DNA and protein evolution is the cornerstone of modern biology. In order to form a new integrated theory, the study incorporates many factors: (1) the large-scale random unequal crossover in eukaryote meiosis have fueled spliceosomal introns, which results in that introns are very common in eukaryotes but very less in prokaryotes; (2) DNA evolution proceeds through two ways: C-to-T (caused by DNA methyltransferase, which mainly existed in vertebrates) and A-to-G substitution (which increased linearly with the A/G gradient); (3) the trend of protein evolution is controlled by the simple trend of coding-DNA evolution. Cys increases in the all species during protein evolution; (4) S. thermophilus is tested to be resistant to most current antibiotics due to horizontal gene transfer; (5) DNA methyltransferase is considered to affect protein evolution, which will promote various cancers prevalence, thus an enzyme inhibitor could be a potential candidate for cancer therapy; (6) Meanwhile, multibase site-directed mutagenesis, heterogeneous DNA transformation and species selection are studied for exploring evolution.