Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology

AbstractTo understand the mechanical forces involved in cell adhesion, molecular force sensors have been developed to study tension through adhesion proteins. Recently, a class of molecular force sensors called tension gauge tether (TGT) have been developed that rely on irreversible force-dependent dissociation of DNA duplex to study cell adhesion forces. While the TGT offer high signal-to-noise ratio and is ideal for studying fast / single molecular adhesion processes, quantitative interpretation of experimental results has been challenging. Here we used computational approach to investigate how TGT fluorescence readout can be quantitatively interpreted. In particular we studied force sensors made of a single TGT, multiplexed single TGTs, and two TGTs connected in series. Our results showed that fluorescence readout using a single TGT can result from drastically different combinations of force history and adhesion event density that span orders of magnitude. In addition, the apparent behaviour of the TGT is influenced by the tethered receptor-ligand, making it necessary to calibrate the TGT with every new receptor-ligand. To solve this problem, we proposed a system of two serially connected TGTs. Our result shows that not only is the ratiometric readout of serial TGT independent of the choice of receptor-ligand, it is able to reconstruct force history with sub-pN force resolution. This is also not possible by simply multiplexing different types of TGTs together. Lastly, we systematically investigated how sequence composition of the two serially connected TGTs can be tuned to achieve different dynamic range. This computational study demonstrated how serially connected irreversible molecular dissociation processes can accurately quantify molecular force, and laid the foundation for subsequent experimental studies.

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Obtaining Precise Molecular Information via DNA Nanotechnology

Membranes ◽

10.3390/membranes11090683 ◽

2021 ◽

Vol 11 (9) ◽

pp. 683

Author(s):

Qian Tang ◽

Da Han

Keyword(s):

Protein Interactions ◽

Measurement Techniques ◽

Protein Structures ◽

Dna Nanotechnology ◽

Molecular Structures ◽

Protein Protein Interactions ◽

Biochemical Processes ◽

Molecular Force ◽

Molecular Information ◽

Resolution Of Imaging

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein–protein interactions, and molecular force.

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Molecular force sensors to measure stress in cells

Journal of Physics D Applied Physics ◽

10.1088/1361-6463/aa6e1e ◽

2017 ◽

Vol 50 (23) ◽

pp. 233001 ◽

Cited By ~ 4

Author(s):

Meenakshi Prabhune ◽

Florian Rehfeldt ◽

Christoph F Schmidt

Keyword(s):

Force Sensors ◽

Molecular Force ◽

In Cells

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Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

Sensors ◽

10.3390/s20247019 ◽

2020 ◽

Vol 20 (24) ◽

pp. 7019

Author(s):

Runjhun Saran ◽

Yong Wang ◽

Isaac T. S. Li

Keyword(s):

Small Molecules ◽

Conformational Changes ◽

Protein Interactions ◽

Dna Nanotechnology ◽

Bending Rigidity ◽

Intrinsic Factors ◽

Cellular Processes ◽

Molecular Force ◽

Sensory Element ◽

Molecular Springs

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA’s bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA’s rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

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Probing mechanotransduction in living cells by optical tweezers and FRET-based molecular force microscopy

10.1101/2021.01.24.427943 ◽

2021 ◽

Author(s):

M. Sergides ◽

L. Perego ◽

T. Galgani ◽

C. Arbore ◽

F.S. Pavone ◽

...

Keyword(s):

Optical Tweezers ◽

Single Molecule ◽

Single Cells ◽

Force Sensors ◽

Force Microscopy ◽

Mechanical Signals ◽

Cell Plasma ◽

Molecular Force ◽

Wide Range ◽

Biochemical Signals

AbstractCells sense mechanical signals and forces to probe the external environment and adapt to tissue morphogenesis, external mechanical stresses, and a wide range of diverse mechanical cues. Here, we propose a combination of optical tools to manipulate single cells and measure the propagation of mechanical and biochemical signals inside them. Optical tweezers are used to trap microbeads that are used as handles to manipulate the cell plasma membrane; genetically encoded FRET-based force sensors inserted in F-actin and alpha-actinin are used to measure the propagation of mechanical signals to the cell cytoskeleton; while fluorescence microscopy with single molecule sensitivity can be used with a huge array of biochemical and genetic sensors. We describe the details of the setup implementation, the calibration of the basic components and preliminary characterization of actin and alpha-actinin FRET-based force sensors.

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Molecular Force Sensors

10.1021/acsinfocus.7e4008 ◽

2022 ◽

Author(s):

Rachel L. Bender ◽

Khalid Salaita

Keyword(s):

Force Sensors ◽

Molecular Force

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Probing mechanotransduction in living cells by optical tweezers and FRET-based molecular force microscopy

The European Physical Journal Plus ◽

10.1140/epjp/s13360-021-01273-7 ◽

2021 ◽

Vol 136 (3) ◽

Author(s):

M. Sergides ◽

L. Perego ◽

T. Galgani ◽

C. Arbore ◽

F. S. Pavone ◽

...

Keyword(s):

Optical Tweezers ◽

Single Molecule ◽

Single Cells ◽

Force Sensors ◽

Force Microscopy ◽

Mechanical Signals ◽

Cell Plasma ◽

Molecular Force ◽

Wide Range ◽

Biochemical Signals

AbstractCells sense mechanical signals and forces to probe the external environment and adapt to tissue morphogenesis, external mechanical stresses and a wide range of diverse mechanical cues. Here, we propose a combination of optical tools to manipulate single cells and measure the propagation of mechanical and biochemical signals inside them. Optical tweezers are used to trap microbeads that are used as handles to manipulate the cell plasma membrane; genetically encoded FRET-based force sensors inserted in F-actin and alpha-actinin are used to measure the propagation of mechanical signals to the cell cytoskeleton, while fluorescence microscopy with single-molecule sensitivity can be used with a huge array of biochemical and genetic sensors. We describe the details of the setup implementation, the calibration of the basic components and preliminary characterization of actin and alpha-actinin FRET-based force sensors.

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