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13344264287
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note
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2 and then ligated for 1 hour at 37°C with 5 units of T4 DNA ligase (Boehringer). The cohesive-right DIG-labeled fragments were then added to the mixture and similarly annealed and ligated
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13344253439
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The DNA construct was incubated with streptavidin-coated paramagnetic beads (Dynal, M280) in phosphate-buffered saline (PBS) buffer for 10 min for binding The DMA-bead assembly was then incubated in wells coated with a polyclonal antibody to digoxigenin (anti-DIG; Boehringer). The wells were formed from glass cover slips and coated with polystyrene (or coated with silane), to which a small polyvinyl chloride ring was glued with paraffin Anti-DIG [2 5 μg in 100 μl of PBS or carbonate buffer (0.1 M, pH 9)] was incubated in each well overnight at 4°C. The anti-DIG was then rinsed thoroughly in phosphate buffer (10 mM, pH B) and 0.1% Tween. Sonicated fish sperm DNA (molecular biology grade; Boehringer) in phosphate buffer was added and incubated for 1 hour at 37°C to prevent nonspecific binding The wells were finally washed in phosphate buffer and Tween before addition of the DNA-magnetic bead assembly. The samples thus prepared and sealed to prevent contamination are stable for more than a week if stored at 4°C. Single DNA molecules can be studied for a few days.
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Superparamagnetic beads are made of many small ferromagnetic domains. Their susceptibility is anisotropic, and therefore their response to a magnetic field is similar to that of a compass needle
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We thank C Bouchiat for proving that relation to be valid even at small extensions where / ∼δx (personal communication).
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2>
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Our DNA construct is ∼20% longer than native λ DNA. The binding of the molecule to the bead and to the surface may not occur on the full length of the of the functionalized extremities We thus observed tethered molecules able to be coiled with maximal extensions between ∼17 μm and ′17 9 μm.
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A shorter persistence length corresponds to a smaller bending stiffness and results in a higher entropic rigidity. 3
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11744311356
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_, Phys. Rev. E52, 2912 (1995).
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Phys. Rev.
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0029416931
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H. Yin et al , Science 270, 1653 (1995).
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Science
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Yin, H.1
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13344257408
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We checked the overall acquisition chain by measuring the drag on the bead-DNA system (from the cutoff frequency in the spectrum of the Brownien motion) and comparing it with the expectations from Stokes law. Agreement within 4% was observed.
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The relative extension is defined as the measured extension of the molecule divided by its maximal extension.
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We thank A. Bememan, C. Bouchiat, A. Chiffaudel, L Jullien, J. Marko, X. Michalet, E. Siggia, J.-L. Sikorav, and S Smith for useful discussions, correspondence, and making available unpublished data. We also thank one of the referees for incisive and helpful comments. We are grateful to Boehringer-Mannheim for a generous gift of photo-digoxigenin
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We thank A. Bememan, C. Bouchiat, A. Chiffaudel, L Jullien, J. Marko, X. Michalet, E. Siggia, J.-L. Sikorav, and S Smith for useful discussions, correspondence, and making available unpublished data. We also thank one of the referees for incisive and helpful comments. We are grateful to Boehringer-Mannheim for a generous gift of photo-digoxigenin.
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