Single molecule statistics and the polynucleotide unzipping transition

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"Single molecule statistics and the polynucleotide unzipping transition"




Micromanipulation of Single Molecule


Fig. 1: Sketch of the DNA unzipping experiment. One of the single strands of a dsDNA molecule with a random base sequence is attached by its end to a solid surface, and the other is pulled away from the surface with a constant force F. As a result, the double strand partially denatures, separating m base pairs (m=2 in the figure). The distance between the ends of the two single strands, or extension, is r. Inset: Schematic phase diagram in the temperature– pulling force (<math>T-F</math>) plane of a <math>ds</math>DNA molecule in three dimensions. At low enough T and F, the polymer is in the native, doublestranded phase. At the phase transition line Fc(T), the DNA denatures and the two strands separate. Thermally induced melting occurs at zero force at a temperature Tm . As indicated by the arrow, this paper considers instead the unzipping transition, in which the phase transition line is crossed at nonzero F.

One of the single strands from a double-stranded DNA molecule is attached to a glass slide, and the other to a bead on which a constant force F is exerted. F could be created, for example, with magnetic tweezers, which have been used to exert constant piconewton-scale forces over hundreds of microns. Optical tweezers or atomic force microscopes (AFM) with appropriate feedback can create a similar effect. As a result of the applied force, the DNA partially ‘‘unzips,’’ breaking m bonds.