Selenium Atom-Specific Mutagenesis (SAM) for Crystallography, DNA Nanostructure Design, and Other Applications - DNA Nanotechnology: From Structure to Function - page 40

nanotechnology. Introducing base-modified nucleotides into oligonucleotides by
rational design can help to selectively enhance or weaken the binding affinity of
targeted region of duplexes, thereby generating complicated nanoscale structures in
well-controlled manner.

3.4.1 Sulfur Modification on Nucleobases

Sulfur-modified DNA and RNA are important classes of atom-specifically modified
nucleic acids. Like selenium, sulfur belongs to chalcogen family but possesses
smaller atomic radius (S: 1.02 A) compared to selenium (Se: 1.16 ˚ A).Thisoffersthe
sulfur-modified nucleic acid unique biophysical and biological properties, thereby
making it a valuable alternative in structure-and-function studies as well as in
therapeutics. Sulfur-modified nucleic acids, especially noncoding RNAs, exist in
nature and involve in biological processes. These naturally occurring thiolations
take place at the nucleobases, particularly 2-thiouridine (s2U), 4-thiouridine (s4U),
and 2-thiocytidine (s2C) in E. coli and yeast. Moreover, the 2-thiouridine is often
located in the wobble position [ 34 ] of tRNA with various other modifications on
position 5, engaging in the decoding process during protein translation [ 60 ].
To further investigate the function and role of the sulfur-modified nucleic acids,
both synthetic and enzymatic methods have been developed for these natural prod-
ucts [ 61 - 65 ]. The investigations were carried out, including biophysical research
[ 66 , 67 ], biological studies [ 59 , 68 , 69 ], as well as crystal structure studies [ 70 ]. The
results indicate that the thio-modification at position 2 of uridine can enhance the
thermostability of the U/A or T/A base pair compared to the native one [ 59 ]. The
in vitro experiments of the s2U derivatives show the preference toward A instead
of G during decoding process [ 68 ]. The synthesis of 4-thiolated nucleic acids
is available through solid-phase synthesis [ 71 ]. Compared to the 2-thiouridine-
containing duplex, the 4-thiouridine-containing duplex has lower stability, because
of the 4-sulfur-disrupted H-bond at the 4-position [ 66 ]. Another possible position to
replace oxygen with sulfur on nucleobase is position 6 of guanosine, and the synthe-
sis was successfully developed previously [ 72 , 73 ]. The most interesting property
of the 6-thioguanosine is the UV red-shift to 330 nm [ 74 ], which is away from
normal protein (280 nm) and nucleobase absorption (260 nm). This modification
is potentially useful in monitoring nucleic acid-nucleic acid interactions as well as
nucleic acid-protein interactions. Besides the replacement of oxygen in nucleobases,
the sulfur functionality has been introduced into nucleobases at other sites, such as
position 5 of thymidine. This S modification has been studied by Benner's group to
examine the ability of polymerases in accepting unnaturally modified nucleic acids
in vitro [ 75 ].