DNA manipulation with elastomeric nanostructures fabricated by soft-moulding of a FIB-patterned stamp

Angeli, Elena; Manneschi, Chiara; Repetto, Luca; Firpo, Giuseppe; Valbusa, U.

doi:10.1039/c1lc20411d

Cited by 37 publications

(33 citation statements)

References 22 publications

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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.…”

Section: Introductionmentioning

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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Section: Introductionmentioning

confidence: 99%

Entropic depletion of DNA in triangular nanochannels

2013

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“…Here we propose a new method that exploits the elastomeric behavior of soft polymeric materials to fabricate tuneable devices for the manipulation and trapping of DNA molecules inside a nanochannel2223. In particular, we present the fabrication process of an elastomeric Lab-On-Chip device and the characterization of the nanochannel resizing in response to a compressive strain.…”

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confidence: 99%

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

Fanzio¹,

Manneschi²,

Angeli³

et al. 2012

Sci Rep

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Several strategies have been developed for the control of DNA translocation in nanopores and nanochannels. However, the possibility to reduce the molecule speed is still challenging for applications in the field of single molecule analysis, such as ultra-rapid sequencing. This paper demonstrates the possibility to alter the DNA translocation process through an elastomeric nanochannel device by dynamically changing its cross section. More in detail, nanochannel deformation is induced by a macroscopic mechanical compression of the polymeric device. This nanochannel squeezing allows slowing down the DNA molecule passage inside it. This simple and low cost method is based on the exploitation of the elastomeric nature of the device, can be coupled with different sensing techniques, is applicable in many research fields, such as DNA detection and manipulation, and is promising for further development in sequencing technology.

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“…In such translocation process, the dynamical nature of the pore enable the polymer chain to translocate more efficiently as compare to the translocation of polymer in static pore [47]. On the experimental side, it has been shown that the translocation of DNA through a nanochannel can be modulated by dynamically changing the cross-section of an elastomeric nanochannel device by applying mechanical stress [48][49][50][51][52]. Time-dependent driving force are also used in the translocation process [53][54][55][56][57][58].…”

Section: Introductionmentioning

confidence: 99%

Polymer translocation through nano-pores: influence of pore and polymer deformation

2018

Preprint

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We have simulated polymer translocation across the a α-hemolysin nano-pore via a coarse grained computational model for both the polymer and the pore. We simulate the translocation process by allowing the protein cross a free-energy barrier from a metastable state, in the presence of thermal fluctuations. The deformation in the channel, which we model by making the radius of pore change from large to small size, can be originated by the random and non-random (systematic) cellular environment, drive out the polymer out of equilibrium during the transport dynamics. We expect that in more realistic conditions, effects originating on the translocation phenomena due to the deformability of the nano-pore can either decrease or increase the transport time of biomolecule passing through the channel. Deformation in channel can occurred because the structure of αhemolysin channel is not completely immobile, hence a small pore deformation can be occurred during translocation process. We also discuss the effects of polymer deformation on the translocation process, which we achieve by varying the value of the empirical and dihedral potential constants. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore under the influence of small and large pore. We observed that a pore with small size can speed down the polymer translocation process, especially at the limit of small pulling force. A drastic increase in translocation time at the limit of low force for small pore clearly illustrate the strong interaction between the transport polymer and pore. Our results can be of fundamental importance for those experiments on DNA-RNA sorting and sequencing and drug delivery mechanism for anti-cancer therapy.

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DNA manipulation with elastomeric nanostructures fabricated by soft-moulding of a FIB-patterned stamp

Cited by 37 publications

References 22 publications

Entropic depletion of DNA in triangular nanochannels

Entropic depletion of DNA in triangular nanochannels

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

Polymer translocation through nano-pores: influence of pore and polymer deformation

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