Selenium Atom-Specific Mutagenesis (SAM) for Crystallography, DNA Nanostructure Design, and Other Applications - DNA Nanotechnology: From Structure to Function - page 29

Fig. 3.1 Selenium
atom-specific mutagenesis
( SAM ) in nucleic acids

(SeNA, Fig. 3.1 ) and its potential usefulness in nucleic acid nanotechnology.
Because of the nature of the virtually atom-specific modification in SeNA, we have
borrowed the term “protein site-specific mutagenesis” from biology and call the
selenium modification as the selenium atom-specific mutagenesis (SAM).

3.2 Selenium-Derivatized Nucleic Acids (SeNA)

Selenium-Derivatized Nucleic Acid at the 5 0 -Position 3.2.1

In 1998, our laboratory pioneered the atom-specific incorporation of selenium
into nucleic acids, and we first synthesized the selenium-derivatized nucleic acids
(SeNA) for structure-and-function studies [ 24 ]. We are also the first to synthesize
selenium-derivatized phosphoramidites and triphosphates for both chemical and
enzymatic syntheses of Se-derivatized nucleic acids [ 15 , 16 ]. In the first attempt,
selenium was introduced to the 5 0 -positions in A, T, C, G, and U for developing
a novel tool [ 24 ] in nucleic acid crystallography for phase determination via
multiwavelength anomalous diffraction (MAD). In this early trial, the incorporation
of the selenium functionality was accomplished in a two-phase system (water-
toluene) using a phase-transfer catalyst (tetrahexylammonium hydrogen sulfate).
The 5 0 -hydroxy groups of nucleosides (A, T, C, G, and U) were activated by
Br-, Ms-, or Ts- group, followed by a nucleophilic substitution reaction using
sodium selenide or methyl selenide as a nucleophile. The resulting 5 0 -MeSe-
labeled (5 0 -Se) nucleosides can be converted to the corresponding phosphoramidites
conveniently by a phosphorylation reaction (shown in Scheme 3.1 ). The 5 0 -Se
functionality was then incorporated into oligonucleotides by solid-phase synthesis
using the standard phosphoramidite method. In the oligonucleotides, the selenium
functionality showed fine stability under various conditions in solid-phase synthesis,
including treatments of strong acid, base, and oxidant. The desired 5 0 -Se-DNAs
can be easily purified by either HPLC or gel electrophoresis to reach over
95% purity.