Elucidating the mechanism of the considerable mechanical stiffening of DNA induced by the couple Zn2+/Calix[4]arene-1,3-O-diphosphorous acid

Abstract

The couple Calix[4]arene-1,3-O-diphosphorous acid (C4diP) and zinc ions (Zn 2+ ) acts as a synergistic DNA binder. Silicon NanoTweezer (SNT) measurements show an increase in the mechanical stiffness of DNA bundles by a factor of >150, at Zn 2+ to C4diP ratios above 8, as compared to Zinc alone whereas C4diP alone decreases the stiffness of DNA. Electroanalytical measurements using 3D printed devices demonstrate a progression of events in the assembly of C4diP on DNA promoted by zinc ions. A mechanism at the molecular level can be deduced in which C4diP initially coordinates to DNA by phosphate-phosphate hydrogen bonds or in the presence of Zn 2+ by Zn 2+ bridging coordination of the phosphate groups. Then, at high ratios of Zn 2+ to C4diP, interdigitated dimerization of C4diP is followed by cross coordination of DNA strands through Zn 2+ /C4diP inter-strand interaction. The sum of these interactions leads to strong stiffening of the DNA bundles and increased inter-strand binding.

Fused Deposition Modeling 3D Printing: Test Platforms for Evaluating Post-Fabrication Chemical Modifications and In-Vitro Biological Properties

“…The ester C=O band is highlighted by a blue oval, the amide C=O bands by red circles, and the amide NH band by a green oval. From the presence of only the ester C=O stretch in PLA and the presence of both C=O amide and NH amide bands in the PLA-ED spectra, it is clear that the amide functionalization reaction has occurred, as was previously observed by time of flight secondary ion mass spectrometry (TOF-SIMS) for the surface modification of poly-ethylene-terephthalate (PET) by adenosine mono-phosphate (AMP) under the same conditions as in the current study [24].…”

“…A total of 1000 mL 1 M solution of each amidation reagent was prepared in deionized water. No coupling reagents were added, as prior work using adenosine monophosphate had shown clean functionalization under the above conditions [24].…”

Fabricating Silicon Resonators for Analysing Biological Samples

“…Using this kind of suspended microchannel resonator, resonance measurements can be performed continuously with the sensor contained in vacuum while the samples can be handled by controlling the flow through the internal channel [11,55,56]. Other researchers have developed systems with the probe tip working at an air-liquid interface to access the samples without immersing the sensitive actuation and sensing elements in the liquid [57,58].…”

“…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.…”

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

“…1B). This allows injection of a series of molecular solutes in order to assemble molecular complexes 38 and/or to determine the mechanical effects as a function of the concentration of a given substrate on DNA packing and rearrangement in terms of stiffness and viscous losses changes 39 .…”