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The efficacy of affinity-based treatments for cancer and other diseases is often limited by poor distribution throughout the targeted tissue. Although lower-affinity antibodies will penetrate more uniformly, these often reach lower concentrations because of their rapid clearance from the tissue. To increase retention and improve distribution, we created low-affinity photocrosslinkable affibodies that can diffuse into dense tumor matrices with limited tumor barrier formation and then be photocrosslinked in place to cell receptors to increase retention. In testing with 3D tumor spheroids, the addition of a 50 nM photocrosslinkable affibody showed a similar level of accumulation at the edges of the spheroid but a higher level near the middle of the spheroid than the wild-type (non-photocrosslinkable) affibody. These results show that target affinity affects protein transport in tumor microenvironments and that covalently cross-linking the ligands to cells may improve both their transport and retention.

Tumor spheroids represent valuable in vitro models for studying cancer biology and evaluating therapeutic strategies. In this study, we investigated the impact of varying lengths of DNA-modified cell surfaces on spheroid formation, cellular adhesion molecule expression, and hypoxia levels within 4T1 mouse breast cancer spheroids. Through a series of experiments, we demonstrated that modifying cell surfaces with biotinylated DNA strands of different lengths facilitated spheroid formation without significantly altering the expression of fibronectin and e-cadherin, key cellular adhesion molecules. However, our findings revealed a notable influence of DNA length on hypoxia levels within the spheroids. As DNA length increased, hypoxia levels decreased, indicating enhanced intercellular spacing and porosity within the spheroid structure. These results contribute to a better understanding of how DNA modification of cell surfaces can modulate spheroid architecture and microenvironmental conditions. Such insights may have implications for developing therapeutic interventions targeting the tumor microenvironment to improve cancer treatment efficacy.

The role of stromal and immune cells in transforming the tumor microenvironment is a key consideration in understanding tumor cell behavior and anticancer drug development. To better model these systems in vitro, 3D coculture tumor spheroids have been engineered using a variety of techniques including centrifugation to microwells, hanging drop, low adhesion cultures, and culture of cells in a microfluidic platform. Aside from using bioprinting, however, it has remained more challenging to direct the spatial organization of heterotypic cells in standalone 3D spheroids. To address this, we present an in vitro 3D coculture tumor model where we modulated the interactions between cancer cells and fibroblasts through DNA hybridization. When native heterotypic cells are simply mixed, the cell aggregates typically show cell sorting behavior to form phase separated structures composed of single cell types. In this work, we demonstrate that when MDA-MB-468 breast cancer and NIH/3T3 fibroblasts are directed to associate via complementary DNA, a uniform distribution of the two cell types within a single spheroid was observed. In contrast, in the absence of specific DNA interactions between the cancer cells and fibroblasts, individual clusters of the NIH/3T3 cells formed in each spheroid due to cell sorting. To better understand the effect of heterotypic cell organization on either cell-cell contacts or matrix protein production, the spheroids were further stained with anti-E-cadherin and antifibronectin antibodies. While the amounts of E-cadherin appeared to be similar between the spheroids, a significantly higher amount of fibronectin secretion was observed in the coculture spheroids with uniform mixing of two cell types. This result showed that different heterotypic cell distributions within 3D architecture can influence the ECM protein production that can again alter the properties of the tumor or tumor microenvironment. The present study thus describes the use of DNA templating to direct the organization of cells in coculture spheroids, which can provide mechanistic biological insight into how heterotypic distribution in tumor spheroids can influence tumor progression, metastasis, and drug resistance.

Hydrophobically-modified silica-coated gold nanorods are presented here as multifunctional theranostic agents. A single modification both increases two-photon fluorescence and promotes cavitation-based acoustic signal for imaging. A two-fold greater release of small molecule drugs was observed under ultrasound-mediated conditions as compared to passive release without ultrasound.

In this work, we demonstrate that a photo-cross-linkable conjugate of upconverting nanoparticles and cytosine deaminase can catalyze prodrug conversion specifically at tumor sites in vivo . Non-covalent association of proteins and peptides with cellular surfaces leads to receptor-mediated endocytosis and catabolic degradation. Recently, we showed that covalent attachment of proteins such as affibodies to cell receptors yields extended expression on cell surfaces with preservation of protein function. To adapt this technology for in vivo applications, conjugates were prepared from upconverting nanoparticles and fusion proteins of affibody and cytosine deaminase enzyme (UC-ACD). The affibody allows covalent photo-cross-linking to epidermal growth factor receptors (EGFRs) overexpressed on Caco-2 human colorectal cancer cells under near-infrared (NIR) light. Once bound, the cytosine deaminase portion of the fusion protein converts the prodrug 5-fluorocytosine (5-FC) to the anticancer drug 5-fluorouracil (5-FU). NIR covalent photoconjugation of UC-ACD to Caco-2 cells showed 4-fold higher retention than observed with cells that were not irradiated in vitro . Next, athymic mice expressing Caco-2 tumors showed 5-fold greater UC-ACD accumulation in the tumors than either conjugates without the CD enzyme or UC-ACDs in the absence of NIR excitation. With oral administration of 5-FC prodrug, tumors with photoconjugated UC-ACD yielded 2-fold slower growth than control groups, and median mouse survival increased from 28 days to 35 days. These experiments demonstrate that enzyme-decorated nanoparticles can remain viable after a single covalent photoconjugation in vivo , which can in turn localize prodrug conversion to tumor sites for multiple weeks.

