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Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
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10.1063/1.2937441
/content/aip/journal/jcp/128/22/10.1063/1.2937441
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/22/10.1063/1.2937441
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Persistence length (solid curve) and effective diameter (dashed curve) vs the ionic strength of the buffer medium calculated with the effective number of charges per unit DNA length from the numerical solution to the nonlinear Poisson–Boltzmann equation for DNA in the -form and 23 base-pairs per YOYO-1 molecule (bare diameter and bare persistence length ).

Image of FIG. 2.
FIG. 2.

Persistence length (solid curve) and effective diameter (dashed curve) vs the number of base-pairs per YOYO-1 molecule calculated with the effective number of charges per unit DNA length from the numerical solution to the nonlinear Poisson–Boltzmann equation for DNA in the -form in buffer (ionic strength ).

Image of FIG. 3.
FIG. 3.

(a): Scanning electron microscopy image of the HSQ master showing a positive standing channel structure with a width of 150 (I) and 200 (II) and a uniform height of (the height was determined by atomic force microscopy). Feature III is a wide “feeder” channel. (b) Atomic force microscopy image of the PDMS replica showing a set of parallel channels with a width and depth of 200 and , respectively.

Image of FIG. 4.
FIG. 4.

Montage of fluorescence images of T4-DNA molecules confined in channels. The buffer concentration decreases from left to right according to 1, , , , , and . The molecules were stained with an intercalation level of 23 base-pairs per YOYO-1 molecule.

Image of FIG. 5.
FIG. 5.

Relative extension of T4-DNA in (a), (b), and (c) channels vs the ionic strength of the solvent medium. The open symbols refer to TBE buffer conditions, whereas the closed symbols pertain to the T buffer system. The error bars denote the width of the distribution following from the measurement of at least 200 different DNA molecules for each data point. The solid curves represent a fit of the theoretically predicted extensions to the data with the persistence lengths and effective diameters displayed in Fig. 1 and optimized scaling constant and bare persistence length . The dashed curves represent the fluctuation bandwidth. The molecules were stained with an intercalation level of 23 base-pairs per YOYO-1 molecule.

Image of FIG. 6.
FIG. 6.

(a) Number of persistence length segments per blob in (dashed-dotted curve), (dashed curve), and (solid curve) channels vs the ionic strength of the solvent pertaining to the fit of the theoretical extension to the data in Fig. 5(b). (b) As in panel (a), but for the repulsive energy per blob (in units ).

Image of FIG. 7.
FIG. 7.

(a) Excluded volume parameter in (dashed-dotted curve), (dashed curve), and (solid curve) channels vs the ionic strength of the solvent pertaining to the fit of the theoretical extension to the data in Fig. 5. (b) As in panel (a), but for the swelling factor .

Image of FIG. 8.
FIG. 8.

Relative extension of T4-DNA stained with the saturating intercalation ratio of 4 base-pairs per YOYO-1 molecule in the channel vs the ionic strength of the TBE medium. The solid curve represents a fit of the theoretically predicted extension calculated with the relevant linear DNA charge density, optimized scaling constant , and bare persistence length . The dashed curve is included for comparison and represents the corresponding theoretical result for T4-DNA with 23 base-pairs per YOYO-1 molecule (see Fig. 5).

Image of FIG. 9.
FIG. 9.

Relative extension of T4-DNA in the channel vs the base-pair to YOYO-1 ratio in buffer. The solid curve represents a fit of the theoretically predicted extension to the data with the persistence lengths and effective diameters shown in Fig. 2 (optimized with a fixed value ).

Image of FIG. 10.
FIG. 10.

Relative extension of T4-DNA vs the ionic strength of the TBE/Mg (◻), TBE/Ca (○), and TBE/Pu (△) buffers in channels. The intercalation ratio is 23 base-pairs per YOYO-1 molecule. The solid curve represents the theoretically predicted extension based on the solution of the nonlinear Poisson–Boltzmann equation including the effect of the divalent salt. The dashed curve is included for comparison and represents the corresponding result for the relative extension in a monovalent salt buffer (see Fig. 5).

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/content/aip/journal/jcp/128/22/10.1063/1.2937441
2008-06-13
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/22/10.1063/1.2937441
10.1063/1.2937441
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