sure what you mean by deformations other than bending. 
Certianly cruciform formation is possible in the context of a longer
DNA.  As for bending we did some work with that a number of years ago
(Koepsel and Khan Science 233:1316-1318, 1986)  Some useful reference
from that general era are 1) Wu and Crothers, Nature 308:509, 1984.  2)
Zhan and Blattner  EMBO J. 4:3605, 1985.
These are gel methods but gave good results for us.  Hope this helps.
Rick