Cellular quiescence is a reversible state of cell cycle arrest whereby cells are temporarily maintained in the nondividing phase. Inducing quiescence in cancer cells by targeting growth receptors is a treatment strategy to slow cell growth in certain aggressive tumors, which in turn increases the efficacy of treatments such as surgery or systemic chemotherapy. However, ligand interactions with cell receptors induce receptor-mediated endocytosis followed by proteolytic degradation, which limits the duration of cellular quiescence. Here, we report the effects of targeted covalent affibody photoconjugation to epidermal growth factor receptors (EGFR) on EGFR-positive MDA-MB-468 breast cancer cells. First, covalently conjugating affibodies to cells increased doubling time two-fold and reduced ERK activity by 30% as compared to cells treated with an FDA-approved anti-EGFR antibody Cetuximab, which binds to EGFR noncovalently. The distribution of cells in each phase of the cell cycle was determined, and cells conjugated with the affibody demonstrated an accumulation in the G1 phase, indicative of G1 cell cycle arrest. Finally, the proliferative capacity of the cells was determined by the incorporation of 5-ethynyl-2-deoxyuridine and Ki67 Elisa assay, which showed that the percentage of proliferative cells with photoconjugated affibody was half of that found for the untreated control., (© 2021 Wiley Periodicals LLC.)

In this work, we report that gold nanorods coated with hydrophobically-modified mesoporous silica shells not only enhance photoacoustic (PA) signal over unmodified mesoporous silica coated gold nanorods, but that the relationship between PA amplitude and input laser fluence is strongly nonlinear. Mesoporous silica shells of ~14 nm thickness and with ~3 nm pores were grown on gold nanorods showing near infrared absorption. The silica was rendered hydrophobic with addition of dodecyltrichlorosilane, then re-suspended in aqueous media with a lipid monolayer. Analysis of the PA signal revealed not only an enhancement of PA signal compared to mesoporous silica coated gold nanorods at lower laser fluences, but also a nonlinear relationship between PA signal and laser fluence. We attribute each effect to the entrapment of solvent vapor in the mesopores: the vapor has both a larger expansion coefficient and thermal resistance than silica that enhances conversion to acoustic energy, and the hydrophobic porous surface is able to promote phase transition at the surface, leading to a nonlinear PA response even at fluences as low as 5 mJ cm -2 . At 21 mJ cm -2 , the highest laser fluence tested, the PA enhancement was >12-fold over mesoporous silica coated gold nanorods.

3D culture is known to provide more faithful tissue models than 2D culture, and thus it is a valuable tool for in vitro evaluation of biological models. However, many cell lines are unable to form desired 3D spheroids by traditional methods because the naturally occurring cell-cell adhesion is too weak. Here, we present a method to produce 3D cell spheroids by using DNA-mediated assembly. We first demonstrate an Affinity Mediated Photoconjugation Approach (AMCP) to covalently modify cell receptors with affibody-streptavidin fusion proteins, where the affibody chemically crosslinks to cell expressed EGFR and the streptavidin is used to attach DNA strands. The DNA conjugated cells were then mixed with complementary DNA 'linker strands' to impart cell-cell interactions. When incubated in wells coated with non-adhesive polymers, cells formed dense spherical aggregates larger than 500 microns in diameter. Each of these studies was carried out using human breast cancer cells (MBA-MB-468), aneuploid human keratinocytes (HaCaT), and human colon cancer cells (Caco-2). Without either DNA on the cells or in solution as linkers, no cell spheroids were observed. After 96 h of incubation, the cultured DNA assembled spheroids were found to be mechanically stable enough to be handled easily for further analysis and confocal imaging. The findings suggest that the proposed DNA assembly method can be considered as an attractive strategy for assembling cells into stable spheroids.

In this work we report the effect of incorporating conducting oligophenylenes and a cobaltocene-based redox mediator on photodriven electron transfer between thioglycolic acid (TGA) capped CdS nanorods (NR) and the native nitrogenase MoFe protein (MoFeP) by following the reduction of H + to H 2 . First, we demonstrate that the addition of benzidine-a conductive diphenylene- to TGA-CdS and MoFeP increased catalytic activity by up to 3-fold as compared to CdS-MoFeP alone. In addition, in comparing the use of oligophenylenes composed of one ( p -phenylenediamine), two (benzidine) or three (4,4''-diamino- p -terphenyl)phenylene groups, the largest gain in H 2 was observed with the addition of benzidine and the lowest with phenylenediamine. As a comparison to the conductive oligophenylenes, a cobaltocene-based redox mediator was also tested with the TGA-CdS NRs and MoFeP. However, adding either cobaltocene diacid or diamine caused negligible gains in H 2 production and at higher concentrations, caused a significant decrease. Agarose gel electrophoresis revealed little to no detectable interaction between benzidine and TGA-CdS but strong binding between cobaltocene and TGA-CdS. These results suggest that the tight binding of the cobaltocene mediator to CdS may hinder electron transfer between CdS and MoFe and cause the mediator to undergo continuous reduction/oxidation events at the surface of CdS., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The cell membrane possesses an extensive library of proteins, carbohydrates, and lipids that control a significant portion of inter- and intracellular functions, including signaling, proliferation, migration, and adhesion, among others. Augmenting the cell surface composition would open possibilities for advances in therapy, tissue engineering, and probing fundamental cell processes. While genetic engineering has proven effective for many in vitro applications, these techniques result in irreversible changes to cells and are difficult to apply in vivo . Another approach is to instead attach exogenous functional groups to the cell membrane without changing the genetic nature of the cell. This review focuses on more recent approaches of nongenetic methods of cell surface modification through metabolic pathways, anchorage by hydrophobic interactions, and chemical conjugation. Benefits and drawbacks of each approach are considered, followed by a discussion of potential applications for nongenetic cell surface modification and an outlook on the future of the field.

Efficient intracellular delivery of biomacromolecules such as proteins continues to remain a challenge despite its potential for medicine. In this work, we show that mScarlet, a non cytotoxic red fluorescent protein (RFP) conjugated to Click Nucleic Acid (CNA), a synthetic analog of DNA, undergo cell uptake significantly more than either native proteins or proteins conjugated with similar amounts of DNA in MDA-MB-468 cells. We further demonstrate that the process of cell uptake is metabolically driven and that scavenger receptors and caveolae mediated endocytosis play a significant role. Co-localization studies using anti-scavenger receptor antibodies suggest that scavenger receptors are implicated in the mechanism of uptake of CNA modified proteins.

