The invention provides a method for stably cross-linking a first nucleic acid sequence selected for being stably cross-linked in the presence of a second nucleic acid sequence selected for not being stably cross-linked in a nucleic acid molecule. The method comprises providing a nucleic acid sequence that is complementary to the first nucleic acid sequence; hybridizing the first nucleic acid sequence to its complementary sequence; and stably cross-linking the first nucleic acid sequence to the complementary sequence.