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pairs for specifying intermolecular interactions (Jorgensen and Pranata 1990; Pranata,
et al. 1990; Murray and Zimmerman 1992). Subsequently, particularly stable hetero-
cyclic complexes with arrays of H bond donors (D) and acceptors (A) were developed
by the groups of Zimmerman (Fenlon et al. 1993; Corbin and Zimmerman 1998) and
others (Beijer, Kooijman, et al. 1998; Beijer, Sijbesma, et al. 1998; Folmer et al.
1999). Many other groups also reported H bonded self-assembling aggregates con-
sisting of multicomponents (Yang et al. 1993; Whitesides et al. 1995; Sessler and
Wang 1996; Vreekamp et al. 1996; Conn and Rebek 1997; Hartgerink et al. 1998;
Kolotuchin and Zimmerman 1998; Orr et al. 1999; Lehn 2000; Percec et al. 2000;
Fenniri et al. 2002; Wu et al. 2002).
The development of DNA-like associating units with strength and specificity that
can be systematically tuned is of great significance for the specific control of intermo-
lecular association. Such units may serve as versatile “molecular glue” that allows the
association or linking of various structural units, including those with no obvious
complementarity. With such associating units, the formation of a self-assembling
architecture can be readily carried out under thermodynamic control, that is, by
simply mixing the components together. In addition to the development of noncova-
lent associating units, an even more exciting possibility is the combination of system-
atically tunable supramolecular linking units and reversible covalent bonds, leading
to covalently linked structures under reversible conditions.
In recent years we have developed a series of information-storing molecular
duplexes based on oligoamides consisting of simple building blocks (Gong et al.
1999; Zeng et al. 2000, 2001, 2002, 2003; Gong 2001; Yang et al. 2003, 2004;
Sanford et al. 2004; Yang and Gong 2005). This system involves oligoamide
strands carrying various arrays (sequences) of amide hydrogens and carbonyl
oxygens as H bond acceptors and donors. These molecular duplexes are featured
by tunable affinity, programmable sequence specificity, and convenient synthetic
availability, offering a novel class of associating units for the instructed assembly
of various discrete, oligomeric, or polymeric structures.
The discussion in this chapter is mostly focused on 1) the development of hydrogen
bonded duplexes that form in a sequence-specific fashion, 2) application of the
duplexes as information-storing molecules for specifying intermolecular association,
and 3) converting the duplexes into sequence-specific dynamic covalent (Rowan
et al. 2002) ligation units in highly competitive media. Many other important duplex
systems (Bisson et al. 2000; Gabriel and Iverson, 2002; Zhao et al. 2003; Jiang et al.
2004; Gong and Krische, 2005) are noteworthy and will not be discussed here.
9.2. GENERAL DESIGN: INFORMATION-STORING MOLECULAR
DUPLEXES BASED ON THE RECOMBINATION OF H BOND
DONORS AND ACCEPTORS
The objective of this research is to develop easily modifiable associating units that can
direct unnatural molecular systems to self-assemble in a highly predictable fashion.
Specifically, hydrogen bonded duplexes with unnatural backbones are chosen to
