Nynke Dekker

Abstract:

We introduce magnetic torque tweezers, which enable direct single-molecule measurements of torque. Our measurements of the effective torsional stiffness C of dsDNA indicated a substantial force dependence, with C = approximately 40 nm at low forces up to C = approximately 100 nm at high forces. The initial torsional stiffness of RecA filaments was nearly twofold larger than that for dsDNA, yet at moderate torques further build-up of torsional strain was prevented.

Abstract:

DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3±1° and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.

Abstract:

Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal.

Abstract:

Single-molecule techniques are powerful tools that can be used to study the kinetics and mechanics of a variety of enzymes and their complexes. Force spectroscopy, for example, can be used to control the force applied to a single molecule and thereby facilitate the investigation of real-time nucleic acid-protein interactions. In magnetic tweezers, which offer straightforward control and compatibility with fluorescence measurements or parallel tracking modes, force-measurement typically relies on the analysis of positional fluctuations through video microscopy. Significant errors in force estimates, however, may arise from incorrect spectral analysis of the Brownian motion in the magnetic tweezers. Here we investigated physical and analytical optimization procedures that can be used to improve the range over which forces can be reliably measured. To systematically probe the limitations of magnetic tweezers spectral analysis, we have developed a magnetic tweezers simulator, whose outcome was validated with experimental data. Using this simulator, we evaluate methods to correctly perform force experiments and provide guidelines for correct force calibration under configurations that can be encountered in typical magnetic tweezers experiments.

Abstract:

Solid-state nanopores are considered a promising tool for the study of biological polymers such as DNA and RNA, due largely to their flexibility in size, potential in device integration and robustness. Here, we show that the precise shape of small nanopores (approximately 5 nm diameter in 20 nm SiN membranes) can be controlled by using transmission electron microscope (TEM) beams of different sizes. However, when some of these small nanopores are immersed in an aqueous solution, their resistance is observed to decrease over time. By comparing nanopores of different shapes using (scanning) TEM both before and after immersion in aqueous solution, we demonstrate that the stability of small nanopores is related to their three-dimensional geometry, which depends on the TEM beam size employed during pore fabrication. Optimal stability is obtained using a TEM beam size of approximately the same size as the intended nanopore diameter. In addition, we show that thermal oxidation can serve as a means to independently control nanopore size following TEM fabrication. These observations provide key guidelines for the fabrication of stable solid-state nanopores on the scale of nucleic acids and small proteins.