Probing Single DNA Molecule Transport Using Fabricated Nanopores

Chen, Peng; Gu, Jian; Brandin, Eric; Kim, Young-Rok; Wang, Qiaoqiao; Branton, Daniel

doi:10.1021/nl048654j

Cited by 357 publications

(403 citation statements)

References 31 publications

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“…This implies that molecules test multiple configurations prior to capture, which is a statistical process governed by energetic considerations. By contrast, Chen et al reported a bias for unfolded translocations that increased with applied voltage [5]. This finding implies that molecules pre-align in the fields outside the pore rather than sample multiple configurations prior to capture.…”

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confidence: 90%

“…The capture location, x ≡ Ls Ls+L l , is the fractional contour distance from the initial fold to the nearest end. The time for each segment to translocate is measurable from the time trace of I [4][5][6] and can be used to estimate x. Storm et al inferred the distribution of x for λ DNA translocations and concluded that folds occur with equal probability everywhere along a molecule's length, but that the DNA is more likely to be captured at its ends because of the lower energetic cost of threading an unfolded molecule [6].…”

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confidence: 99%

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Statistics of DNA Capture by a Solid-State Nanopore

2013

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A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

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confidence: 90%

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confidence: 99%

Statistics of DNA Capture by a Solid-State Nanopore

2013

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“…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.…”

Section: Nanopores and Polynucleotidesmentioning

confidence: 99%

Colloquium: Physical approaches to DNA sequencing and detection

2008

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With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe ͑through chemical elongation, electrophoresis, and optical detection͒ length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field.

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“…In recent years, SAMs found wide applications in chemistry, physics, and especial biology [2][3][4][5] when SAMs combined with microfluidic technology [6][7][8][9][10]; for example, we applied alkanethiolate SAMs on gold surface to study the relationship between the shape of mammalian cells and their migration direction [11]. Recently, when we applied alkanethiolate SAMs combined with microfluidic technology to establish interaction models for multiple types of cells [12], we found that the SAMs diffused on the surfaces of evaporation-coated gold slides which were covered with polydimethylsiloxan (PDMS) stamps [13].…”

Section: Introductionmentioning

confidence: 99%

Diffusion of self-assembled monolayers of thiols on the gold surfaces covered with polydimethylsiloxane stamps

et al. 2014

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Thiols can diffuse and form self-assembled monolayers (SAMs) on the gold surfaces covered with polydimethylsiloxane (PDMS) stamps. For the first time, with cells as the indicator of how far alkanethiols had diffused to form SAM, we studied the growth dynamics of SAMs of HS(CH 2 ) 11 (OCH 2 CH 2 ) 3 OH (EG 3 ) and HS(CH 2 ) 11 (OCH 2 CH 2 ) 6 OH (EG 6 ) on the gold surfaces covered with PDMS stamps. The growth of SAMs is well described by one-dimensional diffusion from a line source of concentration, with surface diffusion coefficient of 193.4 ± 19.2 lm 2 /min (EG 3 ) and 95.8 ± 18.9 lm 2 /min (EG 6 ).

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Probing Single DNA Molecule Transport Using Fabricated Nanopores

Cited by 357 publications

References 31 publications

Statistics of DNA Capture by a Solid-State Nanopore

Statistics of DNA Capture by a Solid-State Nanopore

Colloquium: Physical approaches to DNA sequencing and detection

Diffusion of self-assembled monolayers of thiols on the gold surfaces covered with polydimethylsiloxane stamps

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