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      Janus DNA orthogonal adsorption of graphene oxide and metal oxide nanoparticles enabling stable sensing in serum

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          Abstract

          Sensing DNA in a complex sample matrix using the adsorption difference between DNA and proteins on nanomaterials.

          Abstract

          While DNA/graphene oxide (GO) conjugates have been widely used for DNA detection, they suffer from non-specific DNA displacement by proteins, making their application in biological samples difficult. To find new materials tightly adsorbing DNA but not proteins, we screened seven metal oxide nanoparticles, all interacting with the phosphate backbone of DNA, while DNA uses its nucleobases to interact with GO. In this regard, DNA is a Janus polymer orthogonally adsorbing GO and metal oxides. The DNA adsorption affinity ranks CoO > NiO > Cr 2O 3 > Fe 2O 3 > Fe 3O 4 > TiO 2 > CeO 2 based on a phosphate displacement assay. Among them, CoO is nearly fully resistant to protein displacement, while NiO has the best limit of detection of 0.24 nM DNA. This study provides fundamental insights into the biointerface chemistry of DNA, and reveals new materials useful for bioanalytical chemistry, DNA separation, and DNA-directed assembly.

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          Nanomaterials. Programmable materials and the nature of the DNA bond.

          Matthew Jones, Nadrian Seeman, Chad A. Mirkin (2015)
          For over half a century, the biological roles of nucleic acids as catalytic enzymes, intracellular regulatory molecules, and the carriers of genetic information have been studied extensively. More recently, the sequence-specific binding properties of DNA have been exploited to direct the assembly of materials at the nanoscale. Integral to any methodology focused on assembling matter from smaller pieces is the idea that final structures have well-defined spacings, orientations, and stereo-relationships. This requirement can be met by using DNA-based constructs that present oriented nanoscale bonding elements from rigid core units. Here, we draw analogy between such building blocks and the familiar chemical concepts of "bonds" and "valency" and review two distinct but related strategies that have used this design principle in constructing new configurations of matter.
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            DNA-programmable nanoparticle crystallization.

            Sung Yong Park, Abigail K. R. Lytton-Jean, Byeongdu Lee … (2008)
            It was first shown more than ten years ago that DNA oligonucleotides can be attached to gold nanoparticles rationally to direct the formation of larger assemblies. Since then, oligonucleotide-functionalized nanoparticles have been developed into powerful diagnostic tools for nucleic acids and proteins, and into intracellular probes and gene regulators. In contrast, the conceptually simple yet powerful idea that functionalized nanoparticles might serve as basic building blocks that can be rationally assembled through programmable base-pairing interactions into highly ordered macroscopic materials remains poorly developed. So far, the approach has mainly resulted in polymerization, with modest control over the placement of, the periodicity in, and the distance between particles within the assembled material. That is, most of the materials obtained thus far are best classified as amorphous polymers, although a few examples of colloidal crystal formation exist. Here, we demonstrate that DNA can be used to control the crystallization of nanoparticle-oligonucleotide conjugates to the extent that different DNA sequences guide the assembly of the same type of inorganic nanoparticle into different crystalline states. We show that the choice of DNA sequences attached to the nanoparticle building blocks, the DNA linking molecules and the absence or presence of a non-bonding single-base flexor can be adjusted so that gold nanoparticles assemble into micrometre-sized face-centred-cubic or body-centred-cubic crystal structures. Our findings thus clearly demonstrate that synthetically programmable colloidal crystallization is possible, and that a single-component system can be directed to form different structures.
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              Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns.

              Martin R Larsen, Tine E Thingholm, Ole N. Jensen … (2005)
              Reversible phosphorylation of proteins regulates the majority of all cellular processes, e.g. proliferation, differentiation, and apoptosis. A fundamental understanding of these biological processes at the molecular level requires characterization of the phosphorylated proteins. Phosphorylation is often substoichiometric, and an enrichment procedure of phosphorylated peptides derived from phosphorylated proteins is a necessary prerequisite for the characterization of such peptides by modern mass spectrometric methods. We report a highly selective enrichment procedure for phosphorylated peptides based on TiO2microcolumns and peptide loading in 2,5-dihydroxybenzoic acid (DHB). The effect of DHB was a very efficient reduction in the binding of nonphosphorylated peptides to TiO2 while retaining its high binding affinity for phosphorylated peptides. Thus, inclusion of DHB dramatically increased the selectivity of the enrichment of phosphorylated peptides by TiO2. We demonstrated that this new procedure was more selective for binding phosphorylated peptides than IMAC using MALDI mass spectrometry. In addition, we showed that LC-ESI-MSMS was biased toward monophosphorylated peptides, whereas MALDI MS was not. Other substituted aromatic carboxylic acids were also capable of specifically reducing binding of nonphosphorylated peptides, whereas phosphoric acid reduced binding of both phosphorylated and nonphosphorylated peptides. A putative mechanism for this intriguing effect is presented.
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                Author and article information

                Journal
                Journal ID (publisher-id): MHAOAL
                Title: Materials Horizons
                Abbreviated Title: Mater. Horiz.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 2051-6347
                ISSN (Electronic): 2051-6355
                Publication date Created: 2018
                Publication date (Electronic): 2018
                Volume: 5
                Issue: 1
                Pages: 65-69
                Affiliations
                [1 ]Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo
                [2 ]Ontario
                [3 ]Canada
                [4 ]Analytical & Testing Centre, Sichuan University
                [5 ]Chengdu
                [6 ]China
                Article
                DOI: 10.1039/C7MH00804J
                SO-VID: 44d33226-7f14-4978-ac48-288193c7c421
                Copyright © © 2018
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                http://rsc.li/journals-terms-of-use

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