The site-specific reaction with high efficiency and specificity to DNA or RNA has become of great interests, as such modification may have possibility to induce point mutation of a genetic code. The cross-linking reagents within complementary duplexes and triplexes are one of the tools for site-specific modification by forming covalently bond. However, the existing alkylating agents still need further improvement for application in either in vitro or in vivo study. Previously, we have designed a new cross-linking motif, 2-amino-6-vinylpurine(1), toward cytosine by expecting a proximity effect within the complex resembling a natural G-C pair. In this paper, we wish to describe the development of the novel cross-linking reagents based on the structure of 1.