1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
f
Entropic depletion of DNA in triangular nanochannels
Rent:
Rent this article for
Access full text Article
/content/aip/journal/bmf/7/2/10.1063/1.4794371
1.
1. R. Riehn, M. Lu, Y. M. Wang, S. F. Lim, E. C. Cox, and R. H. Austin, Proc. Natl. Acad. Sci. U.S.A. 102, 10012 (2005).
http://dx.doi.org/10.1073/pnas.0503809102
2.
2. K. Jo, D. M. Dhingra, T. Odijk, J. J. de Pablo, M. D. Graham, R. Runnheim, D. Forrest, and D. C. Schwartz, Proc. Natl. Acad. Sci. U.S.A. 104, 2673 (2007).
http://dx.doi.org/10.1073/pnas.0611151104
3.
3. S. K. Das, M. D. Austin, M. C. Akana, P. Deshpande, H. Cao, and M. Xiao, Nucleic Acids Res. 38, e177 (2010).
http://dx.doi.org/10.1093/nar/gkq673
4.
4. Y. Kim, K. S. Kim, K. L. Kounovsky, R. Chang, G. Y. Jung, J. J. de Pablo, K. Jo, and D. C. Schwartz, Lab Chip 11, 1721 (2011).
http://dx.doi.org/10.1039/c0lc00680g
5.
5. K. H. Rasmussen, R. Marie, J. M. Lange, W. E. Svendsen, A. Kristensen, and K. U. Mir, Lab Chip 11, 1431 (2011).
http://dx.doi.org/10.1039/c0lc00603c
6.
6. E. T. Lam, A. Hastie, C. Lin, D. Ehrlich, S. K. Das, M. D. Austin, P. Deshpande, H. Cao, N. Nagarajan, M. Xiao, and P. Y. Kwok, Nat. Biotechnol. 30, 771 (2012).
http://dx.doi.org/10.1038/nbt.2303
7.
7. W. Reisner, J. N. Pedersen, and R. H. Austin, Rep. Prog. Phys. 75, 106601 (2012).
http://dx.doi.org/10.1088/0034-4885/75/10/106601
8.
8. K. D. Dorfman, S. B. King, D. W. Olson, J. D. P. Thomas, and D. R. Tree, “ Beyond gel electrophoresis: Microfluidic separations, fluorescence burst analysis, and DNA stretching,” Chem. Rev. (published online).
http://dx.doi.org/10.1021/cr3002142
9.
9. D. Huh, K. L. Mills, X. Zhu, M. A. Burns, M. D. Thouless, and S. Takayama, Nature Mater. 6, 424 (2007).
http://dx.doi.org/10.1038/nmat1907
10.
10. E. Angeli, C. Manneschi, L. Repetto, G. Firpo, and U. Valbusa, Lab Chip 11, 2625 (2011).
http://dx.doi.org/10.1039/c1lc20411d
11.
11. P. Fanzio, V. Mussi, C. Manneschi, E. Angeli, G. Firpo, L. Repetto, and U. Valbusa, Lab Chip 11, 2961 (2011).
http://dx.doi.org/10.1039/c1lc20243j
12.
12. P. Fanzio, C. Manneschi, E. Angeli, V. Mussi, G. Firpo, L. Cesaracciu, L. Repetto, and U. Valbusa, Sci. Rep. 2, 791 10.1038/srep00791 (2012).
http://dx.doi.org/10.1038/srep00791
13.
13. T. Odijk, Macromolecules 16, 1340 (1983).
http://dx.doi.org/10.1021/ma00242a015
14.
14. M. Daoud and P. G. de Gennes, J. Phys. (Paris) 38, 85 (1977).
http://dx.doi.org/10.1051/jphys:0197700380108500
15.
15. Y. Wang, D. R. Tree, and K. D. Dorfman, Macromolecules 44, 6594 (2011).
http://dx.doi.org/10.1021/ma201277e
16.
16. P. Cifra, J. Chem. Phys. 131, 224903 (2009).
http://dx.doi.org/10.1063/1.3271830
17.
17. P. Cifra, Z. Benková, and T. Bleha, J. Phys. Chem. B 113, 1843 (2009).
http://dx.doi.org/10.1021/jp806126r
18.
18. D. R. Tree, Y. Wang, and K. D. Dorfman, Phys. Rev. Lett. 108, 228105 (2012).
http://dx.doi.org/10.1103/PhysRevLett.108.228105
19.
19. P. Cifra, J. Chem. Phys. 136, 024902 (2012).
http://dx.doi.org/10.1063/1.3674304
20.
20. T. Odijk, J. Chem. Phys. 125, 204904 (2006).
http://dx.doi.org/10.1063/1.2400227
21.
21. Y. Wang, W. F. Reinhart, D. R. Tree, and K. D. Dorfman, Biomicrofluidics 6, 014101 (2012).
http://dx.doi.org/10.1063/1.3672691
22.
22. C. Bustamante, J. F. Marko, E. D. Siggia, and S. B. Smith, Science 265, 1599 (1994).
http://dx.doi.org/10.1126/science.8079175
23.
23. J. Wang and H. Gao, J. Chem. Phys. 123, 084906 (2005).
http://dx.doi.org/10.1063/1.2008233
24.
24. W. Reisner, K. J. Morton, R. Riehn, Y. M. Wang, Z. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin, Phys. Rev. Lett. 94, 196101 (2005).
http://dx.doi.org/10.1103/PhysRevLett.94.196101
25.
25.See supplementary material at http://dx.doi.org/10.1063/1.4794371 for tabulated simulation data. [Supplementary Material]
26.
26. T. Odijk, Phys. Rev. E 77, 060901R (2008).
http://dx.doi.org/10.1103/PhysRevE.77.060901
27.
27. Y. Zhang, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 136, 014901 (2012).
http://dx.doi.org/10.1063/1.3672103
http://aip.metastore.ingenta.com/content/aip/journal/bmf/7/2/10.1063/1.4794371
Loading
View: Figures

