Editorial

3 pages, 154 KiB

Open AccessEditorial

Special Issue “Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—A Themed Issue in Honor of Prof. Dr. Itamar Willner”

by Di Li

Chemistry 2024, 6(1), 95-97; https://doi.org/10.3390/chemistry6010006 - 11 Jan 2024

Viewed by 538

Abstract

This Special Issue of Chemistry is a themed issue of “Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications” in honor of Itamar Willner to celebrate his innovative research career [...] Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

Research

Jump to: Editorial, Review

12 pages, 2257 KiB

Open AccessArticle

Condensed DNA Nanosphere for DNA Origami Cryptography

by Rui Gao, Zhuang Cai, Jianbang Wang and Huajie Liu

Chemistry 2023, 5(4), 2406-2417; https://doi.org/10.3390/chemistry5040159 - 08 Nov 2023

Viewed by 888

Abstract

Maintaining the confidentiality and integrity of the messages during a transmission is one of the most important aims of encrypted communication systems. Many achievements were made using biomolecules to improve the quality of the messages in communication. At the same time, it is [...] Read more.

Maintaining the confidentiality and integrity of the messages during a transmission is one of the most important aims of encrypted communication systems. Many achievements were made using biomolecules to improve the quality of the messages in communication. At the same time, it is still a challenge to construct cooperative communications based on the interactions between biomolecules to achieve the confidentiality and integrity of the transmitted messages. DNA-based encrypted communications have been developed, and in particular, DNA-origami-based message encryption can combine steganography and pattern encryption and exhibits extremely high confidentiality. Nevertheless, limited by biological characteristics, encrypted messages based on DNA require a strict storage environment in the process of transmission. The integrity of the message encoded in the DNA may be damaged when the DNA is in an unfriendly and hard environment. Therefore, it is particularly significant to improve the stability of DNA when it is exposed to a harsh environment during transmission. Here, we encoded the information into the DNA strands that were condensed for encryption to form a nanosphere covered with a shell of SiO₂, which brings high-density messages and exhibits higher stability than separated DNA. The solid shell of SiO₂ could prevent DNA from contacting the harsh environment, thereby protecting the DNA structure and maintaining the integrity of the information. At the same time, DNA nanospheres can achieve high throughput input and higher storage density per unit volume, which contribute to confusing the message strand (M-strand) with the interference strand in the stored information. Condensing DNA into the nanosphere that is used for DNA origami cryptography has the potential to be used in harsh conditions with higher confidentiality and integrity for the transmitted messages. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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13 pages, 3397 KiB

Open AccessArticle

High Thermal Stability of Enzyme-MOF Composites at 180 °C

by Shitong Cui and Jun Ge

Chemistry 2023, 5(3), 2025-2037; https://doi.org/10.3390/chemistry5030137 - 19 Sep 2023

Cited by 1 | Viewed by 1230

Abstract

Encapsulating enzymes in a tailored scaffold is of great potential in industrial enzymatic catalysis, which can enhance the stability of enzymes thus expanding their applications. Metal–organic frameworks (MOFs) are emerging as promising candidates for enzyme encapsulation due to their precise pore structure, ease [...] Read more.

Encapsulating enzymes in a tailored scaffold is of great potential in industrial enzymatic catalysis, which can enhance the stability of enzymes thus expanding their applications. Metal–organic frameworks (MOFs) are emerging as promising candidates for enzyme encapsulation due to their precise pore structure, ease of synthesis and good biocompatibility. Despite the fact that enzymes encapsulated in MOFs can obtain enhanced stability, there has been little discussion about the thermal stability of enzyme-MOF composites in solid state under extremely high temperatures. Herein, we fabricated the enzyme-MOF composites, CALB-ZIF-8, via a convenient coprecipitation method in aqueous solution, which exhibited good thermal stability at 180 °C. It was found that the activity of CALB encapsulated in ZIF-8 retained nearly ~80% after heating for 10 min at 180 °C. A finite element method was applied to investigate the heat transfer process within a ZIF-8 model, indicating that the air filled in cavities of ZIF-8 played a significant role in hindering the heat transfer and this may be an important reason for the outstanding thermal stability of CALB-ZIF-8 at 180 °C, which paves a new path for expanding the industrial application of enzyme-MOF composites. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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8 pages, 3708 KiB

