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Ashwood B, Tokmakoff A. Kinetics and dynamics of oligonucleotide hybridization. Nat Rev Chem 2025; 9:305-327. [PMID: 40217001 DOI: 10.1038/s41570-025-00704-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2025] [Indexed: 05/15/2025]
Abstract
The hybridization of short nucleic acid strands is a remarkable spontaneous process that is foundational to biotechnology and nanotechnology and plays a crucial role in gene expression, editing and DNA repair. Decades of research into the mechanism of hybridization have resulted in a deep understanding of its thermodynamics, but many questions remain regarding its kinetics and dynamics. Recent advances in experiments and molecular dynamics simulations of nucleic acids are enabling more direct insight into the structural dynamics of hybridization, which can test long-standing assumptions regarding its mechanism. In this Review, we summarize the current state of knowledge of hybridization kinetics, discuss the barriers to a molecular description of hybridization dynamics, and highlight the new approaches that have begun uncovering the dynamics of hybridization and the duplex ensemble. The kinetics and dynamics of hybridization are highly sensitive to the composition of nucleic acids, and we emphasize recent discoveries and open questions on the role of nucleobase sequence and chemical modifications.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - Andrei Tokmakoff
- Department of Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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2
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Foote A, Ishii K, Cullinane B, Tahara T, Goldsmith RH. Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level. ACS PHYSICAL CHEMISTRY AU 2024; 4:408-419. [PMID: 39069982 PMCID: PMC11274281 DOI: 10.1021/acsphyschemau.3c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/30/2024]
Abstract
Quantifying the rapid conformational dynamics of biological systems is fundamental to understanding the mechanism. However, biomolecules are complex, often containing static and dynamic heterogeneity, thus motivating the use of single-molecule methods, particularly those that can operate in solution. In this study, we measure microsecond conformational dynamics of solution-phase DNA hairpins at the single-molecule level using an anti-Brownian electrokinetic (ABEL) trap. Different conformational states were distinguished by their fluorescence lifetimes, and kinetic parameters describing transitions between these states were determined using two-dimensional fluorescence lifetime correlation (2DFLCS) analysis. Rather than combining fluorescence signals from the entire data set ensemble, long observation times of individual molecules allowed ABEL-2DFLCS to be performed on each molecule independently, yielding the underlying distribution of the system's kinetic parameters. ABEL-2DFLCS on the DNA hairpins resolved an underlying heterogeneity of fluorescence lifetimes and provided signatures of two-state exponential dynamics with rapid (
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Affiliation(s)
- Alexander
K. Foote
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kunihiko Ishii
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Brendan Cullinane
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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3
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Li Y, Yu P, Ma W, Mao L. High-Performance Electrochemical Actuator under an Ultralow Driving Voltage with a Mixed Electronic-Ionic Conductive Metal-Organic Framework. ACS APPLIED MATERIALS & INTERFACES 2023; 15:56158-56166. [PMID: 37976422 DOI: 10.1021/acsami.3c12270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Although versatile deformation, high flexibility, and environmental friendliness of electrochemical actuators (EAs) have made them promising in bioinspired soft robots and biomedical devices, the relatively high driving voltages unfortunately impose great restrictions on their applications in low-energy and human-friendly electronics. Here, we find that the uses of a mixed electronic-ionic conductive metal-organic framework (c-MOF), i.e., Ni3(hexaiminotriphenylene)2 (Ni3(HITP)2), largely lower the driving voltage of EAs. The as-fabricated EA can work under a driving voltage as low as 0.1 V, representing the lowest value among those for the c-MOF-based EAs reported so far. The Ni3(HITP)2-based EA shows an excellent actuation performance such as a high bending strain difference of 0.48% (±0.5 V, 0.1 Hz) and long-term durability of >99% after 15,000 cycles due to the improved conductivity up to 1000 S·cm-1 and double-layer capacitance as high as 176.3 F·g-1 stemming from the mixed electronic-ionic conduction of Ni3(HITP)2.
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Affiliation(s)
- Yali Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- Institute of Analysis and Testing (Beijing Center for Physical & Chemical Analysis), Beijing Academy of Science and Technology, Beijing100089, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China
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4
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Rajasooriya T, Ogasawara H, Dong Y, Mancuso JN, Salaita K. Force-Triggered Self-Destructive Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305544. [PMID: 37724392 PMCID: PMC10764057 DOI: 10.1002/adma.202305544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Self-destructive polymers (SDPs) are defined as a class of smart polymers that autonomously degrade upon experiencing an external trigger, such as a chemical cue or optical excitation. Because SDPs release the materials trapped inside the network upon degradation, they have potential applications in drug delivery and analytical sensing. However, no known SDPs that respond to external mechanical forces have been reported, as it is fundamentally challenging to create mechano-sensitivity in general and especially so for force levels below those required for classical force-induced bond scission. To address this challenge, the development of force-triggered SDPs composed of DNA crosslinked hydrogels doped with nucleases is described here. Externally applied piconewton forces selectively expose enzymatic cleavage sites within the DNA crosslinks, resulting in rapid polymer self-degradation. The synthesis and the chemical and mechanical characterization of DNA crosslinked hydrogels, as well as the kinetics of force-triggered hydrolysis, are described. As a proof-of-concept, force-triggered and time-dependent rheological changes in the polymer as well as encapsulated nanoparticle release are demonstrated. Finally, that the kinetics of self-destruction are shown to be tuned as a function of nuclease concentration, incubation time, and thermodynamic stability of DNA crosslinkers.
