Research Activities

Control of DNA dynamics to advance nano-biosensing

The dynamics of DNA conformations induced by mechanical or biochemical constraints is a central issue for biologists and remains challenging for physicists. Indeed, from the biological point of view, it directly concerns the understanding of replication and transcription in vivo, which are out-of-equilibrium processes. On the theoretical side, DNA dynamcis is usually modeled using the classical Rouse dynamics (or Zimm one, if hydrodynamic interactions are taken into account), where DNA is seen as a simple polymer without internal structure. Although this approach is valid on length scales larger than 100 base-pairs (bps), it fails at the smaller scale of interest, where taking the double helical structure into account becomes essential. Moreover, the dynamics becomes much more complex as soon as counterions, hydrodynamics interactions, external constraints (external or induced by partner proteins) are considered.

Several biological and biophysical questions concern the intra-chain DNA dynamics which might be observable in TPM experiments. These issues focuse on the influence of local elastic properties (which varies with the local base-pairing state) on the looping dynamics. For instance, it has been proposed that the extremely slow closure of DNA denaturation bubbles (local DNA segments where bps are broken), observed in experiments, is essentially due to a metastable barrier associated to the bending energy and elastic energy stored in the bubble (which is more flexible than the double-helix segments). This metastable state is relaxed once the double-helix strands have diffused towards an aligned state. Such activation barriers might also play a central role in protein-DNA complexation and biosensing, which are kinetically controlled.

Snapshot of an equilibrated double helix (left panel) and free energy surfaces projected along the maximale width of the bubble and the minimal twist angle in the bubble (middle and right panels), associated with the Temperated-­‐activated closure of the bubble (Sicard et al., 2015).

We consider a minimal mesoscopic model where the double helix is made of two interacting bead-spring freely rotating strands, with a non- zero torsional modulus in the duplex state, and Brownian simulations to study the fundamental of the slow closure mechanism of long equilibrated denaturation bubble in DNA. Despite the relative simplicity of the model many processes are still slow to equilibrate due to the presence of large free energy barrier (rare event). We study accurately the free-energy landscape and the nucleation/closure rates associated to this temperature-activated mechanism with accelerated molecular dynamics simulations. We highlight that this closure mechanism consists in a collective twisting up to a threshold value of the torsional modulus. This free energy barrier is related to geometrical constraints occuring during the zipping regime, and that dynamically impose a small but non-nul torsional modulus to the single-stranded DNA. Contrary to small breathing bubbles, these more than 4 base-pair bubbles are of biological relevance, for example when a preexisting state of denaturation is required by specific DNA-binding proteins. (Sicard et al., 2015).

We have recently extended this previous analysis to tackle the interplay between twist and writhe in the denaturation bubble mechanisms considering DNA minicircles containing between 200 and 400 bps, also named microDNA. We revealed that different structural properties of microDNA could be linked to a broad range of closure/nucleation times, ranging from microseconds to several minutes, which could be used as dynamical bandwidth to advance the specificity of biosensing probes and to reduce further the experimental setup complexity (Sicard et al., 2018).

References:

last update: June 2018