Adsorption of DNA Oligonucleotides by Boronic Acid-Functionalized Hydrogel Nanoparticles

Abstract

Boronic acid-functionalized hydrogels were commonly used for covalent binding of cis-diol-contained molecules such as glucose, but noncovalent adsorption by boronic acids was less studied. DNA as an important polymer has been used to enhance the function of hydrogels including boronic acid-containing gels. In this work, noncovalent interactions between DNA oligonucleotides and boronic acid-containing hydrogel nanoparticles were studied in detail. The gels were composed of either poly­(N-isopropylacrylamide) or with additional 5.6 mol % of 3-acrylamidophenylboronic acid (AAPBA). DNA adsorption on the AAPBA-containing gels was achieved with a high salt concentration, which can be explained by electrostatic repulsion between DNA and boronic acid. The critical role of boronic acid was confirmed by adding competing cis-diol-containing molecules such as glucose, fructose, and cytidine. Hydrogen bonding and hydrophobic interactions are important for DNA adsorption based on inhibited adsorption by urea and dimethyl sulfoxide. Polycytosine DNA showed a higher adsorption capacity compared to the other three types of DNA homopolymers. When T15 and T14-rU were compared, no covalent binding was detected for T14-rU, suggesting that a single terminal diol was insufficient to support covalent binding at the low concentration of DNA used. Finally, the boronic acid-containing gels were able to adsorb an aptamer and inhibit its binding function. Binding was rescued by adding glucose to block the boronic acids. This study demonstrates noncovalent boronic acid interactions with DNA, and this information could be useful for designing and optimization of related biosensors and materials.

Investigation of polyacrylamide hydrogel‐based molecularly imprinted polymers using protein gel electrophoresis

“…7 This is due to their capability of recognising higher molecular weight molecules despite the significant reduction in integral binding strength of non-covalent template/monomer interactions. More recently, the molecular imprinting of large biomolecules, such as nucleic acids, 8,9 viruses, 10,11 and proteins, [12][13][14] has become increasingly topical, especially with the aim of developing MIP-based sensors for the detection of disease markers. MIP-based biosensors have been reported for the determination of a number of protein biomarkers including bovine (and human) serum albumin, [15][16][17] haemoglobin, 18 myoglobin (Mb), 19 and prostate-specific antigen.…”

Boron Isotope Tag-Assisted Ultrahigh-Performance Liquid Chromatography Coupled with High-Resolution Mass Spectrometry for Discovery and Annotation of cis-Diol-Containing Metabolites

“…20−22 Among them, boronate affinity chromatography has been one of the most effective tools for the analysis of cis-diol-containing metabolites, 23 diols by covalently forming a fiveor six-membered ring. 24,25 According to the previous studies, boronic acids were employed as derivatization reagents to improve the selectivity and sensitivity of cis-diol-containing metabolites on the LC− MS platform. For instance, 4-phenylaminomethyl-benzeneboronic acid (4-PAMBA) and 3-(dimethylamino)-phenylboronic acid (DMAPBA) were used to label the cis-diol-containing metabolites for LC−MS analysis of monosaccharides and brassinosteroids.…”

“…Up to now, many efforts have been made to develop analytical methods for the profiling of cis -diol-containing metabolites in various biological samples. − Among them, boronate affinity chromatography has been one of the most effective tools for the analysis of cis -diol-containing metabolites, as boronate affinity media could selectively bind cis -diols by covalently forming a five- or six-membered ring. , According to the previous studies, boronic acids were employed as derivatization reagents to improve the selectivity and sensitivity of cis -diol-containing metabolites on the LC–MS platform. For instance, 4-phenylaminomethyl-benzeneboronic acid (4-PAMBA) and 3-(dimethylamino)-phenylboronic acid (DMAPBA) were used to label the cis -diol-containing metabolites for LC–MS analysis of monosaccharides and brassinosteroids. − Furthermore, the profiling of cis -diol-containing metabolites was pioneeringly exemplified by introducing a pair of boronate reagents, 4-PAMBA and 4-PAMBA- d 5 , to label potential brassinosteroids in plant extracts followed by LC–MS analysis .…”

Novel CD123 polyaptamer hydrogel edited by Cas9/sgRNA for AML-targeted therapy

“…To increase the retention of SS30 in the body, DNA hydrogel, a kind of important DNA materials was chosen. DNA hydrogel could retain the biological function of DNA, and realizes the perfect fusion of structure and function of hydrogel materials, presenting good biocompatibility, adjustable biodegradability and controllable mechanical properties (Li et al, 2019 ; Zhang et al, 2020 ). Moreover, to precisely cleave the DNA hydrogel to generate the precise aptamer for further inhibition function, CRISPR-associated protein 9 (Cas9) was utilized.…”