Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

Modulation of antioxidant enzyme by light and heavy rare earth metals: A case study with catalase

The present study highlights the hazardous effect of heavy and light rare earth elements (REEs) on bovine liver catalase (BLC) using a combination of spectroscopic and computational methods. The presence of Praseodymium chloride (PrCl3) and Gadolinium chloride (GdCl3) resulted in a substantial reduction in catalytic efficiency of BLC by approximately 1.8 and 2.6 fold, respectively. The compromised activity was further accompanied by conformational rearrangements at the secondary and tertiary levels as evidenced by circular dichroism (CD) and fluorescence spectroscopy. These analyses revealed a significant decrease in α-helical content and a simultaneous increase in random coils, disrupting intramolecular hydrogen bonding. Furthermore, the zeta potential (ζ) of BLC demonstrated a reversal from negative to positive ζ values upon the addition of PrCl3 and GdCl3, indicating BLC-lanthanide complex formation. Isothermal titration calorimetry (ITC) supports spontaneous interaction with negative free energy favouring endothermic reaction. This was further supported by docking studies which revealed the binding of PrCl3 and GdCl3 within the active site of BLC thus interfering with the catalytic ability to degrade hydrogen peroxide (H2O2). Nevertheless, a significant decline in the melting temperature (Tm) of BLC was observed in the presence of lanthanides suggesting the thermal instability of the enzyme. Thus, a similar approach could be applied to evaluate the hazardous effects of lanthanides on structural and functional changes in other proteins or similar biomolecules.

Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials

DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.

Self-assembled DNA nanostructure containing oncogenic miRNA-mediated cell proliferation by downregulation of FOXO1 expression

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

Construction and Configuration Analysis of Zelkova Serrata Lenticel-Like Patterns Generated through DNA Algorithmic Self-Assembly

Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.

Configuration Analysis of a Lizard Skin-like Pattern Formed by DNA Self-Assembly

Nature manifests diverse and complicated patterns through efficient physical, chemical, and biological processes. One of the approaches to generate complex patterns, as well as simple patterns, is the use of the cellular automata algorithm. However, there are certain limitations to produce such patterns experimentally due to the difficulty of finding candidate programmable building blocks. Here, we demonstrated the feasibility of generating an ocellated lizard skin-like pattern by simulation considering the probabilistic occurrence of cells and constructed the simulation results on DNA lattices via bottom-up self-assembly. To understand the similarity between the simulated pattern (SP) and the observed pattern (OP) of lizard skin, a unique configuration scheme (unit configuration was composed of 7 cells) was conceived. SPs were generated through a computer with a controlling population of gray and black cells in a given pattern. Experimental patterns (EPs) on DNA lattices, consisting of double-crossover (DX) tiles without and with protruding hairpins, were fabricated and verified through atomic force microscopy (AFM). For analyzing the similarity of the patterns, we introduced deviation of the average configuration occurrence for SP and EP with respect to OP, i.e., σ_α(SO) and σ_α(EO). The configuration and deviation provide characteristic information of patterns. We recognized that the minimum values of <σ_α(SO)> and <σ_α(EO)> occurred when 50% (55%) of black cells in given SPs (DX tiles with hairpins in given EPs) appeared to be most similar to the OP. Our study provides a novel platform for the applicability of DNA molecules to systematically demonstrate other naturally existing complex patterns or processes with ease.

Biophysical interaction between self-assembled branched DNA nanostructures with bovine serum albumin and bovine liver catalase

Branched DNA (bDNA) nanostructures have emerged as self-assembled biomaterials and are being considered for biomedical applications. Herein, we report the biophysical interaction between self-assembled bDNA nanostructure with circulating protein bovine serum albumin (BSA) and cellular enzyme bovine liver catalase (BLC). The binding between bDNA and BSA or BLC was confirmed through the decrease in fluorescence spectra. The Stern-Volmer data supports for non-covalent bonding with ~1 binding site in case of BSA and BLC thus advocating a static binding. Furthermore, FTIR and ITC study confirmed the binding of bDNAs with proteins through hydrogen bonding and van der Waals interaction. The negative free energy observed in ITC represent spontaneous reaction for BLC-bDNA interaction. The biophysical interaction between bDNA nanostructures and proteins was also supported by DLS and zeta potential measurement. With an increase in bDNA concentrations up to 100 nM, no significant change in absorbance and CD spectra was observed for both BLC and BSA which suggests structural stability and unaffected secondary conformation of proteins in presence of bDNA. Furthermore, the catalytic activity of BLC was unaltered in presence of bDNAscr even with increasing the incubation period from 1 h to 24 h. Interestingly, the time-dependent decrease in activity of BLC was protected by bDNAmix. The thermal melting study suggests a higher Tm value for proteins in presence of bDNAmix which demonstrates that interaction with bDNAmix increases the thermal stability of proteins. Collectively these data suggest that self-assembled DNA nanostructure may bind to BSA for facilitating circulation in plasma or binding to intracellular proteins like BLC for stabilization, however the secondary conformation of protein or catalytic activity of enzyme is unaltered in presence of bDNA nanostructure. Thus, the newly established genomic sequence-driven self-assembled DNA nanostructure can be explored for in vitro or in vivo experimental work in recent future.