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Affiliation(s)
| | | | - Yixiao Dong
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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5
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Duan Y, Szlam F, Hu Y, Chen W, Li R, Ke Y, Sniecinski R, Salaita K. Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand. Nat Biomed Eng 2023; 7:1404-1418. [PMID: 37957275 PMCID: PMC11289779 DOI: 10.1038/s41551-023-01114-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Molecular forces generated by cell receptors are infrequent and transient, and hence difficult to detect. Here we report an assay that leverages the CRISPR-associated protein 12a (Cas12a) to amplify the detection of cellular traction forces generated by as few as 50 adherent cells. The assay involves the immobilization of a DNA duplex modified with a ligand specific for a cell receptor. Traction forces of tens of piconewtons trigger the dehybridization of the duplex, exposing a cryptic Cas12-activating strand that sets off the indiscriminate Cas12-mediated cleavage of a fluorogenic reporter strand. We used the assay to perform hundreds of force measurements using human platelets from a single blood draw to extract individualized dose-response curves and half-maximal inhibitory concentrations for a panel of antiplatelet drugs. For seven patients who had undergone cardiopulmonary bypass, platelet dysfunction strongly correlated with the need for platelet transfusion to limit bleeding. The Cas12a-mediated detection of cellular traction forces may be used to assess cell state, and to screen for genes, cell-adhesion ligands, drugs or metabolites that modulate cell mechanics.
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Affiliation(s)
- Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Fania Szlam
- Department of Anesthesiology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Wenchun Chen
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Departments of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Departments of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Roman Sniecinski
- Department of Anesthesiology, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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6
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Rashid SA, Dong Y, Ogasawara H, Vierengel M, Essien ME, Salaita K. All-Covalent Nuclease-Resistant and Hydrogel-Tethered DNA Hairpin Probes Map pN Cell Traction Forces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:33362-33372. [PMID: 37409737 PMCID: PMC10360067 DOI: 10.1021/acsami.3c04826] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Cells sense and respond to the physical properties of their environment through receptor-mediated signaling, a process known as mechanotransduction, which can modulate critical cellular functions such as proliferation, differentiation, and survival. At the molecular level, cell adhesion receptors, such as integrins, transmit piconewton (pN)-scale forces to the extracellular matrix, and the magnitude of the force plays a critical role in cell signaling. The most sensitive approach to measuring integrin forces involves DNA hairpin-based sensors, which are used to quantify and map forces in living cells. Despite the broad use of DNA hairpin sensors to study a variety of mechanotransduction processes, these sensors are typically anchored to rigid glass slides, which are orders of magnitude stiffer than the extracellular matrix and hence modulate native biological responses. Here, we have developed nuclease-resistant DNA hairpin probes that are all covalently tethered to PEG hydrogels to image cell traction forces on physiologically relevant substrate stiffness. Using HeLa cells as a model cell line, we show that the molecular forces transmitted by integrins are highly sensitive to the bulk modulus of the substrate, and cells cultured on the 6 and 13 kPa gels produced a greater number of hairpin unfolding events compared to the 2 kPa substrates. Tension signals are spatially colocalized with pY118-paxillin, confirming focal adhesion-mediated probe opening. Additionally, we found that integrin forces are greater than 5.8 pN but less than 19 pN on 13 kPa gels. This work provides a general strategy to integrate molecular tension probes into hydrogels, which can better mimic in vivo mechanotransduction.
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Affiliation(s)
- Sk Aysha Rashid
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yixiao Dong
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Maia Vierengel
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Mark Edoho Essien
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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7
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Jeong S, Shin W, Park M, Lee JU, Lim Y, Noh K, Lee JH, Jun YW, Kwak M, Cheon J. Hydrogel Magnetomechanical Actuator Nanoparticles for Wireless Remote Control of Mechanosignaling In Vivo. NANO LETTERS 2023; 23:5227-5235. [PMID: 37192537 PMCID: PMC10614426 DOI: 10.1021/acs.nanolett.3c01207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
As a new enabling nanotechnology tool for wireless, target-specific, and long-distance stimulation of mechanoreceptors in vivo, here we present a hydrogel magnetomechanical actuator (h-MMA) nanoparticle. To allow both deep-tissue penetration of input signals and efficient force generation, h-MMA integrates a two-step transduction mechanism that converts magnetic anisotropic energy to thermal energy within its magnetic core (i.e., Zn0.4Fe2.6O4 nanoparticle cluster) and then to mechanical energy to induce the surrounding polymer (i.e., pNiPMAm) shell contraction, finally delivering forces to activate targeted mechanoreceptors. We show that h-MMAs enable on-demand modulation of Notch signaling in both fluorescence reporter cell lines and a xenograft mouse model, demonstrating its utility as a powerful in vivo perturbation approach for mechanobiology interrogation in a minimally invasive and untethered manner.
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Affiliation(s)
- Sumin Jeong
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Wookjin Shin
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Mansoo Park
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-uk Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Yongjun Lim
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Kunwoo Noh
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Jae-Hyun Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Young-wook Jun
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
- Department of Otolaryngology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Helen Diller Family Cancer Comprehensive Center (HDFCCC), University of California, San Francisco, CA, USA
| | - Minsuk Kwak
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), A dvanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
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8
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The Free-Energy Landscape of a Mechanically Bistable DNA Origami. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally.
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