Chemistry Reference
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suggests that the observed dimerization constants are independent of the sequence
and are only proportional to the number of interstrand H bonds in each duplex.
This is in contrast to many previously reported H bonded dimers based on rigid
heterocycles, whose stability depends not only on the number of intermolecular H
bonds but also on the arrangement of H bond donors and acceptors attributable to
secondary electrostatic interactions (Jorgensen and Pranata 1990; Pranata et al.
1990; Murray and Zimmerman 1992).
9.4. TUNING BINDING STRENGTH BY VARYING THE NUMBER
OF INTERSTRAND H BONDS
Because the stability of our duplexes depends only on the number of intermolecular
H bonds, increasing the number of interstrand H bonds in a duplex, which can be
readily realized by adding additional aromatic residues into the oligoamide strands,
should lead to an increase in the stability of a duplex. Such an expectation was con-
firmed by the 6-H bonded, heteroduplex 3†4 (Fig. 9.3a), consisting of two different
strands having complementary H bonding sequences DADDAD and ADAADA
(Zeng et al. 2000). Probing the sequence-specific pairing of 3 and 4 into an H
bonded duplex was investigated to address the following questions: 1) In addition to
those with self-complementary arrays, could duplexes consisting of two different
strands of complementary H bonding sequences still form? 2) Will the backbones of
longer strands stay in register to allow pairing of the duplexes? 3) Compared to the
homologous quadruply H bonded duplexes, what would be the expected enhancement
of the binding strength (association constant) of the longer duplex?
The formation of duplex 3†4 was confirmed by 1-D and 2-D
1
H-NMR. In CDCl
3
,
the
1
H-NMR spectrum of the 1:1 mixture of 3 and 4 revealed very large (2-3 ppm)
downfield shifts of the aniline NH signals compared to those of strands 3 or 4 alone.
The association constant of 3†4 was so high that attempts to measure it by
1
H-NMR
Figure 9.3 (a) Duplex 3†4 consisting of two different strands with complementary
H bonding sequences. (b) Duplex 5†5 consisting of two identical single strands with a self-
complementary H bonding sequence. Interstrand NOE contacts revealed by NOESY are
indicated by arrows.