Open AccessCommunication

Solid State Fabrication of Copper Nanoclusters and Supraparticles

by Rui Wang, Yunyun Zheng and Yunsheng Xia

Chemistry 2023, 5(3), 1990-1997; https://doi.org/10.3390/chemistry5030134 - 06 Sep 2023

Viewed by 1029

Abstract

In this study, we present solid state processes for the fabrication of copper nanoclusters (NCs) and hierarchical supraparticles (SPs). To achieve this, copper salt and thiols are mixed and are then grinded for 10–15 min, and the nano-products are thereby obtained. Interestingly, it [...] Read more.

In this study, we present solid state processes for the fabrication of copper nanoclusters (NCs) and hierarchical supraparticles (SPs). To achieve this, copper salt and thiols are mixed and are then grinded for 10–15 min, and the nano-products are thereby obtained. Interestingly, it was found in this study that the formation of the NCs or SPs is completely dependent on the grinding methods that are used: with mechanical grinding, the products are several nanometer-sized NCs, whereas manual grinding in an agate mortar can obtain Cu SPs with diameters as low as 10 nm all the way up to 200 nm. The photoluminescence emission wavelength of the nano-products is located at ~680 nm. The Stokes shift of the obtained nanomaterials is more than 300 nm. The emission quantum yields of the Cu NCs and SPs are as high as 47.5% and 63%, respectively. Due to their facile fabrication processes and their favorable optical properties, the two as-prepared types of copper nano-materials exhibit great potential for bio-imaging and bio-sensing applications. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 1627 KiB

Open AccessArticle

A Ratiometric Fluorescent Probe for pH Measurement over a Wide Range Composed of Three Types of Fluorophores Assembled on a DNA Scaffold

by Eiji Nakata, Khongorzul Gerelbaatar, Mashal Asif, Hiroaki Konishi, Yuya Shibano, Peng Lin and Takashi Morii

Chemistry 2023, 5(3), 1832-1842; https://doi.org/10.3390/chemistry5030125 - 17 Aug 2023

Viewed by 1167

Abstract

The desirable properties of the sophisticated fluorescent pH probe are ratiometric detection properties and a wide detection range. In this study, three types of fluorophores with different fluorescence properties were assembled on a DNA origami nanostructure. DNA nanostructure has the advantage of being [...] Read more.

The desirable properties of the sophisticated fluorescent pH probe are ratiometric detection properties and a wide detection range. In this study, three types of fluorophores with different fluorescence properties were assembled on a DNA origami nanostructure. DNA nanostructure has the advantage of being a scaffold that can assemble different types of fluorophores with control over their number and position. The defined number of three different fluorophores, i.e., pH-sensitive fluorescein (CF) and Oregon Green (OG), and pH-insensitive tetramethylrhodamine (CR), assembled on the DNA scaffold provided a ratiometric fluorescent pH probe with a wide pH detection range that could cover the variation of intracellular pH. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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15 pages, 1457 KiB

Open AccessFeature PaperArticle

Ratiometric Detection of Zn²⁺ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors

by Yuting Wu, Whitney Lewis, Jing Luen Wai, Mengyi Xiong, Jiao Zheng, Zhenglin Yang, Chloe Gordon, Ying Lu, Siu Yee New, Xiao-Bing Zhang and Yi Lu

Chemistry 2023, 5(3), 1745-1759; https://doi.org/10.3390/chemistry5030119 - 08 Aug 2023

Cited by 1 | Viewed by 2037

Abstract

While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer [...] Read more.

While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn²⁺ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permitted BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn²⁺ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn²⁺ in serum samples and achieved Zn²⁺ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 2432 KiB

Open AccessArticle

Construction of an ATP-Activated Y-Shape DNA Probe for Smart miRNA Imaging in Living Cells

by Wukun Zhong, Yanlin Zheng, Lei Huang, Chao Xing and Chunhua Lu

Chemistry 2023, 5(3), 1634-1644; https://doi.org/10.3390/chemistry5030112 - 27 Jul 2023

Viewed by 974

Abstract

A stringent DNA probe to profile microRNA (miRNA) expression within a specific cell remains a key challenge in biology. To address this issue, an intracellular ATP-activated Y-DNA probe for accurate imaging of miRNA in living cells was designed. Y-DNA was based on the [...] Read more.

