Functional Nucleic Acids for DNA Nanotechnology - DNA Nanotechnology: From Structure to Function - page 7

affinity and selectivity by intermolecular binding forces such as hydrogen bonds,
electrostatic forces, and van der Waals force. They are identified from an initial
library, usually containing 10 13 -10 16 random ssDNA or ssRNA sequences, by an
in vitro evolving process called SELEX (systematic evolution of ligands by expo-
nential enrichment). Aptamers gain advantages over antibodies, which have already
made substantial contributions in various diagnostic assays concerning the specific
immune reactions routinely used in clinics, by the way that while maintaining high
binding affinity and specificity, aptamers are easily synthesized and convenient to
keep and have less immunogenicity. Especially, because of the in vitro selection
of aptamers, they can bind essentially to any target of choice, while antibodies
cannot be obtained for small molecules, toxic molecules or molecules with low
immunogenicity [ 28 , 30 , 31 ]. Moreover, in DNA nanotechnology, aptamers are
ready to be engineered into DNA nanostructures.

2.2.2 DNAzymes

Discovered by Cech and Altman [ 32 , 33 ], ribozymes overturn the fundamental
concept of enzymes. In vitro selection allows the identification of artificial nucleic
acid enzymes. DNAzymes (also termed deoxyribozymes, catalytic DNA), compared
to ribozymes, despite the lack of the 2 0 -hydroxyl group, have also been evolved
to catalyze a diverse range of reactions, including RNA cleavage [ 34 - 36 ], DNA
cleavage [ 37 , 38 ], RNA ligation [ 39 - 41 ], DNA ligation [ 42 , 43 ], and enzymatic
activities as peroxidases [ 44 , 45 ]. In contrast to the thermally unstable protein
enzymes, DNAzymes are robustly stable under ambient temperatures. Furthermore,
it is difficult to conjugate protein enzymes to other functionalities or biomolecules.
By comparison, DNAzymes, for its intrinsic properties of nucleic acids, are simple
to directly label themselves to the desired target through chemical modification,
DNA hybridization. DNAzymes are also isolated by in vitro selection [ 46 - 48 ].
Depending on the nature of each catalytic reaction, there are various designed meth-
ods to perform the selection. The selections followed the similar basic processes
as that of aptamer SELEX: reaction, separation, and amplification. And thus it is
proposed that autonomous selection is possible [ 49 ].

2.2.3 Evolution of Functional Nucleic Acids

Systematic evolution of ligands by exponential enrichment (SELEX) is the most
common methodology for in vitro selection of FNAs. It is based on the combination
chemistry principles in which evolving selection of specific oligonucleotides is
performed in an initial large nucleic acid pool. Before the selection, to determine
the length of the random region in the initial pool is important. Random regions of