We illustrate how intermolecular interactions facilitate ATP-free electron transfer between either native or engineered MoFe protein (MoFeP) from nitrogenase and a CdS nanorod (NR) by following the reduction of H + to H 2 . First, by varying the charge on the surface of the NR, we show the role of electrostatic interactions on MoFeP binding to the particle surface and subsequent H + reduction. Next, the role of strong, semicovalent thiol-CdS interactions was tested using free cysteines on the MoFeP. By blocking free cysteines, we show that the presence of free thiols on the protein has little to no influence on CdS binding and resultant photocatalytic activity. We next studied methods to covalently bind the protein to CdS by modifying the free cysteines with dibenzocyclooctyne (DBCO) and reacting the CdS NRs capped with a mixture of negatively charged thioglycolic acid and thiol-PEG3-azide ligands. As compared to that of the unmodified proteins, a 32.2 ± 1.5% and 61.7 ± 2.1% increase in H 2 production was observed from MoFeP and C-MoFeP, respectively. At last, to test the effect of both charge and covalent tethering, positively charged cysteamine/azide CdS NRs were reacted with DBCO-modified C-MoFeP, which showed little improvement over native C-MoFeP alone under irradiation. These results show the importance of both electrostatic associations between the NR and protein and covalently tethering the protein to the semiconductor surface for enhanced electron transfer and photodriven activity.

In this work, we show that a prodrug enzyme covalently photoconjugated to live cell receptors survives endosomal proteolysis and retains its catalytic activity over multiple days. Here, a fusion protein was designed with both an antiepidermal growth factor receptor (EGFR) affibody and the prodrug enzyme cytosine deaminase, which can convert prodrug 5-fluorocytosine to the anticancer drug 5-fluorouracil. A benzophenone group was added at a site-specific mutation within the affibody, and the fusion protein was selectively photoconjugated to EGFR receptors expressed on membranes of MDA-MB-468 breast cancer cells. The fusion protein was next labeled with two dyes for tracking uptake: AlexaFluor 488 and pH-sensitive pHAb. Flow cytometry showed that fusion proteins photo-cross-linked to EGFR first underwent receptor-mediated endocytosis within 12 h, followed by recycling back to the cell membrane within 24 h. These findings were also confirmed by confocal microscopy. The unique cross-linking of the affibody-enzyme fusion proteins was utilized for two anticancer treatments. First, the covalent linking of the protein to the EGFR led to inhibition of ERK signaling over a two-day period, whereas conventional antibody therapy only led to 6 h of inhibition. Second, when the affibody-CodA fusion proteins were photo-cross-linked to EGFR overexpressed on MDA-MB-468 breast cancer cells, prodrug conversion was found even 48 h postincubation without any apparent decrease in cell killing, while without photo-cross-linking no cell killing was observed 8 h postincubation. These studies show that affinity-mediated covalent conjugation of the affibody-enzymes to cell receptors allows for prolonged expression on membranes and retained enzymatic activity without genetic engineering.

Achieving global sustainability will require balancing encroaching climate changes while maintaining existing quality of life. Using sunlight to purify wastewater while simultaneously generating usable fuels is an opportunity to approach both targets in a cost-efficient manner. In addition, converting biomass products to usable polymers is a sustainable approach for potentially replacing polystyrene or other petroleum derived polymers. Phenols from medical, manufacturing, and agricultural waste are commonly found in many water sources, and they are known to foul common reverse osmosis membranes. Here, we show oxidative polymerization of guaiacol, an aromatic compound derived from biomass, with concurrent hydrogen gas generation by using platinum-seeded cadmium sulfide nanorods (Pt@CdS) as photocatalysts. Rather than forming short oligomers as typically made by enzymes such as laccase and peroxidase, the resulting polymers show higher molecular weights that can more easily flocculate out of water. By comparing guaiacol conversion to molecular weight and dispersity, the guaiacol was found to polymerize via a chain-growth process. We also show that Pt@CdS can polymerize other phenols as well by testing the monomers phenol, 2,6-dihydroxybenzoic acid, gallic acid, and vanillin. Lastly, because the aqueous solubility of these aromatic polymers decreases dramatically with molecular weight, polymerization reactions were also tested in biphasic solutions to determine if chain growth could propagate in the oil phase. We show that the Pt@CdS nanoparticles can form stable Pickering emulsions in various biphasic combinations, and that both H 2 formation and polymer molecular weight correlated with the partition coefficient of guaiacol into the oil phase as well as the solubility of the growing polymer chains. These combined studies demonstrate the possibility of using nanoscale photocatalysts to oxidatively polymerize phenolic substrates via a chain-growth mechanism, thereby providing a path for pretreating water by flocculating out contaminants with concurrent generation of hydrogen.

In this Letter, we report that surface-bound nanobubbles reduce protein denaturation on methylated glass by irreversible protein shell formation. Single-molecule total internal reflection fluorescence (SM-TIRF) microscopy was combined with intramolecular Förster resonance energy transfer (FRET) to study the conformational dynamics of nitroreductase (NfsB) on nanobubble-laden methylated glass surfaces, using reflection brightfield microscopy to register nanobubble locations with NfsB adsorption. First, NfsB adsorbed irreversibly to nanobubbles with no apparent desorption after 5 h. Moreover, virtually all (96%) of the NfsB molecules that interacted with nanobubbles remained folded, whereas less than 50% of NfsB molecules remained folded in the absence of nanobubbles on unmodified silica or methylated glass surfaces. This trend was confirmed by ensemble-average fluorometer TIRF experiments. We hypothesize that nanobubbles reduce protein damage by passivating strongly denaturing topographical surface defects. Thus, nanobubble stabilization on surfaces may have important implications for antifouling surfaces and improving therapeutic protein storage.