A stringent DNA probe to profile microRNA (miRNA) expression within a specific cell remains a key challenge in biology. To address this issue, an intracellular ATP-activated Y-DNA probe for accurate imaging of miRNA in living cells was designed. Y-DNA was based on the fabrication of tripartite function modules, which consisted of a folate (FA)-modified targeting module, an ATP aptamer-sealed driver, and a miRNA sensing module. The Y-DNA probe could be specifically activated by ATP after it efficiently internalized into FA-receptor-overexpressed cells based on caveolar-mediated endocytosis, leading to the activation of the miRNA sensing module. The activated Y-DNA probe allowed for the imaging of miRNA in living cells with high sensitivity. The design of the ATP-activated Y-DNA sensor opens the door for bioorthogonal miRNA imaging and promotes the development of various responsive DNA molecular probes with enhanced anti-interference ability for clinical diagnosis. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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13 pages, 2517 KiB

Open AccessArticle

Constructing a Triangle Ensemble of Pt Clusters for Enhanced Direct-Pathway Electrocatalysis of Formic Acid Oxidation

by Cheng Li, Zheng Tang, Lanlan Shi, Yongjia Li, Yingjie Ji, Kaixin Zhang, Zhiyu Yang and Yi-Ming Yan

Chemistry 2023, 5(3), 1621-1633; https://doi.org/10.3390/chemistry5030111 - 26 Jul 2023

Cited by 1 | Viewed by 976

Abstract

The pursuit of operational advancements in direct formic acid fuel cells (DFAFCs) necessitates the development of high-performance platinum (Pt)-based catalysts for formic acid electrooxidation (FAOR). However, FAOR on Pt-based catalysts follows a dual pathway mechanism, in which the direct pathway is a preferred [...] Read more.

The pursuit of operational advancements in direct formic acid fuel cells (DFAFCs) necessitates the development of high-performance platinum (Pt)-based catalysts for formic acid electrooxidation (FAOR). However, FAOR on Pt-based catalysts follows a dual pathway mechanism, in which the direct pathway is a preferred route due to its efficient dehydrogenation process. Conversely, the indirect pathway results in the generation of adsorbed CO species, a process that deleteriously poisons the active sites of the catalyst, with CO species only being oxidizable at higher potentials, causing a significant compromise in catalyst performance. Herein, we have successfully synthesized Pt-C₃N₄@CNT, where three Pt clusters are precisely dispersed in a triplet form within the C₃N₄ by virtue of the unique structure of C₃N₄. The mass activity for the direct pathway (0.44 V) delivered a current density of 1.91 A

{mg}_{Pt}^{- 1}

, while the indirect pathway (0.86 V) had no obvious oxidation peak. The selectivity of Pt-C₃N₄@CNT catalysts for the direct pathway of FAOR was improved due to the special structure of C₃N₄, which facilitates the dispersion of Pt tri-atoms in the structure and the electronic interaction with Pt. In this study, we provide a new strategy for the development of highly active and selective catalysts for DFAFCs. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 3461 KiB

Open AccessArticle

Coupling 2-Aminopurine with DNA Copper Nanoparticles as a Rapid and Enzyme-Free System for Operating DNA Contrary Logic Pairs

by Jun Wang, Jiawen Han, Xujuan Lv, Jingyu Hou, Daoqing Fan and Shaojun Dong

Chemistry 2023, 5(3), 1577-1587; https://doi.org/10.3390/chemistry5030108 - 23 Jul 2023

Cited by 1 | Viewed by 1012

Abstract

Exploring affordable and efficient platform for innovative DNA computing is of great significance. Herein, by coupling 2-aminopurine (2AP) with DNA copper nanoparticles (CuNPs) as two universal opposite outputs, we, for the first time, fabricated a rapid and enzyme-free system for operating DNA contrary [...] Read more.

