8] Heavy atom derivatives of RNA

Abstract

This chapter discusses the heavy atom derivatives of RNA such as mercury and bromine or iodine. Heavy atom derivatives may be obtained by soaking the compound into preformed crystals or cocrystallized with the molecule. If there are sites within the molecule that tightly bind to the compound, a useful derivative may be obtained. This is the classical method of heavy atom derivatization, and it has been used to solve the majority of the new protein structures. Another methodology is engineering heavy atoms or heavy atom binding sites into the covalent structure of the RNA to create derivatives. The simplest way to create a heavy atom derivative of RNA is to incorporate one of the halogenated pyrimidines in place of its unmodified counterpart. Bromine or iodine substitution at the 5' position of uracil or cytosine residues is an often used modification. The halogenation of RNA for use as heavy atom derivatives is a classical method used in the investigation of transfer RNA (tRNA) structures. The most common means of incorporating bromine or iodine is to chemically synthesize the RNAs and incorporate them in the synthesis. An alternate method of derivation may be accomplished by incorporating a mercury-binding site into RNA via a phosphorothioate in the RNA backbone. This technique has been used to solve crystal structures of DNA–protein complexes.