Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer simulations, that these discrepancies can be resolved if a coupling between twist and bend is introduced. We obtain an estimate of 40 ± 10 nm for the twist-bend coupling constant. Our simulations are in good agreement with high-resolution, magnetic-tweezers torque data. Although the existence of twist-bend coupling was predicted long ago (Marko and Siggia, Macromolecules 27, 981 (1994)), its effects on the mechanical properties of DNA have been so far largely unexplored. We expect that this coupling plays an important role in several aspects of DNA statics and dynamics.Introduction The mechanical properties of doublestranded DNA (dsDNA) are critical for both its structure and function within the cell. The stretching of ds-DNA under applied forces has been measured by single molecule techniques [1, 2] and is accurately reproduced by a simple polymer model, containing the bending stiffness as the only parameter [1]. Elastic polymer models were also successfully employed to study the torsional properties of dsDNA [4] and compared to single-molecule experiments, such as magnetic tweezers (MT) [2] (Fig. 1, right). The currently accepted elastic model for dsDNA is the twistable worm-like chain (TWLC) [6]. Although the TWLC correctly describes the overall response of ds-DNA to applied forces and torques, it fails to quantitatively explain the force-dependence of the effective torsional stiffness [3, 4]. Here, we show that an alternative elastic model proposed by Marko and Siggia (MS) [5], quantitatively describes the force-dependence of the effective torsional stiffness, by taking into account a direct coupling between twist and bend deformations. Furthermore, we demonstrate that the MS model explains an unresolved discrepancy in the measured intrinsic torsional stiffness, obtained from different techniques. Finally, we show that the MS model provides a better description of the pre-buckling torque response of dsDNA, determined in high-resolution magnetic torque tweezers (MTT) experiments, than the TWLC.TWLC and MS models Both the TWLC and MS models describe dsDNA as a continuous, twistable curve by associating an orthonormal frame { e 1 , e 2 , e 3 } with each base pair (Fig. 1) [5]. We choose e 3 tangent to the helical axis and e 1 and e 2 oriented as in Fig. 1. In the continuum limit these vectors are functions of the arc-length variable s. For the stretching forces considered here (f < 10 pN) dsDNA is inextensible, hence 0 ≤ s ≤ L, with L the contour length. A local dsDNA conformation is given by a vector Ω(s) which describes the infinitesimal rotation connecting { e 1 (s), e 2 (s), e 3 (s)} to { e 1 (s + ds), e 2 (s + ds), e 3 (s + ds)}. The direction of Ω(s) identifies the rotation axis, and |Ω(s)|ds the infinitesimal rotation angle. In particular, if Ω(s) is parallel to e 3...

DNA is the carrier of all cellular genetic information and increasingly used in nanotechnology. Quantitative understanding and optimization of its functions requires precise experimental characterization and accurate modeling of DNA properties. A defining feature of DNA is its helicity. DNA unwinds with increasing temperature, even for temperatures well below the melting temperature. However, accurate quantitation of DNA unwinding under external forces and a microscopic understanding of the corresponding structural changes are currently lacking. Here we combine single-molecule magnetic tweezers measurements with atomistic molecular dynamics and coarse-grained simulations to obtain a comprehensive view of the temperature dependence of DNA twist. Experimentally, we find that DNA twist changes by ΔTw(T) = (−11.0 ± 1.2)°/(°C·kbp), independent of applied force, in the range of forces where torque-induced melting is negligible. Our atomistic simulations predict ΔTw(T) = (−11.1 ± 0.3)°/(°C·kbp), in quantitative agreement with experiments, and suggest that the untwisting of DNA with temperature is predominantly due to changes in DNA structure for defined backbone substates, while the effects of changes in substate populations are minor. Coarse-grained simulations using the oxDNA framework yield a value of ΔTw(T) = (−6.4 ± 0.2)°/(°C·kbp) in semi-quantitative agreement with experiments.

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All life on earth depends on the generation and exploitation of ionic and pH gradients across membranes. One theory for the origin of life proposes that geological pH gradients were the prebiotic ancestors of these cellular disequilibria. With an alkaline interior and acidic exterior, alkaline vents match the topology of modern cells, but it remains unknown whether the steep pH gradients persist at the microscopic scale. Herein, we demonstrate the existence of 6 pH-unit gradients across micrometer scales in a microfluidic vent replicate. Precipitation of metal sulfides at the interface strengthens the gradients, but even in the absence of precipitates laminar flow sustains the disequilibria. The gradients drive directed transport at the fluid interface, leading to colloid accumulation or depletion. Our results confirm that alkaline vents can provide an exploitable pH gradient, supporting their potential role at the emergence of chemiosmosis and the origin of life.