Exploring affordable and efficient platform for innovative DNA computing is of great significance. Herein, by coupling 2-aminopurine (2AP) with DNA copper nanoparticles (CuNPs) as two universal opposite outputs, we, for the first time, fabricated a rapid and enzyme-free system for operating DNA contrary logic pairs (D-CLPs). Notably, derived from the rapid and concomitant response of both fluorescent probes, different D-CLPs can be achieved via a “double-results-half-efforts” manner in less than 20 min with low-cost. Moreover, based on the same system, the smart ratiometric analysis of target DNA was realized by employing the high reliability and accuracy of D-CLPs, providing a robust and typical paradigm for the exploration of smart nucleic acid sensors. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 1255 KiB

Open AccessArticle

Photocatalytic Duplex-Based DNAzymes Switched by an Abasic Site

by Longlong Gao, Rui Tian and Yong Shao

Chemistry 2023, 5(3), 1497-1507; https://doi.org/10.3390/chemistry5030102 - 28 Jun 2023

Cited by 1 | Viewed by 945

Abstract

DNAzymes have attracted increasing interest in developments of gene tools, therapies, and biosensors. Among them, G-quadruplexes are widely used as the key structure elements of DNAzymes to activate the catalytic competency of specific cofactors, such as hemin, but there is a great demand [...] Read more.

DNAzymes have attracted increasing interest in developments of gene tools, therapies, and biosensors. Among them, G-quadruplexes are widely used as the key structure elements of DNAzymes to activate the catalytic competency of specific cofactors, such as hemin, but there is a great demand to diversify DNAzymes using other more straightforward DNA structures such as fully matched duplex (FM-DNA). However, the perfect base pairs in duplex limit the DNAzyme activity. In this work, a photocatalytic DNAzyme was developed by introducing an abasic site (AP site) into duplex (AP-DNA) to switch its photocatalytic activity. Palmatine (PAL), a photosensitizer from natural isoquinoline alkaloids, served as a cofactor of the DNAzyme by binding at the AP site. The AP site provides a less polarized environment to favor the PAL fluorescence. As a result, dissolved oxygen was converted into singlet oxygen (¹O₂) via energy transfer from the excited PAL. The oxidation of substrates by the in situ photogenerated ¹O₂ served as a readout for the DNAzyme. In addition, the duplex-based DNAzyme was engineered from FM-DNA by the cascade uracil-DNA glycosylase to generate AP-DNA. Our work provides a new way to construct duplex-based DNAzymes. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 2926 KiB

Open AccessArticle

Rolling-Circle-Amplification-Assisted DNA Biosensors for Sensitive and Specific Detection of Hypochlorous Acid and Myeloperoxidase

by Bo Liu, Jia-Yi Ma, Jing Wang, Dong-Xia Wang, An-Na Tang and De-Ming Kong

Chemistry 2023, 5(2), 1454-1464; https://doi.org/10.3390/chemistry5020098 - 18 Jun 2023

Viewed by 1159

Abstract

Hypochlorous acid (HClO) is a common reactive oxygen species (ROS), with a high chemical reactivity. Myeloperoxidase (MPO) is an enzyme that catalyzes in vivo redox reactions between H₂O₂ and Cl⁻ to produce HClO. Abnormal levels of HClO and MPO [...] Read more.

Hypochlorous acid (HClO) is a common reactive oxygen species (ROS), with a high chemical reactivity. Myeloperoxidase (MPO) is an enzyme that catalyzes in vivo redox reactions between H₂O₂ and Cl⁻ to produce HClO. Abnormal levels of HClO and MPO may lead to oxidative stress, irreversible tissue damage and, thus, serious diseases; they are thus becoming important biomarkers and therapeutic targets. In this work, using HClO-induced site-specific cleavage of phosphorothioate-modified DNA to trigger rolling circle amplification (RCA), RCA-assisted biosensors have been developed for the highly sensitive and specific detection of HClO and MPO. Only two DNA oligonucleotides are used in the sensing systems. The powerful signal-amplification capability of RCA endows the sensing systems with a high sensitivity, and the specific fluorescent response of thioflavin T (ThT) to G-quadruplexes in RCA products makes a label-free signal output possible. The proposed biosensors were demonstrated to work well not only for the sensitive and specific quantitation of HClO and MPO with detection limits of 1.67 nM and 0.33 ng/mL, respectively, but also for the screening and inhibitory capacity evaluation of MPO inhibitors, thus holding great promise in disease diagnosis and drug analysis. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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15 pages, 3783 KiB

