How the chaotropic agents help in purification of DNA molecule?
Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. a chaotropic agent reduces the amount of order in the structure of a protein formed by water molecules, both in the bulk and the hydration shells around hydrophobic amino acids, and may cause its denaturation (biochemistry).
A chaotropic agent is often used in DNA isolation. It's purpose is

a. To degrade membrane lipids

b. To destroy the endoplasmic reticulum

c. To degrade mitochondria

d. To limit the amount of magnesium salts in the lysate

e. To destroy the three dimensional structure of proteins 

To make it simple, a chaotropic agent destroys the 3D structure of a protein, thereby leading to subsequent protein degradation. It serves as a proteinase enzyme, cleaning the cellular proteins in your DNA isolation and purification process.

http://www.hindawi.com/journals/bmri/2009/574398/

http://www.ncbi.nlm.nih.gov/pubmed/16152629