Chemistry Reference
In-Depth Information
CHAPTER 9
SEQUENCE-SPECIFIC HYDROGEN
BONDED UNITS FOR DIRECTED
ASSOCIATION, ASSEMBLY, AND
LIGATION
BING GONG
9.1. INTRODUCTION
Specific association of various structures, either covalently or noncovalently, plays
vital roles in both chemical and biological processes. In natural systems, the association
of molecular components is realized through the cooperative action of multiple non-
covalent interactions, leading to a highly specific formation of assemblies with high
thermodynamic stability. In forming multicomponent assemblies, the unfavorable
loss of entropy is usually offset by the presence of numerous cooperative enthalpic
interactions within the assembled structures. Similar to examples found in Nature,
many nanoscaled structures have been designed and constructed by forming multicom-
ponent assemblies. Most multicomponent assemblies reported thus far were designed
based on a case by case basis, because the information encoded in the corresponding
components only defines the dimension and shape of the specific assembly.
Duplex DNA, consisting of two helical strands with complementary shapes and
H bonding sequences, represents a system that best illustrates the action of multiple
interactions. A unique feature of duplex DNA is its modular, digital nature in
storing and retrieving information, which is realized by arranging the four different
nucleotides along a linear backbone. Inspired by DNA molecules, a systematic
approach to self-assembly has been proposed and tested, which involves associating
units (modules) that store and retrieve information in a digital fashion (Zimmerman
and Corbin, 2000). This field originated from investigation of the molecular associ-
ation of nucleobases that later led to the development of highly specific H bonded
