Chemistry Reference
In-Depth Information
Figure 9.4 Duplex 3†4 and two duplexes 3†6 and 3†7 containing mismatched-binding
sites. The repulsive mismatched binding sites in 3†6 (acceptor-acceptor) and in 3†7
(donor-donor) cause more than a 40-fold decrease in the stabilities of these duplexes
compared to 3†4.
our H bonded duplex, the next objective was to establish the sequence specificity of
this class of information-storing molecules. This could be realized by incorporating
mismatched binding sites into an otherwise fully matched duplex, leading to
“mutant” duplexes that should provide an ideal platform for systematically probing
the effect of sequence specificity on unnatural self-assembling processes, which
had been difficult to investigate because of the lack of appropriate model systems.
Thus, to investigate the sequence specificity of our duplexes, mismatched binding
sites were introduced into duplex 4†5 (Fig. 9.4; Zeng et al. 2001). Single strands
6 and 7, with H bonding sequences of DADDAA and DADDDD, respectively,
were designed and synthesized to pair with 3. Each of the resultant pairs, 3†6 or
3†7, should contain a mismatched binding site. With their mismatched sites, can
duplexes 3†6 and 3†7 still form? Will the single strands in duplexes 3†6 and 3†7
be partially aligned to avoid the mismatched binding sites? What are the stabilities
of 3†6 and 3†7 compared to that of the fully matched 3†4?
1
H-NMR showed poorly defined resonances of individual strands 6 or 7, indicat-
ing a slowly equilibrating mixture of many conformations. Upon mixing with 1 equiv
of 3, both 6 and 7 showed sharp sets of signals that can only be assigned to single
conformers, suggesting the association of 6 or 7 with 3. One interesting observation
was that the aniline NH protons of 4, which show one degenerate signal in the
1
H-NMR spectra of 3 or 3†4 due to the symmetry of the structures, became nonequi-
valent upon mixing 3 with 6 or 7.At25mMinCDCl
3
,
1
H-NMR showed that the
aniline protons of strand 3 in 3†6 or 3†7 appeared as two signals that were separated
