Polynucleotide Cross-linking Methods

The unique properties of oligonucleotides create cross-linking options that are far different from those of any other biological molecule. Nucleic acids are the only major class of macromolecule that can be specifically synthesized in vitro by enzymatic means. The addition of modified nucleoside triphosphates to an existing DNA strand by the action of polymerases or transferases allows addition of spacer arms or detection components at random or discrete sites along the chain. Alternatively, chemical methods that modify nucleotides at selected functional groups can be used to produce spacer arm derivatives or activated intermediates for subsequent coupling to other molecules. 

By contrast, derivatization at the ends of an oligo or at the sugar—phosphate backbone usually produces little interference in base-pairing. Conjugates may be created by enzymatic polymerization of functionalized nucleoside triphosphates off the 3 end or 

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