Selenium Atom-Specific Mutagenesis (SAM) for Crystallography, DNA Nanostructure Design, and Other Applications - DNA Nanotechnology: From Structure to Function - page 35

Synthesis of 2 0 -SeMe-adenosine and 2 0 -SeMe-guanosine phosphoramidite, DNAs, Scheme 3.4

RNAs

First of all, the 2 0 -Se modification shows superior radiation stability over the 5-Br
pyrimidines. UV-induced 5-Br-RNA/protein cross-linking [ 35 ] and X-ray-induced
debromination during MAD data collection have been reported [ 36 ]. The radiation
stability of macromolecules is more critical in SAD/MAD data collection than in
regular single-wavelength experiment. For instance, in MAD data collection, three
data sets at different energies will be collected, which will take longer time in X-ray
radiation. The stability of 2 0 -Se modifications can allow easy completion of the data
collection. In addition, compared to the 5-Br pyrimidine analogs, 2 0 -Se-modified
ones can resist strong basic condition (even in ammonium hydroxide at 65 ı C). The
synthesis, purification, and handling of 2 0 -Se-containing oligonucleotides are more
straightforward than the Br-containing oligonucleotides. Besides the stability issue,
the 5-Br-oligonucleotides may cause perturbation in overall and local structures,
due to alternation of base-stacking and hydration patterns in major groove [ 27 ].
Moreover, the 2 0 -Se-modified DNAs and RNAs can be easily prepared with all
four ribo- or deoxynucleotides, which gives the 2 0 -Se modification more diversified
modification sites over the 5-Br modification, which is limited to pyrimidines. Even
though the crystallographic application of the 2 0 -Se modification is still limited
to A-form DNAs and RNAs due to its 3 0 -endo sugar pucker, this property can be
very useful for designing nucleic acids with A-form conformation for nanostructure
construction.

3.2.3 Synthesis of Selenium-Derivatized Nucleic Acid

at 4 0 -Position

Replacing oxygen atom at the 4 0 -position of nucleosides by a chalcogen atom
was first performed back in 1960s by Goodman lab [ 37 ]. The 4 0 -oxygen on
adenosine was replaced by sulfur. The 4 0 -Se functionality was incorporated into
ribo-oligonucleotides for crystallographic study [ 38 ]aswellassiRNAsinthera-
peutic development [ 39 ]. It is also worth mentioning that the 4 0 -S-DNA can be