DNA confined in a two-dimensional strip geometry

Abstract

-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...

Dynamic Compression of Single Nanochannel Confined DNA via a Nanodozer Assay

“…While, precisely speaking, our method does not probe the statistics of equilibrium (noncompressed) chains, we believe that the statistics observed under compression are related to the statistics obeyed in the equilibrium (noncompressed) regimes. In particular, it is likely that the mean-field behavior we observe is closely connected with the extended de Gennes regime [20,21] for equilibrium chains. The extended de Gennes regime has been posited on theoretical grounds but is challenging to confirm experimentally [12].…”

Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles

“…While one expects that semiflexible chains in wide channels (D ≫ ℓ p ) also are compatible with the Daoud-De Gennes 40 picture of a string of blobs, the crossover from the Odijk regime (D ≪ ℓ p ) where L ∥ differs from L only by a small correction (of order 15,45 (D/ℓ p ) 2/3 ) to this regime is still a matter of debate. 1,[27][28][29][30][31]36 However, we note that Eq. 1is based on the use of the Kratky-Porod model of wormlike chains 62,63 which describes the polymer in terms of a contour ⃗ r(s) in space, s being a coordinate along this contour, and the Hamiltonian involves a single parameter, the bending rigidity κ KP ,…”

“…Also the complication that knots may form (which is relevant for dsDNA in various circumstances 81,82 ) cannot occur in d = 2. Our preliminary work 34,36 on confinement effects on chains in d = 2 already has indicated a rather complex behavior, and hence in the present work, we shall address this problem in more detail, with an emphasis on the question to what extent the phenomena are universal and which aspects are model-dependent. Hence, we shall contrast results for the lattice model of Figs.…”

“…We now study semiflexible polymers in quasi-one-dimensional confinement, extending the discussions that were already given in our preliminary work. 34,36 The considered lattice model is defined in Fig. 2(c), and the continuum model (sketched in Fig.…”

“…Semiflexible polymers confined in narrow channels have found abiding interests recently, both in experiments, [1][2][3][4][5][6][7][8][9][10][11][12][13][14] analytical theory, [15][16][17][18][19][20][21][22][23][24][25] and in computer simulations. [26][27][28][29][30][31][32][33][34][35][36][37][38][39] From the application side, this problem is of great interest for the detection of single DNA molecules, separating them by size, and to develop tools for their sequence analysis. On the theoretical front, confined semiflexible polymers pose a variety of challenging questions: what aspects of the behavior are specific to a particular polymer, and what aspects of the behavior are generic?…”