DNA Fuel for Free-Running Nanomachines

We describe kinetic control of DNA hybridization: loop complexes are used to inhibit the hybridization of complementary oligonucleotides; rationally designed DNA catalysts are shown to be effective in promoting their hybridization. This is the basis of a strategy for using DNA as a fuel to drive free-running artificial molecular machines.

Figure 1

Reactions in which the hybridization of two complementary strands is inhibited by a protective strand, already hybridized to one of them.

Figure 2

Oligonucleotide sequences.

Figure 3

Time-dependence of TET fluorescence during reactions of the $Q\overline{L}$ loop complex. The residual quenched intensity from free $Q$ has been subtracted, so the signal is proportional to the concentration of unreacted loops. Solid lines are fits assuming second-order kinetics. (a) $Q\overline{L}+L\to Q+L\overline{L}$; (b) $Q{\overline{L}}^{\prime }+L\to Q+L{\overline{L}}^{\prime }$ catalyzed by $0.125\mu \mathrm{M}$ $M_{0,6}$; (c) $Q{\overline{L}}^{\prime }+L\to Q+L{\overline{L}}^{\prime }$ catalyzed by $0.5\mu \mathrm{M}$ $M_{0,6}$.

Figure 4

Catalysis of the reaction of a DNA loop with a complementary strand of DNA. The catalyst hybridizes with the $Q{\overline{L}}^{\prime }$ loop complex, opening the loop and lowering the free energy barrier to reaction with complementary strand $L$.

Figure 5

Reaction rate constants as a function of the concentration of DNA catalysts $M_{x,y}$ ($[Q]=[L]=[{\overline{L}}^{\prime }]=0.5\mu \mathrm{M}$). Catalysts have the same 15-base section that competes with $Q$ to open the $Q{\overline{L}}^{\prime }$ loop but different toeholds for initial interaction with the loop complex: $M_{x,y}$ has an internal toehold complementary to $x$ bases in the belly of the loop and an external toehold complementary to $y$ bases in the overhang section of ${\overline{L}}^{\prime }$. ●, $M_{10,6}$; ▲, $M_{0,6}$; △, $M_{0,10}$; ■, $M_{6,0}$; □, $M_{10,0}$.