Sucking genes into pores: Insight into driven translocation

Abstract

Flexible polymers such as long DNA, RNA molecules, and proteins, can pass through a narrow pore whose size is comparable to their molecular thickness. We highlight the richness and complexity involved in the dynamics of this unique mode of molecular transport, called translocation, actively driven by external forces. In particular, the process takes place in the condition far from equilibrium accompanying of large conformational distortion in line with the propagation of the tensile force along the chain backbone. A general framework is proposed, which captures such essential features, whereby can account for reported various experimental data from a unified viewpoint.

Driven translocation of a polymer: Fluctuations at work

“…This scenario has been treated within the linear response theory (that is, for relatively weak driving forces) and the corresponding memory function has been derived explicitly [7,8]. For arbitrary strong driving forces, an interesting approach based on the notion of tensile force propagation along the chain backbone has been suggested by Sakaue [9][10][11]. Sakaue's idea has been used and worked out very recently in other theoretical treatments [12,13].…”

“…It is important to determine the origin of this inconsistency since apparently there is something missing in the aforementioned theoretical consideration which gives room for speculations. For example, in a paper by Ikonen et al [12], the model based on the idea of tensile force propagation [9][10][11] and the role of pore-polymer friction has been numerically investigated. The authors argue that the theoretical value for the exponent, α = 1 + ν, may be seen only for very long chains whereas for the chain lengths used in real experiments or simulations the effective exponent α could be approximately 20% smaller.…”

“…Recently [13] we suggested a theoretical description based on the tensile (Pincus) blob picture of a pulled chain and the notion of a tensile force propagation, introduced by Sakaue [9][10][11]. Assuming that the local driving force is matched by a drag force of equal magnitude, (i.e., in a quasistatic approximation), we derived an equation of motion for the tensile front position.…”

Erratum to: Dynamical diagram and scaling in polymer driven translocation

“…[1]. The same ansatz was also adopted in our earlier publications [2,3], where the basic framework for the driven translocation was proposed. However, as discussed in [4], one should instead set the steady-state velocity V (t) ≡ v(t, x = 0) for the steady-state approximation to be self-consistent.…”

Suspended particle transport through constriction channel with Brownian motion

“…There are many situations where small objects subject to Brownian motion in a fluid are introduced to the constriction of microscopic channels, for example, filtration of colloidal particles through porous media [1][2][3], translocation of DNA molecules through nanopore sequencers [4][5][6][7][8][9][10][11][12][13][14][15][16][17], and lab-on-achip (LOC) devices where analytes are introduced to various domains of nano-and microchannels for analysis [18][19][20][21][22][23][24][25]. It is now well known that the translocation phenomena of polymer molecules through nanopores with a diameter comparable to the monomer size have stochastic nature [5,6].…”