Figures

Image of FIG. 1.

Click to view

FIG. 1.

(a) Schematic representation of an isosceles triangular channel in our simulations. The DNA is represented by beads with hardcore excluded volume interactions with one another and the walls. The area of the channel that is accessible to the bead centers (bounded by the dashed line) is the effective area. The thick black curve schematically depicts a portion of a DNA molecule projected onto the channel cross-section. The semiflexible nature of the chain decreases the probability of having a high radius of curvature and therefore restricts the chain from fitting easily into the corners of the channel. (b) A probability density plot from our simulations (see Sec. II ) for an apex angle of . The effective area boundary from panel (a) is included for reference. Note the entropic depletion in the corners caused by the bending penalty illustrated in (a), which increases as the angle of the corner decreases.

Image of FIG. 2.

Click to view

FIG. 2.

Fractional mean span plotted as a function of the effective area. Black triangles are triangular channels with different apex angles, red circles are circular channels, blue squares are square channels. The symbols' sizes are proximate to the standard error. The dashed line shows the scaling of Eq. (2) . For completeness, the data are tabulated. 25

Image of FIG. 3.

Click to view

FIG. 3.

Mean span in triangles normalized by that of a circular channel of equal effective area as a function of apex angle in the triangle. The particular values of are listed in the legend. The data are separated into two panels for clarity. The relative extension increases with in the left panel and decreases with in the right panel.

Image of FIG. 4.

Click to view

FIG. 4.

Probability density plots of channels with effective area created by binning the configuration data into pixels of size . Black lines indicate channel boundaries. If the probability density in the pixel is less than , the pixel is white. (a) Circular channel. (b) Square channel. (c) Triangular channel with apex angle . (d) Triangular channel with apex angle .

Image of FIG. 5.

Click to view

FIG. 5.

Axial chain density distributions for triangular channels with . Positions are normalized by the span X of each configuration. Each bin has a width of 1% of the total span. Lines are different apex angles.

Image of FIG. 6.

Click to view

FIG. 6.

A probability density plot from the simulation for an apex angle of . The eigenvectors of the covariance of the projected bead positions are overlayed in black. Interpolated data from each of the eigenvectors are shown as histograms in the adjacent panels (vertical on the right, horizontal on top). Lines in the side panels are 4th degree polynomial regressions of data sets. The geometric average of the full width at half maximum of the polynomials is defined as .

Image of FIG. 7.

Click to view

FIG. 7.

Fractional extension plotted as a function of the characteristic size of the probability density in the channel cross-section, . Black triangles are triangular channels, red circles are circular channels, and blue squares are square channels. Symbols are sized proximate to the standard error. The dashed line shows −1 scaling. Tabulated data are also available. 25

Loading

Article metrics loading...

/content/aip/journal/bmf/7/2/10.1063/1.4794371
2013-03-01
2014-04-20

Abstract

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.

Loading

Full text loading...

/deliver/fulltext/aip/journal/bmf/7/2/1.4794371.html;jsessionid=1t0wrym1o7iyi.x-aip-live-01?itemId=/content/aip/journal/bmf/7/2/10.1063/1.4794371&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/bmf
true
true
This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Entropic depletion of DNA in triangular nanochannels
http://aip.metastore.ingenta.com/content/aip/journal/bmf/7/2/10.1063/1.4794371
10.1063/1.4794371
SEARCH_EXPAND_ITEM