Direct Observation of Biaxial Confinement of a Semiflexible Filament in a Channel

Choi, Myung Chul; Santangelo, Christian; Pelletier, O.; Kim, Jung-Hyung; Kwon, Sooyoun; Zhang, Wen; Li, Y.; Pincus, P.; Safinya, Cyrus R.; Kim, M. W.

doi:10.1021/ma051348n

Cited by 40 publications

(60 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[1][2][3][4][5][6][7][8] Recent advances in chip lithography have led to the fabrication of well-defined nanochannels 9,10 so that issues in polymer physics may now be addressed which were elusive in the past. [11][12][13][14][15][16][17][18][19] At the same time, stiff polymers such as DNA and actin can now be well aligned which is of considerable interest in the biosciences. [20][21][22] In order to understand the mechanism of chain elongation, it is crucial to investigate the alignment as a function of the size of the channel cross section and this has been carried out recently by Reisner et al 13 The channel width was of the order of the DNA persistence length.…”

Section: Introductionmentioning

confidence: 99%

DNA confined in nanochannels: Hairpin tightening by entropic depletion

Odijk

2006

The Journal of Chemical Physics

217

View full text Add to dashboard Cite

A theory is presented of the elongation of double-stranded DNA confined in a nanochannel based on a study of the formation of hairpins. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The DNA in the hairpin remains double-stranded. The free energy of the hairpin is significantly larger than what one would expect if this entropic effect were unimportant. As a result, the distance between hairpins or the global persistence length is often tens of micrometer long and may even reach millimeter sizes for 10 nm thin channels. The hairpin shape and size and the DNA elongation are computed for nanoslits and circular and square nanochannels. A comparison with experiment is given.

show abstract

Section: Introductionmentioning

confidence: 99%

DNA confined in nanochannels: Hairpin tightening by entropic depletion

Odijk

2006

The Journal of Chemical Physics

217

View full text Add to dashboard Cite

show abstract

“…This background suggests the case of filament fluctuations confined to a plane but with ampli tudes extending into the regime of large deformation as a starting point for development of a model for large deflection. Other observations of filament fluctuation in a rectangular channel were reported by Choi et al [6]. Significant progress on the simulation of biofilaments as a basis for interpretation of observations has been reported by Doyle and coworkers and by Dorfman and co workers; recent reports are given in Refs.…”

Section: Introductionmentioning

confidence: 83%

Section: G E N E Ra Tio N O F R a N D O M C O N Fig U Ra Tio N Smentioning

confidence: 99%

“…The implication of the foregoing observation is that, if many conformations of a given filament are observed over time then a discrete history of angle values for any particular link-to-link joint must exhibit the distri bution p (6) in Eq. (6). Thus, in order to construct admissible fila ment conformations, it is necessary to adopt a strategy whereby the link-to-link angle 9j for every value of the integer j is chosen randomly from among a set of angle values for which the proba bility of occurrence of any particular values is p (9).…”

Section: G E N E Ra Tio N O F R a N D O M C O N Fig U Ra Tio N Smentioning

confidence: 99%

See 1 more Smart Citation

Large Amplitude Thermal Fluctuations of Confined Semiflexible Biopolymer Filaments

Jónsdóttir

Freund

2014

Journal of Applied Mechanics

View full text Add to dashboard Cite

The phenomenon of thermal fluctuations of biopolymers has been of active interest for some time with a view toward understanding the effect of filament confinement, migra tion, and bonding. In this study, we focus our attention on planar fluctuations of a single filament between parallel confining surfaces. Filament slopes, with respect to the centerline o f the channel, commonly exceed 0.1 in magnitude and therefore fall outside the range o f small amplitude fluctuations. Consequently, large amplitudes are anticipated from the outset. Determination of the partition function leads to the quantitative depend ence of free energy and other thermodynamic parameters on the degree of confinement.

show abstract

“…The devices are used to confine DNA on the nanometer scale and thus elongate genomic-length DNA. Confinement alters the statistical mechanical properties as well as the Brownian motion of the confined biomacromolecules [4,[13][14][15][16]. Since in most nanodevices the widths of confining nanochannels d are smaller than the persistence length L P of DNA (L P ∼ 50 nm), the behavior of the DNA can only be described by a model of confined semiflexible macromolecules [17].…”

Section: Introductionmentioning

confidence: 99%

Characterization of single semiflexible filaments under geometric constraints

2008

View full text Add to dashboard Cite

Abstract. Confinement effects on single semiflexible macromolecules are of central importance for a fundamental understanding of cellular processes involving biomacromolecules. To analyze the influence of confinement on the fluctuations of semiflexible macromolecules we study individual actin filaments in straight and curved microchannels. We experimentally characterize the segment distributions for fluctuating semiflexible filaments in microchannels as a function of the channel width. Moreover, the effect of channel curvature on the filament fluctuations is investigated. We find quantitative agreement between experimental results, Monte Carlo simulations, and the analytical description. This allows for determination of the persistence length of actin filaments, the deflection length, which characterizes the confinement effects, and the scaling exponents for the segment distribution of semiflexible macromolecules.PACS. 87.16.Ka Filaments, microtubules, their networks, and supramolecular assemblies -87.16.Ac Theory and modeling; computer simulation -82.37.Rs Single molecule manipulation of proteins and other biological molecules

show abstract

Direct Observation of Biaxial Confinement of a Semiflexible Filament in a Channel

Cited by 40 publications

References 10 publications

DNA confined in nanochannels: Hairpin tightening by entropic depletion

DNA confined in nanochannels: Hairpin tightening by entropic depletion

Large Amplitude Thermal Fluctuations of Confined Semiflexible Biopolymer Filaments

Characterization of single semiflexible filaments under geometric constraints

Contact Info

Product

Resources

About