Engineering tunable catch bonds with DNA

Abstract

Unlike most adhesive bonds, biological catch bonds strengthen with increased tension. This characteristic is essential to specific receptor-ligand interactions, underpinning biological adhesion dynamics, cell communication, and mechanosensing. While artificial catch bonds have been conceived, the tunability of their catch behaviour is limited. Here, we present the fish-hook, a rationally designed DNA catch bond that can be finely adjusted to a wide range of catch behaviours. We develop models to design these DNA structures and experimentally validate different catch behaviours by single-molecule force spectroscopy. The fish-hook architecture supports a vast sequence-dependent behaviour space, making it a valuable tool for reprogramming biological interactions and engineering force-strengthening materials.

Fig. 1. Schematics of DNA catch bond design and expected behaviour.

a Schematic of a two-state mechanism that allows the DNA construct to dissociate via two pathways directed by force above or below a crossover force (F_c). In the weak pathway, the closed jaw locks the hook in the unzipping geometry. In the strong pathway, the open jaw switches the hook to the shearing geometry. b The lifetimes (τ_F) of the hook unzipping and jaw opening are designed to intersect, enabling force-dependent pathway selection. c Below F_c, the construct follows the weak pathway, as the jaw remains closed, and thus the hook unzips. Above F_c, the jaw opens before the hook, steering the construct into the strong pathway, thereby increasing the proportion of constructs with an open jaw (P_jaw-open) as force escalates. d As the force increases, the transition from the hook unzipping to shearing creates a slip-catch-slip behaviour. e Slip bonds are characterized by a unimodal rupture force probability density function (PDF) at a specific loading rate. f In contrast, catch bonds exhibit a bimodal rupture force PDF (catch-slip-catch shown here). Here, the high rupture force population (red) corresponds to high-force slip behaviour and the low rupture force population (green) arises from the catch behaviour. For comparison, a slip-only PDF is represented by a grey dashed line. The catch behaviour shifts subpopulations from high-force to low-force ruptures (grey arrows). g Additionally, the fraction of high rupture force in the bimodal distribution increases with force ramp speed or loading rate.

Fig. 2. Experimental setup and catch bond sequence design.

a Schematic representation of the dual-trap optical tweezers experiment. The hook is attached to bead A, and the fish is attached to bead B via DNA handles of 2633 and 272 bp, respectively. Both handles are attached to the beads by a biotin-streptavidin linkage on the 5′ end of each handle (top inset). Bead B undergoes an oscillatory motion with a dwell period before retraction (bottom inset) to increase the fishing success rate (binding between the hook and the fish). b The construct sequence. A 9-mer polyethylene glycol (PEG) linker attaches the hook to its DNA handle to minimize nonspecific base interactions with the fish and increase flexibility. c Schematic showing the weak and strong pathways. d The expected τ_F of the selected construct sequence based on our analytical model, showing the overall expected slip-catch-slip behaviour resulting from transitioning from hook unzipping to hook shearing around the intersection of the jaw opening and the hook unzipping τ_F at F_c = 13.6 pN. The anticipated force-extension curves differ for the weak (e) and strong (f) pathways, as predicted by the extensible worm-like chain model (XWLC). In the weak pathway, we expect a singular low-force rupture event indicative of hook unzipping (e). In the strong pathway, we expect a jaw-opening transition preceding a high-force rupture event corresponding to hook shearing (f).

Fig. 3. Experimental and simulation results from the optical tweezers.

a Experimental force-extension curves in chronological order from a medium ramp experiment, showing non-history dependent switching between strong (red) and weak (blue) rupture events for the hook9/9-jaw 8/18 construct shown in Fig. 2b. Traces end when the hook unbinds. Fishing attempts that do not yield single tethers are not shown. b The same force-extension curves in (A), but with theoretical worm-like chain curves overlaid for the two possible states (dashed lines). The distribution of ΔL_c (inset) from all medium pulls with a jaw opening event, as compared with the theoretical ΔL_c of 20.20 nm. c Rupture force distributions at three pulling rates compared to the Monte-Carlo simulation. The slow pulling rate has a higher proportion of hook unzipping, while the fastest pulling rate has a higher proportion of hook shearing. d Rupture force plotted against force loading rate for the three ramps, calculated at the moment of rupture. Due to the long DNA handles, each pulling speed (nm s⁻¹) has a range of loading rates (pN s⁻¹) obtained from the worm-like chain model. e The proportion of open-jawed constructs as a function of pulling rate compared to the simulation. Two additional catch bonds were tested in addition to the one shown in the rest of Figs. 2 and 3 (h_9/9j_8/18), one with an 11/11 CG content hook (h_11/11j_8/18; yellow; n = 101, 178, 130 for slow, medium, and fast ramp speed) and one with a 10/18 CG content jaw (h_9/9j_10/18; green; n = 253, 490, 187 for slow, medium, and fast ramp speed). Error bars are the 95% confidence interval of the proportion; n = 1000 for each simulated point.

Fig. 4. Fish-hook catch bond design space.

a Catch regions of fish-hook catch bonds within the biologically relevant window of 0.01 <τ < 100 s and 0 <F_start < 10 pN, simplified to a straight line between the lowest and highest τ_F. The tallest and widest catch behaviours are marked with * and #, respectively. b The characteristic Δlog(τ_F) and ΔF parameters of the catch regions. c, d The tallest and widest catch regions from (a, b). e Jaw lengths and CG contents that create catch behaviour are shown, coloured by the number of hook sequences that form catch bonds with them. The most versatile jaw, with a 0 bp CG content and a 27 bp length of (jaw_0/27), is marked by a black box. f The hook sequence space that forms catch behaviour with the most versatile jaw in (e). g, h The same as (e, f), but for the hook design space and the jaws, which catch with the most versatile hook, which has an 8 bp CG content and an 8 bp length (hook_8/8). Colours in (a–d, f, h) are coded by the 2D colour bar of the (b) inset.