Nucleic Acid Enzyme-Based DNA Nanomachine for Biosensing - DNA Nanotechnology: From Structure to Function - page 301

that are added externally or carried by the motor itself. Programmable motion will
allow the development of computing networks, molecular systems that can sort and
process cargoes according to instructions that they carry, and assembly lines.

14.3 Restriction Endonuclease-Assisted DNA Machine

Endonucleases are enzymes that cleave the phosphodiester bond within a polynu-
cleotide chain. Typically, endonucleases could recognize a restriction site embedded
in DNA strands. Most restriction endonucleases cleave the DNA strand unevenly,
leaving complementary single-stranded ends. These ends can reconnect through
hybridization and are termed “sticky ends.” There are hundreds of restriction
endonucleases known, each attacking a different restriction site.
The ability of restriction endonucleases to cleave DNA strand could induce struc-
tural changes of DNA nanostructure, resulting the release of the chemical enthalpies
embedded in DNA nanostructures. Up to now, several restriction endonucleases
have been successfully used in DNA nanomachines.

14.3.1 Fok I-Assisted DNA Nanomachine

Fok I, naturally found in Flavobacterium okeanokoites , is a special kind of
restriction endonucleases. It could specially bind at the 5 0 -GGATG-3 0 /5 0 -CATCC-3 0
recognition domain then cleaves, without further sequence specificity, the first
strand 9 nucleotides downstream and the second strand 13 nucleotides upstream
of the nearest nucleotide of the recognition site.
Fok I was first introduced in DNA nanotechnology by Shapiro et al. as “hard-
ware” to construct programmable and autonomous DNA computing machines in
2001 [ 20 ]. Later on, this configuration was further used to realize a spectrum of
applications including data storage [ 21 ] and molecule cryptosystem [ 22 ].
Willner and coworkers further employed Fok I in designing an autonomous
fueled DNA replication machine for optical DNA detection [ 23 ]. Principle of the
proposed DNA machine is outlined in Fig. 14.3 . A ss-DNA 1 with two hairpin
structures is predesigned to analyze DNA analyte. The hairpin structure 1 includes
the built-in sequence for the association of the endonuclease Fok I. The larger
loop of 1 and part of the double-stranded stem include the encoded base sequence
that is complementary to the analyzed nucleic acid. The hybridization of 1 with
analyte 2 opens the loop structure and yields the double-stranded complex A. The
latter complex includes the specific base sequence that is cleaved by Fok I to yield
the products B, C, and D. The product D consists of a Fok I/DNA template that
acts as the catalytic cutting machine. The interaction of D with the FAM/TAMRA
fluorophore/quencher-functionalized nucleic acid structure 3, which acts as the fuel,
results in the formation of the double-stranded complex E. The latter complex