Open AccessFeature PaperArticle

Fe Doping Enhances the Peroxidase-Like Activity of CuO for Ascorbic Acid Sensing

by Boyu Yan, Ying Yang, Yinyun Xie, Jinzhao Li and Kun Li

Chemistry 2023, 5(2), 1302-1316; https://doi.org/10.3390/chemistry5020088 - 23 May 2023

Cited by 1 | Viewed by 1657

Abstract

Although significant advances have been witnessed in the application of nanozymes in recent years, exploring new strategies to enhance the enzyme-like activity of nanozymes is of urgent importance. Herein, we investigate the feasibility of accelerating the peroxidase-like reaction rate of CuO nanostructures through [...] Read more.

Although significant advances have been witnessed in the application of nanozymes in recent years, exploring new strategies to enhance the enzyme-like activity of nanozymes is of urgent importance. Herein, we investigate the feasibility of accelerating the peroxidase-like reaction rate of CuO nanostructures through Fe doping. The coprecipitation method was used to synthesize Fe-doped CuO (Fe-CuO) nanozymes, and the results indicate that the diversified valence of Fe benefits the redox reaction driven by CuO-based nanozymes. With the improved peroxidase-like activity, the Fe-CuO nanozyme enables the significant chromogenic oxidation reaction of 3,3′,5,5′-tetramethylbenzidine (TMB), facilitating the construction of a visual sensing platform for the sensitive and selective determination of ascorbic acid. Under optimal conditions, the absorbance at 652 nm decreases linearly with the concentration of ascorbic acid in the range of 5–50 μM, with a limit of detection as low as 4.66 μM. This work exemplifies the activity enhancement for peroxidase-mimicking nanozymes with a metal-doping strategy and provides a broad prospect for the design of more high-performance nanozymes for biosensing applications. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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11 pages, 2716 KiB

Open AccessArticle

Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics

by Yang Zhou and Juewen Liu

Chemistry 2023, 5(2), 789-799; https://doi.org/10.3390/chemistry5020056 - 04 Apr 2023

Cited by 1 | Viewed by 1562

Abstract

Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This [...] Read more.

Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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Review

Jump to: Editorial, Research

23 pages, 4651 KiB

Open AccessReview

Recent Advances in the Preparation and Application of DNA-Encoded Metal Nanoclusters

by Fang Yin, Jiangtao Ren and Erkang Wang

Chemistry 2023, 5(4), 2418-2440; https://doi.org/10.3390/chemistry5040160 - 10 Nov 2023

Viewed by 862

Abstract

DNA as an intriguing organic ligand has been widely employed for synthesizing metal nanoclusters and engineering their properties. This review aims to present recent progress on DNA-encoded metal (Ag, Cu, Au, Ag/Pt, Cu/Ag, etc.) nanoclusters (DNA-MNCs), focusing on their applications in the fields [...] Read more.

DNA as an intriguing organic ligand has been widely employed for synthesizing metal nanoclusters and engineering their properties. This review aims to present recent progress on DNA-encoded metal (Ag, Cu, Au, Ag/Pt, Cu/Ag, etc.) nanoclusters (DNA-MNCs), focusing on their applications in the fields of analysis, logic operation, and therapy based on properties including fluorescence, electrochemiluminescence (ECL), and antibacterial and catalytic activity, and summarizes the attractive features of the latest research. The key points are briefly described as follows. (1) Analytical systems have been constructed based on fluorescence regulation, and nuclease-assisted and enzyme-free amplification strategies have been extensively adopted with fluorescent DNA-MNCs for amplified analysis. (2) DNA-MNCs may play more than one role (emitter, quencher, or catalyst) in ECL-based analytical systems. (3) Apart from antibacterial activity, DNA-MNCs also possess apparent catalytic capability, such as enzyme-like activity (i.e., nanozymes), which has been applied in colorimetric systems. (4) Reversibly regulating the catalytic activity of DNA-MNCs has been attained with DNA systems. It is believed that through in-depth investigation of the relationship between atomic structure and property, more novel DNA-MNCs will be explored and applied in the future. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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23 pages, 7815 KiB

Open AccessReview

Responsive DNA Nanostructures for Bioanalysis and Therapy

by Yingfei Wang, Yue Zhang, Huangxian Ju and Ying Liu

Chemistry 2023, 5(4), 2182-2204; https://doi.org/10.3390/chemistry5040147 - 13 Oct 2023

Cited by 1 | Viewed by 1019

Abstract

DNA nanostructures have been widely explored as an encouraging tool for bioanalysis and cancer therapy due to its structural programmability and good biocompatibility. The incorporation of stimulus-responsive modules enables the accurate targeting and flexible control of structure and morphology, which is benefit to [...] Read more.

