Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase

You, Huijuan; Zhou, Yu; Yan, Jie

doi:10.1007/978-1-0716-0935-4_12

Cited by 6 publications

(3 citation statements)

References 45 publications

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“…Nowadays, there are several methods to realize the manipulation of micro-nano particles, such as atomic force microscope (AFM) [5][6][7], magnetic tweezers [8,9] and optical tweezers [10][11][12]. However, the methods either are unable to implement large-area manipulation or easily damage samples.…”

Section: Introductionmentioning

confidence: 99%

Implementation of flexible virtual microchannels based on optically induced dielectrophoresis

Yang

Song

et al. 2022

Nanotechnology

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Micro-nano particle manipulation methods in liquid environments have been widely used in the fields such as medicine, biology and material science. Nevertheless, the methods usually rely on pre-prepared physical microfluidic channels. In this work, virtual electrodes based on the optically induced dielectrophoresis (ODEP) method were used as virtual microchannels instead of traditional physical microfluidic channels. Virtual microchannels with different shapes were implemented by the designs of projected light patterns, which made the virtual microchannels have great flexibility and controllability. The relationship between the ODEP force and the alternating current (AC) voltage or the AC frequency exerted on the cells was assessed. The experimental results indicated that the ODEP force was increased with the increase of the AC voltage, and it was reduced with the increase of the AC frequency. Moreover, different virtual microchannels were designed to carry out the transportation, aggregation and sorting of yeast cells and rat basophilic leukemia cells (RBL-2H3 cells). This work shows that the virtual microchannels can be flexibly realized by ODEP in liquid environments.

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Section: Introductionmentioning

confidence: 99%

Implementation of flexible virtual microchannels based on optically induced dielectrophoresis

Yang

Song

et al. 2022

Nanotechnology

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“…Single-molecule approaches including force-based and fluorescence-based techniques enable the detection of folding/unfolding dynamics in real time and the discovery of diverse G4 topologies in a heterogeneous sample [ 40 , 41 , 42 , 43 , 44 , 45 ]. Force-based techniques (also called single-molecule force spectroscopy), such as optical tweezers (OT), magnetic tweezers (MT), and atomic force microscopy (AFM), allow direct manipulation of single molecules of DNA, RNA, and proteins.…”

Section: Introductionmentioning

confidence: 99%

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

2021

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G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force–spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.

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“…For analyzing the dsDNA lengthened by intercalated DNA adducts, we performed wash-off experiments to analyze the extension change of dsDNA caused by adduct formation using single-molecule magnetic tweezers (Figure A). , The feasibility of a single-molecule stretching assay for various intercalative DNA adducts has been analyzed, including four anthracyclines, two PSOs, and an AFB 1 –DNA adduct. Previous single-molecule studies suggested that the lengthening by 0.2–0.5 nm per intercalation is a common feature for most intercalators. , X-ray or NMR structures of intercalative DNA adducts, such as daunomycin (DAU)–DNA adducts, PSO–DNA adducts, and AFB 1 –DNA adducts, revealed that for each intercalated moiety, the DNA lengthens by ∼0.34 nm (Figure S1).…”

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confidence: 99%

Force-Dependent Intercalative Bulky DNA Adduct Formation Detected by Single-Molecule Stretching

Liu

Pei

et al. 2022

Anal. Chem.

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Quantitatively analyzing the binding topology and reactivity is essential for understanding the cytotoxic or tumorigenic activities of bulky DNA adducts formed by chemotherapeutic drugs or carcinogens. Biochemical methods require purification of DNA and discontinuous steps to digest or label the adducts and thus have difficulties in identifying the binding topology and are not suitable for detecting unstable adducts. Herein, we used a single-molecule stretching assay to characterize the number of intercalative adducts, the formation kinetics, and the mechanical properties of intercalative DNA adducts based on measuring adduct-induced DNA elongation. We analyzed various reactive conditions, including formaldehyde-mediated anthracycline–DNA adducts, UV light-catalyzed psoralen–DNA adducts, and liver S9 fraction-catalyzed aflatoxin B1–DNA adducts. We showed that adduct formation abilities are correlated with the noncovalent intercalation binding ability. External forces on double-stranded DNA increased the intercalation of ligands and can result in a 1.8- to 5.3-fold increase in DNA adduct formation.

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Using Magnetic Tweezers to Unravel the Mechanism of the G-quadruplex Binding and Unwinding Activities of DHX36 Helicase

Cited by 6 publications

References 45 publications

Implementation of flexible virtual microchannels based on optically induced dielectrophoresis

Implementation of flexible virtual microchannels based on optically induced dielectrophoresis

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

Force-Dependent Intercalative Bulky DNA Adduct Formation Detected by Single-Molecule Stretching

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