Glycol nucleic acids as duplex scaffold for the design of self-assembeld and self-organized architectures
In this thesis, GNA is explored as a simplified duplex scaffold for arranging different chromophores and the properties of the resulting chromophore assemblies are investigated. Chromophore nucleotides were incorporated into GNA by automated solid phase synthesis of oligonucleotides. The synthes...
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|Summary:||In this thesis, GNA is explored as a simplified duplex scaffold for arranging
different chromophores and the properties of the resulting chromophore assemblies
Chromophore nucleotides were incorporated into GNA by automated solid phase
synthesis of oligonucleotides. The synthesis of different chromophore glycol
nucleoside GNA building blocks was presented in chapter 2. The key step for
synthesizing these glycol nucleosides was the regioselective and stereospecific
ring-opening of dimethoxytrityliated (S)-glycidol (3). As shown in Scheme 7.1A,
compounds 5, 9, 14 and 17 were synthesized by three efficient methods, namely, the
application of Grignard reagents, Grignard reagents containing a
metallation/transmetallation protocol, and organolithum reagents. Among these
compounds, compound 17c can be also synthesized by Pd-catalyzed Sonogashira
coupling reaction of compound 30 with compound 17d (Scheme 7.1 B), thus any
chromophore with alkyne groups can be introduced to GNA by this method.
In chapter 3, we investigated GNA duplexes containing fluorescent pyrene (Pyr)
and pyrene acetylide nucleotides (Pyr′) (Figure 7.1A). Duplexes with one or two
adjacent Pyr:Me or Pyr′:H base pairs were synthesized, all resulting in thermally
stable duplexes at room temperature. The incorporation of pyrene or pyrene acetylide
to GNA duplexes did not distort the overall GNA duplex structure.
Interestingly, only the pyrene acetylides but not the related pyrene nucleotides,
could form strong excimers upon interstrand stacking within the GNA duplexes
(Figure 7.1B). The reason for this may be a combination of structural effects,
influence of the stacking of adjacent pyrene acetylides nucleobases, and electronic
effects due to the conjugation of the aromatic pyrene with the acetylide π-system.
As an application of excimer emission upon duplex formation with pyrene
acetylide containing GNA strands, we developed a metal ion sensor by additionally
incorporating a metal-mediated base pair: hydroxypyridone homo-base pair (M:M) or hydroxypyridone-pyridylpurine hetero-base pair (M:P). As shown in Figure 7.2, D15
and D19 are very sensitive and selective Cu2+ “turn-on” fluorescent sensors.
Unfortunately, our attempt to develop a Cu2+ sensor for a complex biological
In chapter 4, the porphyrin acetylide nucleotide (P) was incorporated into GNA
duplexes opposite ethylene glycol abasic sites and the duplexes were analyzed by
UV-melting, UV-vis, fluorescence spectroscopy, and circular dichroism. The modified duplexes display lower thermal stabilities, however the thermal
stabilities of duplex containing P:H base pairs could be modulated by the
incorporation of zinc(II), manganes(II) or nickel(II) ions into P (Figure 7.3B). The
incorporation of zinc(II) or manganes(II) ion led to a decrease in duplex stability, but
the incorporation of nickel(II) resulted in increased duplex stability. These
modulations of duplex stabilities by the nature of the metal ion can be interpreted
by their differenct coordination behavior. Zn2+ or Mn2+ prefers to coordinate to
axial ligands when incorporated into a porphyrin in an octahedral fashion and
needs to dissociate these ligands if it wants to stack within GNA between
neighboring base pairs. In contrast, Ni2+ prefers square planar coordination and can
therefore be accommodated easily in the base stacking.
Furthermore, GNA duplexes provided a suitable scaffold to bring two
porphyrins into close contact and to allow the interaction of porphyrins with
different coordinated metal ions. The obvious change of the Soret bands accompanied
by a blue shift (Figure 7.4B), together with the decrease of fluorescence intensity
upon duplex formation revealed that a ground state interaction between two porphyrin
moieties occurred in GNA, performing in face-to-face (H-dimer) fashion. In chapter 5, Electron donor-acceptor chromophores systems, mainly composed
of perylene bisimide (PBI) and porphyrin (P) units were organized in duplex GNA
The GNA duplexes which contain B-Pyr, B-Pyr′, B-Pe′ and B-P were
investigated. The thermal stabilities revealed that B-P pair stabilizes the GNA duplex
the most significantly, exceeding the stability of the native GNA duplex by additional
10 oC. The significantly increased duplex stability together with the red-shifted
absorption band and induced CD signal at Soret band indicated the interstrand π-π
stacking of B-P pair in the duplex.
Subsequently, we investigated the systems which contain a couple of porphyrin
and PBI building blocks. As shown in Figure 7.6B, the intensity of the CD signal
accompanying the blue-shift of the bisignate CD spectra in the Soret band increased
with the increasing amount of chromophore moieties. This continuous shift in a CD
spectrum with increased amounts of chromophores indicated the interaction between
PBI and porphyrin resulted in a highly ordered helical structure. In addition, we also synthesized some single strands which consisted of entirely
PBIs or porphyrins. However, combining these single strands did not give us desired
helical structure according to CD analysis. It seems that flanking natural base pairs or
natural overhangs play a key role in affording helical structures.
Considering the significantly decreased yield of modified GNA strand with
multi-incorporated chromophores, photochemical ligation of GNA was developed in
order to address this problem. In chapter 6, the photochemical ligation of GNA via
anthracene cyclodimer formation was explored. Anthrancenes were introduced into
GNA not only as artificial nucleosidic bases but also as phototriggered joints (Figure
7.7A). Upon the duplex formation, the two adjacent anthracene nucleobases get close
to each other, and the duplex was expected to generate a hairpin structure via
anthracene cyclodimer formation as a result of the photoirradiation (366 nm).
The photochemical ligation of GNA via anthracene cyclodimer formation was
investigated in terms of three aspects, namely, template-supported GNA ligation,
interstrand crosslinking in the middle of the GNA duplex, and end capping of the
GNA duplex. The template-supported GNA photoligation did not occur, probably due to the
inefficient dimerization of anthracenes in tandem duplex. However, both the
crosslinking in the middle of duplex and end capping of duplex proved to be feasible.
Resulting intramolecular duplexes exhibited high melting temperature (Figure 7.7B),
which was consistent with the formation of an intramolecular duplex with a hairpin
structure. In addition, the CD spectra suggested that end capping did not disrupt
overall GNA duplex structure.
In this study, the GNA duplex was employed as scaffold for the design of
self-assembled and self-organized architectures. Several chromophores had been
successfully introduced into the interior of GNA duplexes. GNA as a simplified
general duplex scaffold proves to be useful for the defined chromophores
Future work will be focused on applications of porphyrin-GNA conjugates as
well as modified GNA containing porphyrin and PBI for light harvesting and charge
transport. In addition, the photochemical ligation of GNA via anthracene cyclodimer
formation is a useful tool for the interstrand crosslinking of GNA, which may provide
a new method for the construction of functional GNA-supramolecules.|