The simultaneous delivery of multiple therapeutics to a single site has shown promise for cancer targeting and treatment. However, because of the inherent differences in charge and size between drugs and biomolecules, new approaches are required for colocalization of unlike components in one delivery vehicle. In this work, we demonstrate that triblock copolymers containing click nucleic acids (CNAs) can be used to simultaneously load a prodrug enzyme (cytosine deaminase, CodA) and a chemotherapy drug (doxorubicin, DOX) in a single polymer nanoparticle. CNAs are synthetic analogs of DNA comprised of a thiolene backbone and nucleotide bases that can hybridize to complementary strands of DNA. In this study, CodA was appended with complementary DNA sequences and fluorescent dyes to allow its encapsulation in PEG-CNA-PLGA nanoparticles. The DNA-modified CodA was found to retain its enzyme activity for converting prodrug 5-fluorocytosine (5-FC) to active 5-fluorouracil (5-FU) using a modified fluorescent assay. The DNA-conjugated CodA was then loaded into the PEG-CNA-PLGA nanoparticles and tested for cell cytotoxicity in the presence of the 5-FC prodrug. To study the effect of coloading DOX and CodA within a single nanoparticle, cell toxicity assays were run to compare dually loaded nanoparticles with nanoparticles loaded only with either DOX or CodA. We show that the highest level of cell death occurred when both DOX and CodA were simultaneously entrapped and delivered to cells in the presence of 5-FC.

While thermal ablation of various solid tumors has been demonstrated using high intensity focused ultrasound (HIFU), the therapeutic outcomes of this technique are still unsatisfactory because of common recurrence of thermally ablated cancers and treatment side effects due to the high ultrasound intensity and acoustic pressure requirements. More precise ablation of tumors can be achieved by generating cavitating bubbles in the tissue using shorter pulses with higher acoustic pressures, which induce mechanical damage rather than thermal. However, it has remained as a challenge to safely deliver the acoustic pressures required for mechanical ablation of solid tumors. Here, we report a method to achieve mechanical ablation at lower acoustic pressures by utilizing phospholipid-stabilized hydrophobic mesoporous silica nanoparticles (PL-hMSN). The PL-hMSNs act as seeds for nucleation of cavitation events and thus significantly reduce the peak negative pressures and spatial-average temporal-average HIFU intensities needed to achieve mechanical ablation. Substantial mechanical damage was observed in the red blood cell or tumor spheroid containing tissue mimicking phantoms at PL-hMSN concentrations as low as 10 μg mL -1 , after only 5 s of HIFU treatment with peak negative pressures ∼11 MPa and duty cycles ∼0.01%. Even the application of HIFU (peak negative pressure of 16.8 MPa and duty cycle of 0.017%) for 1 min in the presence of PL-hMSN (200 μg mL -1 ) did not cause any detectable temperature increase in tissue-mimicking phantoms. In addition, the mechanical effects of cavitation promoted by PL-hMSNs were observed up to 0.5 mm from the center of the cavitation events. This method may thus also improve delivery of therapeutics or nanoparticles to tumor environments with limited macromolecular transport.

Due to the ability to generate oligomers of precise sequence, sequential and stepwise solid-phase synthesis has been the dominant method of producing DNA and other oligonucleotide analogues. The requirement for a solid support, however, and the physical restrictions of limited surface area thereon significantly diminish the efficiency and scalability of these syntheses, thus, negatively affecting the practical applications of synthetic polynucleotides and other similarly created molecules. By employing the robust photoinitiated thiol-ene click reaction, we developed a new generation of clickable nucleic acids (CNAs) with a polythioether backbone containing repeat units of six atoms, matching the spacing of the phosphodiester backbone of natural DNA. A simple, inexpensive, and scalable route was utilized to produce CNA monomers in gram-scale, which indicates the potential to dramatically lower the cost of these DNA mimics and thereby expand the scope of these materials. The efficiency of this approach was demonstrated by the completion of CNA polymerization in 30 seconds, as characterized by size-exclusive chromatography (SEC) and infrared (IR) spectroscopy. CNA/DNA hybridization was demonstrated by gel electrophoresis and used in CdS nanoparticle assembly.

A significant challenge for solid tumor treatment is ensuring that a sufficient concentration of therapeutic agent is delivered to the tumor site at doses that can be tolerated by the patient. Biomolecular targeting can bias accumulation in tumors by taking advantage of specific interactions with receptors overexpressed on cancerous cells. However, while antibody-based immunoconjugates show high binding to specific cells, their low dissociation constants ( K D ) and large Stokes radii hinder their ability to penetrate deep into tumor tissue, leading to incomplete cell killing and tumor recurrence. To address this, we demonstrate the design and production of a photo-cross-linkable affibody that can form a covalent bond to epidermal growth factor receptor (EGFR) under near UV irradiation. Twelve cysteine mutations were created of an EGFR affibody and conjugated with maleimide-benzophenone. Of these only one exhibited photoconjugation to EGFR, as demonstrated by SDS-PAGE and Western blot. Next this modified affibody was shown to not only bind EGFR expressing cells but also show enhanced retention in a 3D tumor spheroid model, with minimal loss up to 24 h as compared to either unmodified EGFR-binding affibodies or nonbinding, photo-cross-linkable affibodies. Finally, in order to show utility of photo-cross-linking at clinically relevant wavelengths, upconverting nanoparticles (UCNPs) were synthesized that could convert 980 nm light to UV and blue light. In the presence of UCNPs, both direct photoconjugation to EGFR and enhanced retention in tumor spheroids could be obtained using near-infrared illumination. Thus, the photoactive affibodies developed here may be utilized as a platform technology for engineering new therapy conjugates that can penetrate deep into tumor tissue and be retained long enough for effective tumor therapy.

