Microfluidic Tools for DNA Analysis - DNA Nanotechnology: From Structure to Function - page 137

Fig. 7.22 Characterization of genome structural variations by optical mapping ( a )PDMS
microfluidic device used for capillary-driven flow. ( b ) Restriction maps of single DNA molecule
give evidence to support a 90 kb insertion. The DNA was extracted from a lymphoblast-derived
cell line. Chr 7, chromosome 7; b35. NCBI Build 35 human genome reference sequence (Reprinted
with permission from Ref. [ 96 ] Copyright (2010) National Academy of Sciences, USA)

up into some knots or some hairpin structures. The nanochannel systems worked at
micro/nanofluidic conditions provide a way to fully stretch DNA and hence help
researchers to study the dynamic structures of DNA molecules which are essential
to understanding many molecular biological events.
DNA elongation can be accomplished by reducing dimensions of nano-
confinement; however, smaller nanochannels require more advanced and more
expensive nanofabrication technologies. Takayama and coworkers developed a
fabrication method for nanoscale fluidic channels (Fig. 7.23 a). The architecture
of nanochannels can be reversibly adjusted in response to compressive forces
applied perpendicularly to the nanochannels (Fig. 7.23 b). This is an extremely cost-
effective method for fabrication of a device that contains millimeter-, micrometer-,
and nanometer-scaled structures together (Fig. 7.23 c). It is hard to accomplish
by traditional top-down (e.g., lithography) or bottom-up (e.g., self-assembly)
approaches. Using this device, single DNA molecules can be stretched or relaxed
along the channel, and consequently, the lengths of

œ DNA (48.5 kbp) can be

determined at different stages (Fig. 7.23 d-f). The œ DNA stained with YOYO-1 was

stretched to 5.6 m when it was electrophoretically driven into the nanochannels,

and was elongated to an equilibrium length of 13.6 m when the channel size was

reduced by applying 22 kPa of pressure. However, the full contour length of œ DNA

stained with YOYO-1 is determined to be 21.8 m[ 98 ]. The conformation of DNA

is correlated to local environments. By optimizing the nanochannel dimensions and
ionic strengths of buffer solution, Schwartz and Jo et al. stretched the YOYO-1-
stained œ DNA as long as 19.1 m ˙ 1.1 m which is almost to the full contour

length [ 99 ].