Characterization of Nucleic Acids by Nanopore Analysis

Abstract

Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field. As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Information about length, composition, structure, and dynamic motion of the molecule can be deduced from modulations of the current blockade.

Colloquium: Physical approaches to DNA sequencing and detection

“…These authors detected the translocation of the PN via measurement of the blockade current, discussed below. Since this pioneering experiment, nanopores have been used to extract a variety of information characterizing the translocation, dynamics, and interactions of both single-and double-stranded PNs in nanopores ͑Kasianowicz et Akeson et al, 1999;Henrickson et al, 2000;Meller et al, 2000Meller et al, , 2001Deamer and Branton, 2002;Chang et al, 2004;Chen et al, 2004;Fologea, Gershow, Ledden, et al, 2005;Mathé et al, 2005;Butler et al, 2006͒. Further 2003; Wanunu and Meller, 2007͒.…”

“…The electronic methods proposed so far are based on the ionic blockade current in the nanopore ͑Kasianowicz et Deamer and Branton, 2002͒, embedding nanoscale electrodes in the nanopore to measure transverse transport across ss-DNA ͑Zwolak and Di Ventra, 2005;Lagerqvist et al, 2006;Lee and Meller, 2007͒, or measuring the voltage fluctuations in a capacitor across the longitudinal direction of the pore ͑Heng, Aksimentiev, Ho, Dimitrov, et al, 2005;Gracheva, Xiong, Aksimentiev, et al, 2006͒. Three specific proposals using these techniques are shown in Fig.…”

“…With the promising first results of Kasianowicz et al ͑1996͒, it was speculated that it may be possible to sequence DNA by measuring the ionic blockade in a very particular pore under the right conditions ͑see Kasianowicz et al, 1996;Deamer and Akeson, 2000;and Deamer and Branton, 2002͒. With this idea in mind, researchers started to examine what kind of information can be extracted from the nanopore experiments.…”

“…There are several candidates that may fill this role ͑Kasianowicz et Akeson et al, 1999;Deamer and Akeson, 2000;Deamer and Branton, 2002;Heng, Aksimentiev, Ho, Dimitrov, et al, 2005;Zwolak and Di Ventra, 2005;Gracheva, Xiong, Aksimentiev, et al, 2006;Lagerqvist et al, 2006;NHGRI, 2006;Lee and Meller, 2007;Lindsay et al, 2007͒. All these candidates have one trait in common: they employ nanoscale probes to examine the structural or electronic signatures of individual DNA bases.…”

Probing surface hydrophobicity of individual protein at single-molecule resolution using solid-state nanopores

“…Nanopores, both biological nanopore [1][2][3][4][5] and solid-state nanopore [6][7][8], have been developed to be very promising candidates for biological detection at single molecule level, such as DNA [7,[9][10][11], RNA [12,13] and proteins [14][15][16][17][18][19][20][21][22][23]. The detection of single molecules is realized through monitoring the temporary ionic current blockage during single molecule translocation through nanopore which is driven by external electric field.…”