Near infrared (NIR)-absorbing noble metal nanostructures are being extensively studied as theranostic agents, in particular for photoacoustic imaging and photothermal therapy. Because of the electric field enhancement at the tips of anisotropic metal nanostructures, positioning photoactive species at these sites can lead to increased energy absorption. Herein, we show the site-specific placement of NIR-active photosensitizers at the ends of gold nanorods (AuNRs) by growing porous TiO 2 caps. The surface plasmon resonance of the AuNRs was carefully tuned to overlap with the exciton absorption of indocyanine green (ICG), a NIR photosensitizer with low quantum yields and poor photostability. In conjugating high amounts of ICG to the TiO 2 caps, increased amounts of singlet oxygen ( 1 O 2 ) were generated as compared to when ICG was attached to sidewalls of the AuNRs. Because the AuNRs also cause local increases in temperature upon NIR excitation, DNA strands were next attached to the AuNRs sidewalls and loaded with doxorubicin (DOX). We found that the synergistic effect of increased 1 O 2 and photothermal-induced drug delivery led to significant improvements in tumor cell killing. This work demonstrates that with careful design over hybrid nanostructure synthesis, higher levels of tumor therapy may be achieved.

Small molecule/DNA hybrids (SMDHs) have been considered as nanoscale building blocks for engineering 2D and 3D supramolecular DNA assembly. Herein, we report an efficient on-bead amide-coupling approach to prepare SMDHs with multiple oligodeoxynucleotide (ODN) strands. Our method is high yielding under mild and user-friendly conditions with various organic substrates and homo- or mixed-sequenced ODNs. Metal catalysts and moisture- and air-free conditions are not required. The products can be easily analyzed by LC-MS with accurate mass resolution. We also explored nanometer-sized shape-persistent macrocycles as novel multitopic organic linkers to prepare SMDHs. SMDHs bearing up to six ODNs were successfully prepared through the coupling of arylenethynylene macrocycles with ODNs, which were used to mediate the assembly of gold nanoparticles.

Synthetic biomacromolecules that mimic natural polymeric structures are of significant interest. For most applications of these materials, however, aqueous solubility is a necessity. Here, we present the synthesis of an intrinsically water soluble single stranded DNA analog formed by the synthesis of a Clickable Nucleic Acid (CNA). These molecules are formed with pendant hydroxyl groups present on the main polymer backbone, and subsequent modification of those hydroxyls with sulfonate moieties further enhances the hydrophilicity of these molecules.

DNA-mediated assembly of core-satellite structures composed of Zr(IV)-based porphyrinic metal-organic framework (MOF) and NaYF 4 ,Yb,Er upconverting nanoparticles (UCNPs) for photodynamic therapy (PDT) is reported. MOF NPs generate singlet oxygen ( 1 O 2 ) upon photoirradiation with visible light without the need for additional small molecule, diffusional photosensitizers such as porphyrins. Using DNA as a templating agent, well-defined MOF-UCNP clusters are produced where UCNPs are spatially organized around a centrally located MOF NP. Under NIR irradiation, visible light emitted from the UCNPs is absorbed by the core MOF NP to produce 1 O 2 at significantly greater amounts than what can be produced from simply mixing UCNPs and MOF NPs. The MOF-UCNP core-satellite superstructures also induce strong cell cytotoxicity against cancer cells, which are further enhanced by attaching epidermal growth factor receptor targeting affibodies to the PDT clusters, highlighting their promise as theranostic photodynamic agents., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Co-delivery of both chemotherapy drugs and siRNA from a single delivery vehicle can have a significant impact on cancer therapy due to the potential for overcoming issues such as drug resistance. However, the inherent chemical differences between charged nucleic acids and hydrophobic drugs have hindered entrapment of both components within a single carrier. While poly(ethylene glycol)-block-poly(lactic-co-glycolic acid) (PEG-PLGA) copolymers have been used successfully for targeted delivery of chemotherapy drugs, loading of DNA or RNA has been poor. It is demonstrated that significant amounts of DNA can be encapsulated within PLGA-containing nanoparticles through the use of a new synthetic DNA analog, click nucleic acids (CNAs). First, triblock copolymers of PEG-CNA-PLGA are synthesized and then formulated into polymer nanoparticles from oil-in-water emulsions. The CNA-containing particles show high encapsulation of DNA complementary to the CNA sequence, whereas PEG-PLGA alone shows minimal DNA loading, and non-complementary DNA strands do not get encapsulated within the PEG-CNA-PLGA nanoparticles. Furthermore, the dye pyrene can be successfully co-loaded with DNA and lastly, a complex, larger DNA sequence that contains an overhang complementary to the CNA can also be encapsulated, demonstrating the potential utility of the CNA-containing particles as carriers for chemotherapy agents and gene silencers., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Ethanol is a ubiquitous fermentation product well-tolerated by microbes, but purification from growth media requires multiple distillations or other energy intensive processes. Converting such metabolites to larger, hydrophobic products would both yield higher energy products and facilitate separation. Here, we demonstrate the conversion of C 2 ethanol to C 8 2-ethylhexenal via a sequential oxidation-aldol-hydrogenation-aldol process with solar energy as the only required input. Photocatalysis was utilized to drive enzymatic oxidation of ethanol, while biphasic media in conjunction with aldol coupling and Pd assisted hydrogenation kept the oxidation and reduction processes physically and chemically separated. Using this process, 2-ethylhexenal was produced from ethanol in both buffer and diluted yeast media.

This paper reports the design and preparation of a biohybrid photoelectrochemical cell (PEC) that can drive the tandem enzymatic oxidation and aldol condensation of n -butanol (BuOH) to C 8 2-ethylhexenal (2-EH). In this work, BuOH was first oxidized to n -butyraldehyde (BA) by the alcohol oxidase enzyme (AOx), concurrently generating hydrogen peroxide (H 2 O 2 ). To preserve enzyme activity and increase kinetics nearly 2-fold, the H 2 O 2 was removed by oxidation at a bismuth vanadate (BiVO 4 ) photoanode. Organocatalyzed aldol condensation of C 4 BA to C 8 2-EH improved the overall BuOH conversion to 6.2 ± 0.1% in a biased PEC after 16 h. A purely light-driven, unbiased PEC showed 3.1 ± 0.1% BuOH conversion, or ~50% of that obtained from the biased system. Replacing AOx with the enzyme alcohol dehydrogenase (ADH), which requires the diffusional nicotinamide adenine dinucleotide cofactor (NAD + /NADH), resulted in only 0.2% BuOH conversion due to NAD + dimerization at the photoanode. Lastly, the application of more positive biases with the biohybrid AOx PEC led to measurable production of H 2 at the cathode, but at the cost of lower BA and 2-EH yields due to both product overoxidation and decreased enzyme activity.