DNA nanostructures have been widely explored as an encouraging tool for bioanalysis and cancer therapy due to its structural programmability and good biocompatibility. The incorporation of stimulus-responsive modules enables the accurate targeting and flexible control of structure and morphology, which is benefit to precise bioanalysis and therapy. This mini review briefly discusses the advancements in stimuli-responsive DNA nanostructures construction and their applications in biomolecules sensing and cancer treatment. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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29 pages, 10492 KiB

Open AccessReview

Self-Assembled DNA Nanospheres: Design and Applications

by Jing Li, Xiaojun Liu, Jiaoli Wang, Qi Jiang, Minhui Chen, Wei Zhang, Yu Chen, Ying Pu and Jin Huang

Chemistry 2023, 5(3), 1882-1910; https://doi.org/10.3390/chemistry5030129 - 29 Aug 2023

Viewed by 1544

Abstract

Self-assembled DNA nanospheres, as versatile and ideal vehicles, have offered new opportunities to create intelligent delivery systems for precise bioimaging and cancer therapy, due to their good biostability and cell permeability, large loading capacity, and programmable self–assembly behaviors. DNA nanospheres can be synthesized [...] Read more.

Self-assembled DNA nanospheres, as versatile and ideal vehicles, have offered new opportunities to create intelligent delivery systems for precise bioimaging and cancer therapy, due to their good biostability and cell permeability, large loading capacity, and programmable self–assembly behaviors. DNA nanospheres can be synthesized by the self–assembly of Y–shaped DNA monomers, ultra–long single-stranded DNA (ssDNA), and even metal–DNA coordination. Interestingly, they are size–controllable by varying some parameters including concentration, reaction time, and mixing ratio. This review summarizes the design of DNA nanospheres and their extensive biomedical applications. First, the characteristics of DNA are briefly introduced, and different DNA nanostructures are mentioned. Then, the design of DNA nanospheres is emphasized and classified into three main categories, including Y–shaped DNA unit self-assembly by Watson–Crick base pairing, liquid crystallization and the dense packaging of ultra–long DNA strands generated via rolling circle amplification (RCA), and metal–DNA coordination–driven hybrids. Meanwhile, the advantages and disadvantages of different self–assembled DNA nanospheres are discussed, respectively. Next, the biomedical applications of DNA nanospheres are mainly focused on. Especially, DNA nanospheres serve as promising nanocarriers to deliver functional nucleic acids and drugs for biosensing, bioimaging, and therapeutics. Finally, the current challenges and perspectives for self-assembled DNA nanospheres in the future are provided. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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17 pages, 3648 KiB

Open AccessReview

DNA Nanotechnology-Empowered Fluorescence Imaging of APE1 Activity

by Hui He, Xiaojun Liu, Yuchen Wu, Lanlin Qi, Jin Huang, Yan Zhou, Jiahao Zeng, Kemin Wang and Xiaoxiao He

Chemistry 2023, 5(3), 1815-1831; https://doi.org/10.3390/chemistry5030124 - 17 Aug 2023

Viewed by 1492

Abstract

Apurinic/apyrimidinic endonuclease 1 (APE1), also known as redox factor-1 (Ref-1), is a multifunctional protein that exists widely in living organisms. It can specifically recognize and cleave the DNA in apurinic/apyrimidinic (AP) sites in the base excision repair (BER) pathway, as well as regulate [...] Read more.

