Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene

Abstract

By means of Silicon Nano Tweezers (SNTs) the effects on the mechanical properties of λ-phage DNA during interaction with calf thymus nucleosome to form an artificial chromatin analog were measured. At a concentration of 100 nM, a nucleosome solution induced a strong stiffening effect on DNA (1.1 N m −1 ). This can be compared to the effects of the histone proteins, H1, H2A, H3 where no changes in the mechanical properties of DNA were observed and the complex of the H3/H4 proteins where a smaller increase in the stiffness is observed (0.2 N m −1 ). Para -sulphonato-calix[4]arene, SC4, known for epigenetic activity by interacting specifically with the lysine groups of histone proteins, was studied for its effect on an artificial chromatin. Using a microfluidic SNT device, SC4 was titrated against the artificial chromatin, at a concentration of 1 mM in SC4 a considerable increase in stiffness, 15 N m −1 , was observed. Simultaneously optical microscopy showed a physical change in the DNA structure between the tips of the SNT device. Electronic and Atomic Force microscopy confirmed this structural re-arrangement. Negative control experiments confirmed that these mechanical and physical effects were induced neither by the acidity of SC4 nor through nonspecific interactions of SC4 on DNA.

Magnetic polymer models for epigenetics-driven chromosome folding

“…We hope that technical advances will soon make it possible to perform experiments with epigenetic marks on reconstituted chromatin in vitro [53]; this should give more hints on how to extend polymer magnetic models to improve our understanding of both epigenetic spreading processes [21,53] and the generic interplay between different read-write protein complexes.…”

Fabricating Silicon Resonators for Analysing Biological Samples

“…Microgrippers have one or two tips to manipulate a target sample, which can be as small as a single microtubule [86] or as large as a fruit fly [15]. Due to the possibility of mechanical stimulation, analyses are performed using mechanical parameters, such as force [15,48,87], stiffness [57,58,[87][88][89][90][91], and viscosity [57]. The demonstrated devices are fabricated with standard silicon micromachining techniques, which make electrostatic actuation and capacitive sensing easily accessible as no extra fabrication steps are needed.…”

“…About a decade later, a similar device was used to assess drug sensitivity of single cancer cells by measuring mass accumulation rate [38]. Similarly, it took over a decade for microgrippers to progress from capturing their first DNA bundle [93] to constructing a chromatin analogue for testing the epigenetic effects of chemicals [90]. Quantitative detection of proteins, nucleic acids, exosomes, or viral particles is required in a wide range of activities such as drug dosing, clinical diagnostics, or protein characterisation.…”

“…Furthermore, the same setup can be used to monitor DNA repair processes by mimicking cell conditions or using cell lysates. A similar technique was used to provide a chromatin analogue and monitor its mechanical properties to test epigenetic effects of para-sulphonato-calix [4]arene [90]. With this platform, DNA can be used for drug testing or combined therapy tests (radiotherapy and chemotherapy).…”

Job Opening for Nucleosome Mechanic: Flexibility Required

“…Do active sites stand out from the rest of the genome? One possibility that has been explored in recent years is that modified nucleosomal patches [92][93][94] create a unique local chromatin environment, simply by having distinct material properties that cause them to extrude locally from the rest of the genome. A simple analogy is to alter a stitch when knitting, which generates an identifiable pattern that pops out from the background.…”