Wringing Out DNA

The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a stretched DNA molecule increases linearly by 0.42 nm per excess turn applied to the double helix. This result contradicts the intuition that DNA should lengthen as it is unwound and get shorter with overwinding. We then present numerical results of energy minimizations of torsionally restrained DNA that display a behavior similar to the experimental data and shed light on the molecular details of this surprising effect.

Figure 1

(a) Two adjacent base pairs are schematically drawn as two pairs of plates (blue), connected by the two backbones (thick red lines). Notice the negative value of the shift in $B$-DNA, i.e., the displacement of the base pair from the helical axis towards the minor groove (marked by “m”). “M” marks the major groove. (b) Principle of the magnetic tweezers (not to scale).

Figure 2

(a) Extension $L$ versus rotation $n$ curve of DNA (pLacD1, 7.4 kbp; $20\mathrm{m}M$ Tris $p\mathrm{H}$ 7.9, $25\mathrm{m}M$ NaCl, $0.625\mathrm{m}M$ ${\mathrm{MgCl}}_2$, $0.1\%\mathrm{w}/\mathrm{v}$ BSA; $F=7\mathrm{pN}$). In the $B$-DNA stability region (black overlay), the curve displays a linear behavior, with a slope of $0.28\mathrm{nm}/\mathrm{\text{turn}}$. (b) Effect of the buffer conditions, exerted force, and DNA sequence content on the twist-stretch coupling. Since the slope value does not display any significant variation, we extract its average value (S.D.) in nm/turn from each set of data: solid squares: 0.52 (0.13), black line: 0.39 (0.05), open circles: 0.70 (0.24), solid gray circles: 0.43 (0.21).

Figure 3

(a) Twist-stretch coupling extracted from energy minimizations ($F=0$), for different dinucleotide sequences. Fitting each curve in its linear region to a line yields the value of the slope in nm/turn: 0.9 (average), 1.15 (GC), 0.97 (AT), 1.33 (AC), and 0.76 (GA). $\sigma =0$ refers to the relaxed twist per base pair for the average sequence (34.5°). (b) Rise (dashed) and inclination (solid) versus induced twist for the GA sequence. $\sigma =0$ refers to the relaxed twist per base pair for the GA sequence (36.75°).

Figure 4

Axial and lateral views of the structures obtained by energy minimizations (14 base pairs; average sequence). Left: relaxed $B$-DNA state, $\theta =34.5°$. Right: $B$-DNA under positive supercoiling ($\theta =40.5°$) displays a smaller diameter, an increased length, a negative base pair inclination, and a less negative shift value.