Microbes produce low-molecular-weight alcohols from sugar, but these metabolites are difficult to separate from water and possess relatively low heating values. A combination of photo-, organo-, and enzyme catalysis is shown here to convert C 4 butanol (BuOH) to C 8 2-ethylhexenal (2-EH) using only solar energy to drive the process. First, alcohol dehydrogenase (ADH) catalyzed the oxidation of BuOH to butyraldehyde (BA), using NAD + as a cofactor. To prevent back reaction, NAD+ was regenerated using a platinum-seeded cadmium sulfide (Pt@CdS) photocatalyst. An amine-based organocatalyst then upgraded BA to 2-EH under mild aqueous conditions rather than harsh basic conditions in order to preserve enzyme and photocatalyst stability. The process also simultaneously increased total BuOH conversion. Thus, three disparate types of catalysts synergistically generated C 8 products from C 4 alcohols under green chemistry conditions of neutral pH, low temperature, and pressure., Competing Interests: The authors declare no competing financial interest.

Here we describe novel covalent conjugates of antibody-phage for the detection of multiple cancer biomarkers using real time immuno-polymerase chain reaction (immuno-PCR). While the conventional process of immuno-PCR utilizes DNA-conjugated antibodies, chemical modification of antibodies not only reduces antibody affinity but also creates a heterogeneous population of products. However, phage naturally encapsulate genomic DNA, which can be used as a PCR template. To produce covalently conjugated antibody-phage constructs without recombinant antibody expression or chemical modification of antibodies, we incorporated a photocrosslinkable non-canonical amino acid within an antibody-binding domain displayed on one of the phage coat proteins. To correlate antigen presence to a specific DNA sequence, the phage genomes were modified with domains that recognized specific sets of primers. The crosslinked antibody-phage conjugates were then tested in a sandwich-type immunoassay using real-time PCR where low pg ml -1 concentrations of antigen could be detected and identified from a single solution containing a mixture of three different types of cancer biomarkers.

There has been active interest to identify new methods to reduce CO 2 into usable fuel sources. In this work, we demonstrate two types of photo-electrochemical cells (PECs) that photoreduce CO 2 directly to formate in aqueous solutions both in the presence and absence of external bias or additional electron sources. The photocathodes were either a CuFeO 2 /CuO electrode or a bilayer of CdTe on NiO, whereas the photoanode was a bilayer of NiO x on CdS. The PECs were characterized by using both electrochemistry and spectroscopy, and the products formed from CO 2 reduction were characterized and quantified by using 1 H NMR spectroscopy and ESI-MS. In addition, an organohydride catalyst was tested in conjunction with the PECs, which not only showed a significant gain of 85 times in CO 2 reduction (27 μm formate without the catalyst, 2.3 mm formate with it) compared to the NiO/CdTe photocathode system but could also generate methanol under an external bias (10 μm)., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A grand challenge for medicine is to develop tools to selectively image and treat diseased cells. Rare earth doped upconverting nanoparticles (UCNPs) have been extensively studied for imaging applications because of their ability to absorb near infrared radiation (NIR) and emit visible light, but these particles cannot induce therapy alone. Recently, we developed methods to couple the UCNPs to visible and NIR-absorbing gold nanostructures through nucleic acid interactions. Here, we show that gold-UCNP clusters with optimized plasmon resonance and particle compositions provide both in vitro imaging contrast and combination cell killing through simultaneous photothermal (PTT) and photodynamic (PDT) therapy. PDT was induced by embedding singlet oxygen photosensitizers in silica shells on the UCNPs. Upon photoexcitation with 980 nm light, the NIR absorbing gold-UCNP clusters both increased the local temperature and generated singlet oxygen, increasing cell killing relative to either modality alone. The multifunctional polyethylene glycol (PEG) coated gold-NaYF 4 :Yb/Er clusters exhibited high biocompatibility without irradiation but synergistic cell killing of MCF-7 cancer cells under light excitation. Finally, we also demonstrate that an optimal gold plasmon resonance is critical for minimizing absorbance overlap with the photosensitizers.

Integrating non-enzymatic chemistry with living systems has the potential to greatly expand the types and yields of chemicals that can be sourced from renewable feedstocks. The in situ conversion of microbial metabolites to higher order products will ensure their continuous generation starting from a given cellular reaction mixture. We present here a systematic study of different organocatalysts that enable aldol condensation in biological media under physiological conditions of neutral pH, moderate temperature, and ambient pressure. The relative toxicities of each catalyst were tested against bacteria, and the catalysts were found to provide good yields of homoaldol products in bacterial cultures containing aldehydes. Lastly, we demonstrate that a biocompatible oil can be used to selectively extract the upgraded products, which enabes facile isolation and decreases the product toxicity to microbes.

Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on photoluminescence. These studies showed that while UCNP fluorescence enhancement was observed from the AuNPs conjugated UCNPs, AuNSs tended to quench fluorescence. However, conjugating lower ratios of AuNSs to UCNPs led to reduced quenching. Simulation studies both confirmed the experimental results and demonstrated that the orientation and distance of the UCNP with respect to the core and arms of the gold nanostructures played a significant role in PL. In addition, the AuNS-UCNP assemblies were able to cause rapid gains in temperature of the surrounding medium enabling their potential use as a photoimaging-photodynamic-photothermal agent.

