Rigid DNA Beams for High‐Resolution Single‐Molecule Mechanics

Pfitzner, Emanuel; Wachauf, Christian; Kilchherr, Fabian; Pelz, Benjamin; Shih, William M.; Rief, Matthias; Dietz, Hendrik

doi:10.1002/anie.201302727

Cited by 110 publications

(126 citation statements)

References 39 publications

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“…The 20-30% error predicted by the theory matches well with the error found empirically in previous work by Chang et al (14). Large bead-size or linker-stiffness increases may lead to larger artifacts, however, as noted previously (15)(16)(17)(18); this is unfortunate because stiff linkers in particular allow for easier reconstruction of free-energy profiles (10,11,24,25). Optimizing assay design for one purpose (e.g., landscape reconstruction) may thus degrade its suitability for others (e.g., measuring kinetic properties).…”

supporting

confidence: 85%

Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy

Neupane

Woodside

2016

Biophysical Journal

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Force spectroscopy is commonly used to measure the kinetics of processes occurring in single biological molecules. These measurements involve attaching the molecule of interest to micron-sized or larger force probes via compliant linkers. Recent theoretical work has described how the properties of the probes and linkers can alter the observed kinetics from the intrinsic behavior of the molecule in isolation. We applied this theory to estimate the errors in measurements of folding made using optical tweezers. Errors in the folding rates arising from instrument artifacts were only ∼20% for constant-force measurements of DNA hairpins with typical choices of linker length and probe size. Measurements of transition paths using a constant trap position at high trap stiffness were also found to be in the low-artifact limit. These results indicate that typical optical trap measurements of kinetics reflect the dynamics of the molecule fairly well, and suggest practical limitations on experimental design to ensure reliable kinetic measurements.

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supporting

confidence: 85%

Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy

Neupane

Woodside

2016

Biophysical Journal

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“…One way to increase handle stiffness is to use shorter handles (42). An alternative is to replace the handle material with something stiffer, as done by Pfitzner et al (96), who showed that using rigid DNA origami beams in place of the double-stranded DNA handles typically used in optical trapping experiments sharpened the distributions and improved the reconstruction.…”

Section: Landscape Reconstructions From Equilibrium Measurements Of Ementioning

confidence: 99%

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

Woodside

Block

2014

Annu. Rev. Biophys.

205

184

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Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate.

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“…For example, Kauert et al 46 measured the torsional persistence length of 4-helix and 6-helix bundles to be 390 nm and 530 nm, respectively; Plesa and co-workers 58 demonstrated that the bending stiffness of DNA origami nanoplates was critical to their functional ion conductance; and Pfitzner et al 59 exploited the stiffness of DNA origami beams to improve the resolution of force spec-troscopy experiments. For example, Kauert et al 46 measured the torsional persistence length of 4-helix and 6-helix bundles to be 390 nm and 530 nm, respectively; Plesa and co-workers 58 demonstrated that the bending stiffness of DNA origami nanoplates was critical to their functional ion conductance; and Pfitzner et al 59 exploited the stiffness of DNA origami beams to improve the resolution of force spec-troscopy experiments.…”

Section: Designing and Characterizing Mechanical Stiffness Of Dna Orimentioning

confidence: 99%

Mechanical design of DNA nanostructures

et al. 2015

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Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.

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Rigid DNA Beams for High‐Resolution Single‐Molecule Mechanics

Cited by 110 publications

References 39 publications

Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy

Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

Mechanical design of DNA nanostructures

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