Single Molecule Detection with an Aptamer-Integrated Nanopore - Nanopores: Sensing and Fundamental Biological Interactions - page 63

3.3.3 Significance and Impacts

Any membrane protein can be used in the ion channel chip for single molecule
detection, such as screening of enzymes or detection of glucose or neural transmit-
ters. The areas of research where the chip will be of the greatest use include DNA
and protein detection in genomics and proteomics, and screening for membrane
protein-targeting pharmaceuticals. The chip could also be a valuable tool for
investigating the long-term dynamics of membrane proteins, including ion chan-
nels, which otherwise are difficult to study by traditional electrophysiology tech-
niques. After improvement, the volume of sample cell on this modular device can
be reduced to smaller than 1

L to significantly reduce reagent consumption, and
the chip could be coupled with a micro-fluidic system to rapidly control the sample
exchange. This speculation is possible because the protein pore-incorporated lipid
membrane has been shown to form across a microfluidic channel [ 76 ]. As micro-
patterned hydrogels have been created [ 66 , 80 ], the chip is speculated to be able to
provide a micro-array in future for high throughput screening with each array
element containing a single stochastic sensor. The possibility of indexing each
individual ion channel on the array is supported by the ability to quickly transfer
ion channels into membrane for single channel assay [ 44 ].

m

3.4 Detection of Single Protein Molecules
with Aptamer-Encoded Nanopore

3.4.1 Detection of Binding, but not Translocation

Protein detection is an essential task in most fields including medical diagnosis and
biodefense. In the nanopore approach, most protein targets are larger than the size
of proteins pores [ 104 ]. Such limitations would prevent the pore from accommo-
dating bulky protein targets, therefore in the current stage, the protein pores may not
be universally suitable for the detection of large protein target. Alternatively, the
stable synthetic nanopores with flexible pore sizes can circumvent these limitations,
but almost all past studies on synthetic nanopores have focused on the measurement
of single DNA or protein molecule translocation. With the translocation-based
detection, any molecules smaller than the nanopore may generate indistinguishable
transient pore blocks. This low specificity limits the ability to identify and isolate
molecular processes [ 78 ]. This may be overcome by coating a layer of probing
molecules to the nanopore [ 50 , 69 , 87 , 103 , 117 ] to force specific targeting. For
example, DNA transport was enhanced in nanopores modified with an complemen-
tary oligonucleotide probe [ 50 , 69 ]; a biosensing nanopore coated with antibodies
can detect target proteins by measuring the time spent for fully blocking the pore