The present invention provides for a method of treating or preventing ischemic or liver disease in a subject by administering a composition reconstituted from a lyophilized hepatocyte growth factor (HGF) DNA formulation, where the DNA formulation comprises an HGF plasmid DNA, salt and a carbohydrate. The invention further provides for a method of making such a lyophilized DNA formulation that preserves or enhances gene expression both in vitro and in vivo, thus maintaining or stimulating the biological activity of the expressed protein. The invention also provides for the DNA formulation, or the lyophilized DNA formulation according to the methods disclosed.