The present invention provides a novel lyophilized pharmaceutical composition that maintains the stability of a DNA plasmid while forming a uniform and elegant cake during lyophilization. The novel lyophilization formulation further allows uniform reconstitution of the DNA plasmid in a pharmaceutically acceptable solution, enabling complete recover of the active ingredients, minimizing partial loss of potency and allowing administration of the active ingredients in an accurate and consistent manner. Additionally provided herein include methods of making the lyophilized pharmaceutical composition and methods of administering the composition for treatment of various diseases.