A wide range of inorganic nanostructures have been used as photocatalysts for generating H2. To increase activity, Z-scheme photocatalytic systems have been implemented that use multiple types of photoactive materials and electron mediators. Optimal catalysis has previously been obtained by interfacing different materials through aggregation or epitaxial nucleation, all of which lowers the accessible active surface area. DNA has now been used as a structure-directing agent to organize TiO2 and CdS nanocrystals. A significant increase in H2 production compared to CdS or TiO2 alone was thus observed directly in solution with no sacrificial donors or applied bias. The inclusion of benzoquinone (BQ) equidistant between the TiO2 and CdS through DNA assembly further increased H2 production. While the use of a second quinone in conjunction with BQ showed no more improvement, its location within the Z-scheme was found to strongly influence catalysis., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In this work, isothermal rolling circle amplification (RCA) of the multi-kilobase genome of engineered filamentous bacteriophage is used to report the presence and identification of specific protein analytes in solution. First, bacteriophages were chosen as sensing platforms because peptides or antibodies that bind medically relevant targets can be isolated through phage display or expressed as fusions to their p3 and p8 coat proteins. Second, the circular, single-stranded genome contained within the phage serves as a natural large DNA template for a RCA reaction to rapidly generate exponential amounts of double stranded DNA in a single isothermal step that can be easily detected using low-cost fluorescent nucleic acid stains. Amplifying the entire phage genome also provides high detection sensitivities. Furthermore, since the sequence of the viral DNA can be easily modified with multiple restriction enzyme sites, a simple DNA digest can be applied to detect and identify multiple antigens simultaneously. The methods developed here will lead to protein sensors that are highly scalable to produce, can be run without complex biological equipment and do not require the use of multiple antibodies or high-cost fluorescent DNA probes or nucleotides.

Electrostatic assembly is used here to couple CdS nanorods with Co3 O4 nanoparticles into photocatalytic systems that simultaneously oxidize water and mediate electron transfer. Layered films of CdS nanorods and Co3 O4 nanoparticles are first used to generate high photo-currents electrochemically as opposed to CdS or Co3 O4 alone. Dispersed clusters of CdS nanorods conjugated with Co3 O4 nanoparticles are next shown to efficiently oxidize water and reduce methylene blue in solution., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

For early detection of many diseases, it is critical to be able to diagnose small amounts of biomarkers in blood or serum. One of the most widely used sensing assays is the enzyme-linked immunosorbent assay (ELISA), which typically uses detection monoclonal antibodies conjugated to enzymes to produce colorimetric signals. To increase the overall sensitivities of these sensors, we demonstrate the use of a dually modified version of filamentous bacteriophage Fd that produces significantly higher colorimetric signals in ELISAs than what can be achieved using antibodies alone. Because only a few proteins at the tip of the micron-long bacteriophage are involved in antigen binding, the approximately 4000 other coat proteins can be augmented-by either chemical functionalization or genetic engineering-with hundreds to thousands of functional groups. In this article, we demonstrate the use of bacteriophage that bear a large genomic fusion that allows them to bind specific antibodies on coat protein 3 (p3) and multiple biotin groups on coat protein 8 (p8) to bind to avidin-conjugated enzymes. In direct ELISAs, the anti-rTNFα (recombinant human tumor necrosis factor alpha)-conjugated bacteriophage show approximately 3- to 4-fold gains in signal over that of anti-rTNFα, demonstrating their use as a platform for highly sensitive protein detection., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Studies focused on understanding the role of matrix biophysical signals on cells, especially those when cells are encapsulated in hydrogels that are locally remodelled, are often complicated by appropriate methods to measure differences between the bulk and local material properties. From this perspective, stress-relaxing materials that allow long-term culture of embedded cells provide an opportunity to elucidate aspects of this biophysical signalling. In particular, rheological characterization of the stress relaxation properties allows one to link a bulk material measurement to local aspects of cellular functions by quantifying the corresponding cellular forces that must be applied locally. Here, embryonic stem cell-derived motor neurons were encapsulated in a well-characterized covalently adaptable bis-aliphatic hydrazone crosslinked PEG hydrogel, and neurite outgrowth was observed over time. Using fundamental physical relationships describing classical mechanics and viscoelastic materials, we calculated the forces and energies involved in neurite extension, the results of which provide insight to the role of biophysical cues on this process.

The development of strategies to couple biomolecules covalently to surfaces is necessary for constructing sensing arrays for biological and biomedical applications. One attractive conjugation reaction is hydrazone formation--the reaction of a hydrazine with an aldehyde or ketone--as both hydrazines and aldehydes/ketones are largely bioorthogonal, which makes this particular reaction suitable for conjugating biomolecules to a variety of substrates. We show that the mild reaction conditions afforded by hydrazone conjugation enable the conjugation of DNA and proteins to the substrate surface in significantly higher yields than can be achieved with traditional bioconjugation techniques, such as maleimide chemistry. Next, we designed and synthesized a photocaged aryl ketone that can be conjugated to a surface and photochemically activated to provide a suitable partner for subsequent hydrazone formation between the surface-anchored ketone and DNA- or protein-hydrazines. Finally, we exploit the latent functionality of the photocaged ketone and pattern multiple biomolecules on the same substrate, effectively demonstrating a strategy for designing substrates with well-defined domains of different biomolecules. We expect that this approach can be extended to the production of multiplexed assays by using an appropriate mask with sequential photoexposure and biomolecule conjugation steps.

Crystalline silicon nanotubes (Si NTs) provide distinctive advantages as electrical and biochemical analysis scaffolds through their unique morphology and electrical tunability compared to solid nanowires or amorphous/non-conductive nanotubes. Such potential is investigated in this report. Gate-dependent four-probe current-voltage analysis reveals electrical properties such as resistivity to differ by nearly 3 orders of magnitude between crystalline and amorphous Si NTs. Analysis of transistor transfer characteristics yields a field effect mobility of 40.0 cm(2) V(-1) s(-1) in crystalline Si NTs. The hollow morphology also allows selective inner/outer surface functionalization and loading capability either as a carrier for molecular targets or as a nanofluidic channel for biomolecular assays. We present for the first time a demonstration of internalization of fluorescent dyes (rhodamine) and biomolecules (BSA) in Si NTs as long as 22 μm in length.

