Unravelling a Direct Role for Polysaccharide β‐Strands in the Higher Order Structure of Physical Hydrogels

Abstract

The mechanical properties of agarose-derived hydrogels depend on the scaffolding of the polysaccharide network. To identify and quantify such higher order structure, we applied Raman optical activity (ROA)-a spectroscopic technique that is highly sensitive toward carbohydrates-on native agarose and chemically modified agarose in the gel phase for the first time. By spectral global fitting, we isolated features that change as a function of backbone carboxylation (28, 40, 50, 60, 80, and 93 %) from other features that remain unchanged. We assigned these spectral features by comparison to ROA spectra calculated for different oligomer models. We found a 60:40 ratio of double- and single-stranded α-helix in the highly rigid hydrogel of native agarose, while the considerably softer hydrogels made from carboxylated agarose use a scaffold of unpaired β-strands.

Simulation of Raman and Raman optical activity of saccharides in solution

“…20 One of the largest systems studied is the agarose hexamer. 21 However, in the paper only continuum solvation without explicit water molecules is used, which was shown to be insufficient to properly capture Raman/ROA spectral features. 13 All these studies clearly hint at the necessity of including explicit waters when computing Raman and ROA spectra.…”

A DNA origami plasmonic sensor with environment-independent read-out

“…To evaluate the read-out of the tetrahedral DNA origami plasmonic sensor in a viscous environment, which is a better approximation of the extracellular matrix [37,38] and the cytosol, we purified, concentrated and then measured in agarose gel the same structure, before and after hybridization in solution [30]. Thick agarose gel may scatter light significantly, resulting in poor transmission, thus hindering UV-vis extinction measurements; therefore, the portion containing the tetrahedral DNA origami plasmonic sensor was cut to the thinnest possible section.…”

Tracking Conformational Changes in Phosvitin throughout a Crowding‐Agent‐Based Titration

“…In the past, CID has been used as a method to determine the similarity between calculated and experimentally measured ROA spectra . However, in this study it is used as a method to validate the claims about the amounts of structural elements present in the described samples, because deviating CID intensities might indicate the presence, in the spectra, of artifacts originating in the subtraction method used during these experiments.…”