Disclosed are methods for use in transferring nucleic acids into cells at a wound site associated with a fluid space. These gene transfer protocols are suitable for use in transferring various nucleic acids into cartilage, cardiac muscle, and other tissues, and have many uses including treating diseases such as arthritis and ischemic heart disease, and promoting wound healing. The invention further disclosed pharmaceutical compositions that may be used in the practice of the invention to transfer the nucleic acid of interest. Such compositions include any multi-partitioned biocompatible matrix in combination with multiple nucleic acids of interest.