We report the effect of DNA-templation on aniline-catalyzed N-acylhydrazone formation. The reaction occurs in both two-component and three-component systems. Through systematic catalyst modifications, we are able to increase the efficiency of the DNA-templated variant to 85-fold above that of the uncatalyzed reaction at physiological pH.

Presented here is a cytocompatible covalently adaptable hydrogel uniquely capable of mimicking the complex biophysical properties of native tissue and enabling natural cell functions without matrix degradation. Demonstrated is both the ability to control elastic modulus and stress relaxation time constants by more than an order of magnitude while predicting these values based on fundamental theoretical understanding and the simulation of muscle tissue and the encapsulation of myoblasts., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The use of microbubbles as ultrasound contrast agents is one of the primary methods to diagnose deep venous thrombosis. However, current microbubble imaging strategies require either a clot sufficiently large to produce a circulation filling defect or a clot with sufficient vascularization to allow for targeted accumulation of contrast agents. Previously, we reported the design of a microbubble formulation that modulated its ability to generate ultrasound contrast from interaction with thrombin through incorporation of aptamer-containing DNA crosslinks in the encapsulating shell, enabling the measurement of a local chemical environment by changes in acoustic activity. However, this contrast agent lacked sufficient stability and lifetime in blood to be used as a diagnostic tool. Here we describe a PEG-stabilized, thrombin-activated microbubble (PSTA-MB) with sufficient stability to be used in vivo in circulation with no change in biomarker sensitivity. In the presence of actively clotting blood, PSTA-MBs showed a 5-fold increase in acoustic activity. Specificity for the presence of thrombin and stability under constant shear flow were demonstrated in a home-built in vitro model. Finally, PSTA-MBs were able to detect the presence of an active clot within the vena cava of a rabbit sufficiently small as to not be visible by current non-specific contrast agents. By activating in non-occlusive environments, these contrast agents will be able to detect clots not diagnosable by current contrast agents., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

We demonstrate here a DNA-based conformationally switchable nanodumbell structure that modulates the interparticle distance between two gold-silver core-shell nanoparticles to induce significant changes in the SERS signal.

While the remarkable chemical and biological properties of DNA have been known for decades, these properties have only been imparted into materials with unprecedented function much more recently. The inimitable ability of DNA to form programmable, complex assemblies through stable, specific, and reversible molecular recognition has allowed the creation of new materials through DNA's ability to control a material's architecture and properties. In this review we discuss recent progress in how DNA has brought unmatched function to materials, focusing specifically on new advances in delivery agents, devices, and sensors.

We report the synthesis, characterization, and protein sensing capabilities of M13 bacteriophage-DNA bioconjugates. DNA oligonucleotides were conjugated to M13 through acyl hydrazone linkages. In one case, DNAzymes retained their catalytic ability when anchored to the virus coat, and in a separate study, the dynamic nature of the hydrazone allowed for liberation of DNA from the phage under mild conditions.

Nanodumbbell gold nanoparticle (AuNP) dimers connected by DNA show significant change in interparticle distance in the presence of a specific analyte, ATP. The nanodumbbell begins in an extended state, but after the addition of the analyte, the DNA connecting the AuNPs forms a stable hairpin, which causes a large decrease in the interparticle distance., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Thrombosis, or malignant blood clotting, is associated with numerous cardiovascular diseases and cancers. A microbubble contrast agent is presented that produces ultrasound harmonic signal only when exposed to elevated thrombin levels. Initially silent microbubbles are activated in the presence of both thrombin-spiked and freshly clotting blood in three minutes with detection limits of 20 nM thrombin and 2 aM microbubbles., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Sensitive protein detection and accurate identification continues to be in great demand for disease screening in clinical and laboratory settings. For these diagnostics to be of clinical value, it is necessary to develop sensors that have high sensitivity but favorable cost-to-benefit ratios. However, many of these sensing platforms are thermally unstable or require significant materials synthesis, engineering, or fabrication. Recently, we demonstrated that naturally occurring M13 bacteriophage can serve as biological scaffolds for engineering protein diagnostics. These viruses have five copies of the pIII protein, which can bind specifically to target antigens, and thousands of pVIII coat proteins, which can be genetically or chemically modified to react with signal-producing materials, such as plasmon-shifting gold nanoparticles (Au NPs). In this report, we show that DNA-conjugated M13 bacteriophage can act as inexpensive protein sensors that can rapidly induce a color change in the presence of a target protein yet also offer the ability to identify the detected antigen in a separate step. Many copies of a specific DNA oligonucleotide were appended to each virus to create phage-DNA conjugates that can hybridize with DNA-conjugated gold nanoparticles. In the case of a colorimetric positive result, the identity of the antigen can also be easily determined by using a DNA microarray. This saves precious resources by establishing a rapid, quantitative method to first screen for the presence of antigen followed by a highly specific typing assay if necessary.

Large-area films of vertically-aligned semiconductor nanorods have the potential to be useful, active materials for optoelectronic devices. We demonstrate here a highly facile thermal annealing approach for reversibly assembling 28 nm long CdSe nanorods into vertically aligned arrays in solution. Using temperature to control solvent strength, aggregated nanorods in a marginally poor solvent mixture were first dispersed at elevated temperatures and then reassembled into freely suspended, ordered sheets of aligned nanorods up to 24 μm in diameter upon slow cooling. The assembly method was tolerant of nanorod polydispersity and was effective over a wide range of solvents and nanorod concentrations. The pre-assembled nanorods could be directly drop-cast from solution onto a substrate and rapidly dried to obtain a film of vertically aligned nanorods., (This journal is © The Royal Society of Chemistry 2012)