This monograph is based on the research done at Department of Physics, DDU Gorakhpur University Gorakhpur,India on unusual DNA structures.Department?s laboratory is pioneer in the field of Computational Modeling, Quantum mechanics and Molecular Mechanics simulations (QM/MM) on bio-molecules. Several high end research articles and theses have been produced during last 10 years form the laboratory. The aim of writing this book is to provide an easy tool/manual to understand nucleic acids, its modeling, QM/MM simulations, conformation and biological functions to the graduate level students and research scholars. This book may also be helpful as a self-study material. Different software and its methodology and compression are also elaborated.