Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Fanzio, Paola; Manneschi, Chiara; Angeli, Elena; Mussi, Valentina; Firpo, Giuseppe; Ceseracciu, Luca; Repetto, Luca; Valbusa, U.

doi:10.1038/srep00791

Cited by 44 publications

(49 citation statements)

References 36 publications

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“…J Nanomed Nanotechnol 8: 437. doi: 10.4172/2157-7439.1000437 Page 4 As shown in Figure 3, the presence of proper nanopatterns (bars I and II) can positively affect the miR-21 capturing. This performance was possible when nanostructures and biomolecule have comparable dimensions, as in accordance with the nanostructures' properties of influencing biomolecules behaviour described in literature [36,39]. The presence of conforming nano-hole pattern is an improvement with respect to the random roughness present on a PDMS surface obtained by spin-coating (bar "S", Figure 3), a surface that we previously studied for RNA capture from biological samples [21,31].…”

supporting

confidence: 83%

Enhancing miRNAs Capture on Polydimethylsiloxane Surface with Nanostructuration

Guida¹,

Savio²,

Potrich³

et al. 2017

J Nanomed Nanotechnol

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IntroductionIn the last years, predictive and preventive medicine took advantage on the novel discoveries in nano-diagnostics and smart therapies, mainly based on the specific identification of molecular biomarkers, such as nucleic acids (DNA, miRNA) and proteins. The possibility to detect low amount of biomarkers directly in biological fluids gives a great advantage in the early diagnosis and therapy of malignant diseases, which have high social impact. In fact, a correlation between degenerative, contagious, or inflammatory illnesses with the presence of specific biomarkers like miRNAs is now well established [1][2][3][4][5]. However, this remains a challenging task since in each biological sample several different biomolecular species co-exist, and moreover it is very hard to treat them in order to achieve the degree of purity and concentration required for a quantitative, specific, and reliable identification. To overcome these obstacles, several nanotechnologybased systems are being developed and tested for miRNAs detection. Nanobiosensor development is particularly relevant for such miRNAs, whose aberrant expression has been shown to correlate with the pathogenesis and progression of several diseases including cancer [6,7]. , in particular, is largely studied since is overexpressed in a variety of solid [8,9] and hematological tumors [10,11]. For these reasons, miR-21 was selected as a microRNA prototype in this study.Recently, it has been proposed that nanotechnology-based approaches [12][13][14] alternative to conventional methods [15][16][17][18][19] for miRNA detection and quantification can be developed using innovative biosensors made of Polydimetylsiloxane (PDMS) [20][21][22]. PDMS is known to have numerous advantages, supporting its development as a useful platform for biosensor and biomedical applications [20,[23][24][25]. Particularly, the attractiveness of such polymer lies in the fact that its chemical and physical properties and also the surface topography can be modulated [26]. These features combined with the manufacturing of biomolecule-specific topographies contribute to the improvement of PDMS performance in terms of sensitivity and efficiency. Recently, the fabrication of PDMS-based devices has introduced significant advances in several analytical techniques in terms of sensitivity, time consuming, and sample volume. Since PDMS material revealed characteristic properties and reliability, PDMS-nanotechnology has therefore gained great attention in developing new generation of research tools. However, both traditional and technology-based approaches have yet limitations mainly related to sample processing, purification, separation and enrichment of the small RNA fraction [12,27]. In fact, advanced biosensors still require specific conjugation steps [28] and expensive equipment which need to be overcome before they can have a real clinical application.PDMS nanostructures manufacturing may be useful to enhance the efficient purification of miRNA circulating bio-markers present at low Abstrac...

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confidence: 83%

Enhancing miRNAs Capture on Polydimethylsiloxane Surface with Nanostructuration

Guida¹,

Savio²,

Potrich³

et al. 2017

J Nanomed Nanotechnol

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“…Similar strategies have been used to create triangular nanochannels to stretch DNA or control its transport rate. [9][10][11][12] In the present contribution, we show that the extension of DNA in these triangular nanochannels can be mapped onto the models developed for circular and rectangular nanochannels, provided that we account for the role of the corners in a triangular channel.…”

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confidence: 99%

Entropic depletion of DNA in triangular nanochannels

2013

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Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes. V C 2013 American Institute of Physics.

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“…36,37 Further, the b obtained from our calculations is very similar to other reported experimental values. 45 Thus, our experimental system is closer to the nanopore 27 system than the DNA than the entropic trap array of Han and Craighead 46 as the translocation time through the nanochannel is the predominant time scale (by design) and is proportional to the DNA contour length. The a and b values for the simulated data (Figure 3(b)) were: 499.8 and À1.1 for k DNA and 2128 and À1.5 for T4 DNA.…”

Section: A Translocation Timementioning

confidence: 98%

DNA translocation through short nanofluidic channels under asymmetric pulsed electric field

et al. 2014

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Investigation of single molecule DNA dynamics in confined environments has led to important applications in DNA analysis, separation, and sequencing. Here, we studied the electrophoretic transport of DNA molecules through nanochannels shorter than the DNA contour length and calculated the associated translocation time curves. We found that the longer T4 DNA molecules required a longer time to traverse a fixed length nanochannel than shorter λ DNA molecules and that the translocation time decreased with increasing electric field which agreed with theoretical predictions. We applied this knowledge to design an asymmetric electric pulse and demonstrate the different responses of λ and T4 DNA to the pulses. We used Brownian dynamics simulations to corroborate our experimental results on DNA translocation behaviour. This work contributes to the fundamental understanding of polymer transport through nanochannels and may help in designing better separation techniques in the future.

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Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Cited by 44 publications

References 36 publications

Enhancing miRNAs Capture on Polydimethylsiloxane Surface with Nanostructuration

Enhancing miRNAs Capture on Polydimethylsiloxane Surface with Nanostructuration

Entropic depletion of DNA in triangular nanochannels

DNA translocation through short nanofluidic channels under asymmetric pulsed electric field

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