Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy

Lin, Szu-Ning; Qin, Liang; Wuite, Gijs J. L.; Dame, Remus T.

doi:10.1007/978-1-4939-8675-0_16

Cited by 3 publications

(2 citation statements)

References 13 publications

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“…The bottom glass reflects the acoustic wave, producing a standing wave over the flow cell. The bead exposed to this standing wave experiences a force along the vertical direction that applies tension to the interaction between the protein–DNA complex and the interacting protein (Lin et al ., 2018). See Fig.…”

Section: State Of the Artmentioning

confidence: 99%

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Sanchez

Robeson

Carrasco

et al. 2022

Quart. Rev. Biophys.

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Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

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Section: State Of the Artmentioning

confidence: 99%

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Sanchez

Robeson

Carrasco

et al. 2022

Quart. Rev. Biophys.

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“…Measurements of chromatin persistence length vary from approximately 200 nm, for highly compacted heterochromatic regions, to approximately 5 nm for ssDNA, and the average L p of a naked double-stranded B-form DNA molecule is approximately 50 nm [48][49][50]. The presence of histones, scaffolding proteins, and chromatin modifiers on DNA allows for modulation of local persistence length in the range from 5 nm to 220 nm [50][51][52][53][54]. The resistance to bending of chromatin by its stiff form can result in far-ranging effects on chromatin loops, their sizes, and stability [55].…”

Section: Introductionmentioning

confidence: 99%

Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops

Kolbin,

Walker,

Hult

et al. 2023

Genes

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Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead–spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.

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How to Quantify DNA Compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence Microscopy

Martucci

Debar

Wildenberg

et al. 2023

Methods in Molecular Biology

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Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy

Cited by 3 publications

References 13 publications

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Determination of protein–protein interactions at the single-molecule level using optical tweezers

Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops

How to Quantify DNA Compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence Microscopy

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