miRNA-mediated alteration of sulfatase modifying factor 1 expression using self-assembled branched DNA nanostructures

Sulfatase enzymes catalyze sulfate ester hydrolysis, thus deficiencies of sulfatases lead to the accumulation of biomolecules resulting in several disorders. One of the important sulfatases is estrone sulfatase that converts inactive estrone sulfate to active estradiol. Posttranslational modification of highly conserved cysteine residue leads to unique formylglycine in the active site of sulfatases being critical for its catalytic activity. The essential factor responsible for this modification of sulfatase is Sulfatase-Modifying Factor 1 (SUMF1). The role of estrone sulfatase is well evident in breast cancer progression. However, the function and regulation of SUMF1 in cancer are not studied. In the present study, for the first time, we have assessed the expression of SUMF1 in breast cancer and report the oncogenic behavior upon overexpression of SUMF1. Although increased expression or activity of SUMF1 is anticipated based on its function, the expression of SUMF1 was found to be reduced in breast cancer cells at both mRNA and protein levels. An estrogen receptor (ER) dependent expression of SUMF1 was observed and higher SUMF1 expression is associated with improved breast cancer patient survival in ER-positive cases. However, high SUMF1 expression leads to reduced median survival in ER-negative breast cancer patients. Putative binding sites for miRNAs-106b-5p, 128-3p and 148b-3p were found at 3′-UTR of SUMF1. Since self-assembled branched DNA (bDNA) structures have emerged as a highly efficient strategy for targeting multiple miRNAs simultaneously, we studied the alteration in SUMF1 expression using bDNA nanostructures with a complementary sequence to miRNAs. The findings suggest the involvement of co-regulators and repressors in miRNA-mediated SUMF1 expression in breast cancer cells and reveal the therapeutic potential of SUMF1 in endocrine-related malignancies.

Reduced expression of SUMF1 was evidenced in MCF-7 cells transfected with antimiR-bDNA. Expression of miRNA-106 and 148 have positive correlation with the expression of SUMF1. miRNA-106 and 148 blocks the repressor protein controls SUMF-1 expression.

Bioinspired pyrimidine-containing cationic polymers as effective nanocarriers for DNA and protein delivery

Cationic polymers have shown great potential in the delivery of nucleic acids and proteins. In this study, a series of pyrimidine-based cationic polymers were synthesized via the Michael addition reaction from pyrimidine-based linkages and low molecular weight polyethyleneimine (PEI). The structure-activity relationship (SAR) of these materials in DNA and protein delivery was investigated. These materials could condense both DNA and protein into nanoparticles with proper sizes and zeta-potentials. In vitro experiments indicated that such polymers were efficient in transporting DNA and proteins into cells. Furthermore, the bioactivity of the genes and proteins encapsulated in these polymers were maintained during the delivery processes. Among the polymers, U-PEI600 synthesized from a uracil-containing linker and PEI 600 Da mediated comparable gene expression to PEI 25 kDa. Moreover, the activities of β-galactosidase delivered by U-PEI600 were well maintained after entering the cells. Evaluation using an immune response assay showed that the U-PEI600/OVA polyplex could stimulate greater production of immune factors with low cytotoxicity. Our study provides a strategy for the construction of cationic polymeric gene and cytosolic protein vectors with high efficiency and low toxicity.

Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications

Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.

The design and biomedical applications of self-assembled two-dimensional organic biomaterials

Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.

Streptavidin-Decorated Algorithmic DNA Lattices Constructed by Substrate-Assisted Growth Method

The ultimate goal of DNA computing is to store information at higher density and solve complex problems with less computational time and minimal error. Most algorithmic DNA lattices have been constructed using the free-solution growth (FSG) annealing method, and hairpin-embedded DNA rule tiles have been introduced in most algorithmic implementations to differentiate 0- and 1-bit information. Here, we developed streptavidin (SA)-decorated algorithmic COPY (produced line-like patterns with biotinylated 1-bit rule tiles) and XOR (triangle-like patterns) lattices constructed by a substrate-assisted growth (SAG) method and FSG. SA decoration in algorithmic lattices provides an efficient platform for visualizing bit information, and the SAG method in algorithmic assembly offers full coverage of algorithmic lattices on a substrate with a relatively lower DNA concentration than previous methods. The algorithmic COPY and XOR lattices assembled with various ratios of 0- and 1-bit rule tiles were verified by atomic force microscopy. We found that even asymmetric DNA patterns produced by certain algorithmic logic gates could be easily constructed by SAG. Finally, we evaluated sorting factors and error rates of algorithmic COPY and XOR lattices to determine the bit population and quality of the algorithmic assembly. Because of the catalytic effect of the substrate, the sorting factor of algorithmic DX-DNA lattices did not greatly influence the specific rules (i.e., COPY and XOR logic gates) annealed by SAG. Additionally, we found that the overall error rates of algorithmic DX-DNA lattices prepared by the FSG and SAG methods were low, within the range of 1-3%. Hence, the self-assembled algorithmic patterns generated with DNA molecules may serve as a scaffold for molecular demultiplexing circuits and computing.

Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials

The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.