Nanopore Recordings to Quantify Activity-Related Properties of Proteins - Nanopores: Sensing and Fundamental Biological Interactions - page 223

and flexibility may accelerate the use of solid-state nanopores for protein-ligand
binding assays because the efficiency of immobilizing a variety of ligands is crucial
for the acceptance of this technique [ 54 ]. In addition, surface chemistries that
reduce non-specific interactions of the protein with the surface will minimize
clogging of nanopores and solve some of the problems mentioned above.
Developing nanopores that mimic biological pores such as porins and ion channel
proteins is an intriguing future perspective [ 29 ]. Topics range from replicating the ion
current rectifying properties of many ion channels (perhaps the most advanced aspect
at the moment) to replicating the natural selectivity of nucleopores and ion channels,
and possibly, to gate nanopores for signal amplification in analogy to ligand-gated ion
channels in nerve endings. Recent, inspiring work has advanced this area of research
in replicating the basic nucleopore complex found in a yeast cell [ 23 ]. Furthermore,
the ability of ion channel proteins to undergo conformational changes in response to
external stimuli is intriguing, since triggers for these responses are not limited to
ligand binding but may include electric potentials, mechanical stresses, and chemical
reactions such as phosphorylations [ 19 , 52 ].
Finally, electrical noise remains a challenge for most nanopore sensing experi-
ments; in particular for studying small proteins with very short translocation times.
Developing nanofabrication techniques that permit the fabrication of nanopores
in materials with low capacitance will help reduce electrical noise and may
potentially increase the sensitivity of nanopores for detecting proteins with short
translocation times [ 48 ].
Acknowledgments The authors acknowledge the following funding sources: National Institutes
of Health (M.M., grant no. 1RO1GM081705), NSF Career Award (M.M., grant no. 0449088),
AISIN/IMRA America Inc., and Thermo Fisher - CCG Collaborative Pilot Project Initiative.
References
1. Ali M, Schiedt B, Healy K et al . (2008) Modifying the surface charge of single track-etched
conical nanopores in polyimide . Nanotechnology, 19: 085713
2. Ali M, Yameen B, Neumann R et al . (2008) Biosensing and supramolecular bioconjugation in
single conical polymer nanochannels. Facile incorporation of biorecognition elements into
nanoconfined geometries . J. Am. Chem. Soc., 130: 16351-16357
3. Blake S, Capone R, Mayer M et al . (2008) Chemically reactive derivatives of gramicidin a for
developing ion channel-based nanoprobes . Bioconjug. Chem., 19: 1614-1624
4. Capone R, Blake S, Restrepo M R et al . (2007) Designing nanosensors based on charged
derivatives of gramicidin a . J. Am. Chem. Soc., 129: 9737-9745
5. Chang H, Venkatesan B M, Iqbal S M et al . (2006) DNA counterion current and saturation
examined by a mems-based solid state nanopore sensor . Biomed. Microdevices, 8: 263-269
6. Chun K Y and Stroeve P (2002) Protein transport in nanoporous membranes modified with
self-assembled monolayers of functionalized thiols . Langmuir, 18: 4653-4658
7. Chun K Y, Mafe S, Ramirez P et al . (2006) Protein transport through gold-coated, charged
nanopores: effects of applied voltage . Chem. Phys. Lett., 418: 561-564
8. Clarke J, Wu HC, Jayasinghe L et al . (2009) Continuous base identification for single-molecule
nanopore DNA sequencing . Nat. Nanotechnol., 4: 265-270