In this work the inference performed on DNA molecules is considered. The process known as self-assembling of DNA strands is fundamental to achieve longer chains of molecules encoding knowledge base. By proper organization of this process any logic operations can be accomplished. In particular, systems based on decision trees may be easy assembled. A severe problem of nano-systems is to provide communication between nano-world and real-world. To solve this problem it is proposed to make use of colorimetric change phenomenon. Here an inference procedure is proposed that allows to check the knowledge base in form of decision tree. Although DNA strands react in the nano-world, due to optical read-out the inference result is attained quickly and easy. Thus, complicated and expensive operations of genetic engineering laboratory are eliminated.