Conformations of DNA in Triangular Nanochannels

Manneschi, Chiara; Angeli, Elena; Ala-Nissilä, Tapio; Repetto, Luca; Firpo, Giuseppe; Valbusa, U.

doi:10.1021/ma4000545

Cited by 25 publications

(35 citation statements)

References 51 publications

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“…Such simulations for circular confinement are driven more by curiosity, since fabrication of transparent circular nanochannels suitable for fluorescence microscopy is challenging but possible [125]. In contrast, triangular channels are easily fabricated [123,124] and provide a stronger extension than a square channel for a given cross-sectional area [126,127]. Moreover, hydrodynamic interactions may play a crucial role for the strong stretching found in “normally closed” triangular nanochannels [124].…”

Section: Discussionmentioning

confidence: 99%

Hydrodynamics of DNA confined in nanoslits and nanochannels

Dorfman

Gupta

Jain

et al. 2014

Eur. Phys. J. Spec. Top.

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Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and “read” a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.

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Section: Discussionmentioning

confidence: 99%

Hydrodynamics of DNA confined in nanoslits and nanochannels

Dorfman

Gupta

Jain

et al. 2014

Eur. Phys. J. Spec. Top.

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“…Along with optical maps [2,7], recently DNA melting characteristics inside a nanochannel have been studied showing further promises [9]. These recent experiments have generated renewed interests in theoretical and computational studies of confined polymers [13]- [24].Confined DNAs inside nanochannels often studied in high salt concentrations [1] where the charges of the individual nucleotides are heavily screened [5,16]. Besides, the resolution of optical studies set by the diffraction limit is typically of the order of 100 base pairs.…”

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confidence: 99%

DNA confined in a two-dimensional strip geometry

Huang¹,

Bhattacharya²

2014

EPL

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-Semiflexible polymers characterized by the contour length L and persistent length ℓp confined in a spatial region D have been described as a series of "spherical blobs" and "deflecting lines" by de Gennes and Odjik for ℓp < D and ℓp ≫ D respectively. Recently new intermediate regimes (extended de Gennes and Gauss-de Gennes) have been investigated by Tree et al. [Phys. Rev. Lett. 110, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in d-dimension as a function of L, ℓp, and D, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor A used to describe the chain extension in the Odjik limit is independent of physical dimension d and is the same as previously found by Conformations and dynamics of DNA inside a nanochannel have attracted considerable attention among various disciplines of science and engineering [1]. Important biomolecules, such as, chromosomal DNAs, or proteins whose functionalities are crucially dependent on the exact sequence of the nucleotides or amino acids usually exist in highly compact conformations. By straightening these molecules on a two dimensional sheet [2][3][4] or inside a nanochannel [5][6][7][8][9][10] it is possible to obtain the structural details of these molecules. It is believed that a complete characterization of the DNA sequence for each individual and a proper understanding the role of genetic variations will lead to personalized medicine for diseases, such as, cancer [11]. DNA confined and stretched inside a nanochannel offers significant promise towards this goal. Unlike, traditional sequencing using Sangers method [12] which requires fragmentation and replication, analysis of a single DNA will be free from statistical errors and sequence gaps while reconstruction [11]. Naturally quests for efficient but low cost techniques have attracted considerable attention. Along with optical maps [2,7], recently DNA melting characteristics inside a nanochannel have been studied showing further promises [9]. These recent experiments have generated renewed interests in theoretical and computational studies of confined polymers [13]- [24].Confined DNAs inside nanochannels often studied in high salt concentrations [1] where the charges of the individual nucleotides are heavily screened [5,16]. Besides, the resolution of optical studies set by the diffraction limit is typically of the order of 100 base pairs. Under these conditions a double-stranded DNA is often described as a worm-like chain (WLC) [25] whose end-to-end distanceHowever, for a very long chain eventually the excluded volume (EV) effect becomes important [26,27], and for L ≫ ℓ p the end-to-end distance in d dimensions should be characterized by the bulk conformation of a swollen semiflexible chain [28,29] where a is the effective width of the...

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“…The extension of a long DNA molecule confined in a nanochannel has attracted tremendous attention 1-4 in large part because it couples a fundamental polymer physics problem to an important application in genomics, namely DNA barcoding. [5][6][7][8][9] The theoretical basis for the equilibrium extension of DNA in a nanochannel has been addressed to varying degrees of accuracy by theory and simulation for strong, 5,10-18 moderate, 17,[19][20][21][22][23][24][25][26][27][28][29][30][31][32] and relatively weak [33][34][35][36] confinement, leading to the reconciliation 26,30 between early experimental observations 37 and the predictions of the classic theories from Odijk 10 and de Gennes. 33 Due to both the paucity of dynamic data in strong confinement and the computational difficulty of simulating the dynamics of long chains, there is little work validating the computational predictions of confined DNA dynamics in nanochannels with hydrodynamic interactions.…”

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confidence: 99%

Modeling the relaxation time of DNA confined in a nanochannel

Tree

Wang²,

Dorfman³

2013

Biomicrofluidics

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Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.

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Conformations of DNA in Triangular Nanochannels

Cited by 25 publications

References 51 publications

Hydrodynamics of DNA confined in nanoslits and nanochannels

Hydrodynamics of DNA confined in nanoslits and nanochannels

DNA confined in a two-dimensional strip geometry

Modeling the relaxation time of DNA confined in a nanochannel

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