Generating aptamers that bind to specific metal ions is challenging because existing aptamer discovery methods typically require chemical labels or modifications that can alter the structure and properties of the ions. In this work, we report an aptamer discovery method that enables us to generate high-quality structure-switching aptamers (SSAs) that undergo a conformational change upon binding a metal ion target, without the requirement of labels or chemical modifications. Our method is more efficient than conventional selection methods because it enables direct measurement of target binding via fluorescence-activated cell sorting (FACS), isolating only the desired aptamers with the highest affinity. Using this strategy, we obtained a highly specific DNA SSA with ~30-fold higher affinity than the best aptamer for Hg2+ in the literature. We also discovered DNA aptamers that bind to Cu2+ with excellent affinity and specificity. Both aptamers were obtained within four rounds of screening, demonstrating the efficiency of our aptamer discovery method. Given the growing availability of FACS, we believe our method offers a general strategy for discovering high-quality aptamers for other ions and small-molecule targets in an efficient and reproducible manner.

We derive an analytic expression for the bending elastic energy of short DNA molecules, valid in the entire range from low to high energies. The elastic energy depends on three parameters: the length of the molecule (2L), the bending modulus B, and a critical torque τc at which the molecule develops a kink. In the kinked state, the elastic energy is linear in the kink angle, i.e. the torque at the kink is constant (= τc). τc depends (weakly) on the sequence around the nick, but is about 27 pN × nm. We measure it for a specific sequence, through experiments where the elastic energy of constrained DNA molecules is directly measured.

We obtain measurements of the elastic energy of short (18-30 bp) molecules of ds DNA constrained into a sharply bent conformation, using a thermodynamic method with the DNA in solution. We consider the case where there is one nick in the ds DNA, and find that the system develops a kink at a critical torque τc ≈ 27 pN × nm. In this regime the elastic energy is linear in the end-to-end distance (EED). For smaller torques the DNA is smoothly bent and described by the worm-like-chain energy, which is also approximately linear in the EED, but with a different slope. Thus we access both the high and low elastic energy regimes, and the transition between the two.

We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque c at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find c ¼ 31 pN Â nm. This critical torque corresponds to a characteristic energy scale ð =2Þ c ¼ 12 kT room relevant for molecular biology processes associated with DNA bending.

Multifunctionality of ILFR-fBNNS, i.e. curing, thermal conduction and flame retardation.