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Amplified stretch of bottlebrush-coated DNA in nanofluidic channels.

Zhang C, Hernandez-Garcia A, Jiang K, Gong Z, Guttula D, Ng SY, Malar PP, van Kan JA, Dai L, Doyle PS, Vries Rd, van der Maarel JR - Nucleic Acids Res. (2013)

Bottom Line: The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy.Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA.The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

ABSTRACT
The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.

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Orientation correlation of the tangent vectors at a pair of points separated by distance L along the contour. The lines represent exponential fits, and the polypeptide to DNA N/P ratios are noted. The fitted values of the persistence lengths P = 60 ± 5, 95 ± 5, 190 ± 10 and 240 ± 10 nm for N/P = 0, 0.1, 1.0 and 2.0, respectively.
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gkt783-F7: Orientation correlation of the tangent vectors at a pair of points separated by distance L along the contour. The lines represent exponential fits, and the polypeptide to DNA N/P ratios are noted. The fitted values of the persistence lengths P = 60 ± 5, 95 ± 5, 190 ± 10 and 240 ± 10 nm for N/P = 0, 0.1, 1.0 and 2.0, respectively.

Mentions: Experimental and fitted tangent correlation functions are shown in Figure 7. With increasing C4K12 to DNA ratio, fitted values of the persistence length P increase from 60 (bare DNA) to 240 nm at the highest polypeptide concentration. The value obtained for bare DNA agrees with the commonly accepted value of ∼50 nm (31). We have measured the length of the molecules by tracing the contour. No change in contour length induced by the binding of the polypeptide on DNA was observed.Figure 7.


Amplified stretch of bottlebrush-coated DNA in nanofluidic channels.

Zhang C, Hernandez-Garcia A, Jiang K, Gong Z, Guttula D, Ng SY, Malar PP, van Kan JA, Dai L, Doyle PS, Vries Rd, van der Maarel JR - Nucleic Acids Res. (2013)

Orientation correlation of the tangent vectors at a pair of points separated by distance L along the contour. The lines represent exponential fits, and the polypeptide to DNA N/P ratios are noted. The fitted values of the persistence lengths P = 60 ± 5, 95 ± 5, 190 ± 10 and 240 ± 10 nm for N/P = 0, 0.1, 1.0 and 2.0, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814371&req=5

gkt783-F7: Orientation correlation of the tangent vectors at a pair of points separated by distance L along the contour. The lines represent exponential fits, and the polypeptide to DNA N/P ratios are noted. The fitted values of the persistence lengths P = 60 ± 5, 95 ± 5, 190 ± 10 and 240 ± 10 nm for N/P = 0, 0.1, 1.0 and 2.0, respectively.
Mentions: Experimental and fitted tangent correlation functions are shown in Figure 7. With increasing C4K12 to DNA ratio, fitted values of the persistence length P increase from 60 (bare DNA) to 240 nm at the highest polypeptide concentration. The value obtained for bare DNA agrees with the commonly accepted value of ∼50 nm (31). We have measured the length of the molecules by tracing the contour. No change in contour length induced by the binding of the polypeptide on DNA was observed.Figure 7.

Bottom Line: The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy.Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA.The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore, Laboratory of Physical Chemistry and Colloid Science, Wageningen University, 6703 HB Wageningen, The Netherlands, Food and Biobased Research, Wageningen University, 6700 AA Wageningen, The Netherlands, BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), 117576 Singapore and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

ABSTRACT
The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.

Show MeSH
Related in: MedlinePlus