Unraveling the Dual-Stretch-Mode Impact on Tension Gauge Tethers’ Mechanical Stability

Liu, Jingzhun; Yan, Jie

doi:10.1021/jacs.3c10923

Cited by 2 publications

(1 citation statement)

References 37 publications

(79 reference statements)

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“…With the rapid development of deoxyribonucleic acid (DNA) nanotechnology over the past decades, DNA has evolved far beyond its conventional roles as genetic materials. − It has been engineered to build diverse two-dimensional (2D) or three-dimensional (3D) structures with nanoscale precision. − Additionally, numerous DNA nanodevices and reaction networks have also been created capable of executing tasks, such as mechanical motion, biosensing, biocomputing, and smart drug delivery. − While most DNA nanodevices were actuated in response to chemical or physical stimuli, , they can also be programmed into ultrasmall instruments to sense and measure the input forces and energies at molecular scales. For example, a suite of DNA-based molecular sensors has been introduced to measure the pulling and compressive forces in living systems. − DNA-based calorimeters and thermometers have also been created for measuring heat changes in small open systems. − …”

Section: Introductionmentioning

confidence: 99%

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Wu,

Wang,

Yang

et al. 2024

J. Am. Chem. Soc.

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Folding thermodynamics, quantitatively described using parameters such as ΔG fold °, ΔH fold °, and ΔS fold °, is essential for characterizing the stability and functionality of noncanonical nucleic acid structures but remains difficult to measure at the molecular level. Leveraging the programmability of dynamic deoxyribonucleic acid (DNA) chemistry, we introduce a DNAbased molecular tool capable of performing a free energy shift assay (FESA) that directly characterizes the thermodynamics of noncanonical DNA structures in their native environments. FESA operates by the rational design of a reference DNA probe that is energetically equivalent to a target noncanonical nucleic acid structure in a series of toehold-exchange reactions, yet is structurally incapable of folding. As a result, a free energy shift (ΔΔG rxn °) is observed when plotting the reaction yield against the free energy of each toehold-exchange. We mathematically demonstrated that ΔG fold °, ΔH fold °, and ΔS fold °of the analyte can be calculated based on ΔΔG rxn °. After validating FESA using six DNA hairpins by comparing the measured ΔG fold °, ΔH fold °, and ΔS fold °values against predictions made by NUPACK software, we adapted FESA to characterize noncanonical nucleic acid structures, encompassing DNA triplexes, G-quadruplexes, and aptamers. This adaptation enabled the successful characterization of the folding thermodynamics for these complex structures under various experimental conditions. The successful development of FESA marks a paradigm shift and a technical advancement in characterizing the thermodynamics of noncanonical DNA structures through molecular tools. It also opens new avenues for probing fundamental chemical and biophysical questions through the lens of molecular engineering and dynamic DNA chemistry.

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Section: Introductionmentioning

confidence: 99%

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Wu,

Wang,

Yang

et al. 2024

J. Am. Chem. Soc.

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Measuring Integrin Force Loading Rates Using a Two-Step DNA Tension Sensor

Combs,

Foote,

Ogasawara

et al. 2024

J. Am. Chem. Soc.

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Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (piconewton) integrin-ECM forces have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical events. MTFM has revealed the force magnitude for integrin receptors in a variety of cell models including primary cells. However, force dynamics and specifically the force loading rate (LR) have important implications in receptor signaling and adhesion formation and remain poorly characterized. Here, we develop an LR probe composed of an engineered DNA structure that undergoes two mechanical transitions at distinct force thresholds: a low force threshold at 4.7 pN (hairpin unfolding) and a high force threshold at 47 pN (duplex shearing). These transitions yield distinct fluorescence signatures observed through single-molecule fluorescence microscopy in live cells. Automated analysis of tens of thousands of events from eight cells showed that the bond lifetime of integrins that engage their ligands and transmit a force >4.7 pN decays exponentially with a τ of 45.6 s. A subset of these events mature in magnitude to >47 pN with a median loading rate of 1.1 pN s–1 and primarily localize at the periphery of the cell–substrate junction. The LR probe design is modular and can be adapted to measure force ramp rates for a broad range of mechanoreceptors and cell models, thus aiding in the study of molecular mechanotransduction in living systems.

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Unraveling the Dual-Stretch-Mode Impact on Tension Gauge Tethers’ Mechanical Stability

Cited by 2 publications

References 37 publications

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Measuring Integrin Force Loading Rates Using a Two-Step DNA Tension Sensor

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