Apurinic/apyrimidinic endonuclease 1 (APE1), also known as redox factor-1 (Ref-1), is a multifunctional protein that exists widely in living organisms. It can specifically recognize and cleave the DNA in apurinic/apyrimidinic (AP) sites in the base excision repair (BER) pathway, as well as regulate the expression of genes to activate some transcription factors. The abnormal expression and disruptions in the biological functions of APE1 are linked to a number of diseases, including inflammation, immunodeficiency, and cancer. Hence, it is extremely desired to monitor the activity of APE1, acquiring a thorough understanding of the healing process of damaged DNA and making clinical diagnoses. Thanks to the advent of DNA nanotechnology, some nanodevices are used to image the activity of APE1 with great sensitivity and simplicity. In this review, we will summarize developments in DNA-nanotechnology-empowered fluorescence imaging in recent years for APE1 activity according to different types of DNA probes, which are classified into linear DNA probes, composite DNA nanomaterials, and three-dimensional (3D) DNA nanostructures. We also highlight the future research directions in the field of APE1 activity imaging. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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23 pages, 5605 KiB

Open AccessReview

Recent Advances in Dynamic DNA Nanodevice

by Qin Fan, Linzi Yang and Jie Chao

Chemistry 2023, 5(3), 1781-1803; https://doi.org/10.3390/chemistry5030122 - 10 Aug 2023

Viewed by 1617

Abstract

DNA nanotechnology has been widely used to fabricate precise nanometer-scale machines. In particular, dynamic DNA nanodevices have demonstrated their ability to mimic molecular motions and fluctuations in bion-anomic systems. The elaborately designed DNA nanomachines can conduct a variety of motions and functions with [...] Read more.

DNA nanotechnology has been widely used to fabricate precise nanometer-scale machines. In particular, dynamic DNA nanodevices have demonstrated their ability to mimic molecular motions and fluctuations in bion-anomic systems. The elaborately designed DNA nanomachines can conduct a variety of motions and functions with the input of specific commands. A dynamic DNA nanodevice with excellent rigidity and unprecedented processability allows for structural transformation or predictable behavior, showing great potential in tackling single-molecule sensing, drug delivery, molecular systems, and so on. Here, we first briefly introduce the development history of DNA nanotechnology. The driving energy of dynamic DNA nanomachines is also discussed with representative examples. The motor pattern of DNA nanomachines is classified into four parts including translational motion, shear motion, 360° rotation, and complex motion. This review aims to provide an overview of the latest reports on the dynamic DNA nanomachine and give a perspective on their future opportunities. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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23 pages, 5246 KiB

Open AccessReview

Peptide-Based Vectors for Gene Delivery

by Juan Yang and Guo-Feng Luo

Chemistry 2023, 5(3), 1696-1718; https://doi.org/10.3390/chemistry5030116 - 05 Aug 2023

Cited by 3 | Viewed by 1820

Abstract

Gene therapy is the ultimate therapeutic technology for diseases related to gene abnormality. However, the use of DNA alone has serious problems, such as poor stability and difficulty in entering target cells. The development of a safe and efficient gene delivery system is [...] Read more.

Gene therapy is the ultimate therapeutic technology for diseases related to gene abnormality. However, the use of DNA alone has serious problems, such as poor stability and difficulty in entering target cells. The development of a safe and efficient gene delivery system is the cornerstone of gene therapy. Of particular interest, multifunctional peptides are rationally designed as non-viral vectors for efficient gene delivery. As components of gene delivery vectors, these peptides play critically important roles in skeleton construction, the implementation of targeting strategies, cell membrane penetration, endosome rupture, and nuclear transport. In recent years, the research of functional peptide-based gene delivery vectors has made important progress in improving transfection efficiency. The latest research progress and future development direction of peptide-based gene delivery vectors are reviewed in this paper. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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25 pages, 6722 KiB

Open AccessReview

Aptamer-Based Immune Drug Systems (AptIDCs) Potentiating Cancer Immunotherapy

by Hongjie Xiong, Liu Liu, Xiaohui Liu, Hui Jiang and Xuemei Wang

Chemistry 2023, 5(3), 1656-1680; https://doi.org/10.3390/chemistry5030114 - 30 Jul 2023

Viewed by 1726

Abstract

Aptamers are artificial oligonucleotides with excellent molecule-targeting ability. Compared with monoclonal antibodies, aptamers have the advantages of low cost, no batch effect, and negligible immunogenicity, making them promising candidates for cancer immunotherapy. To date, a series of aptamer agonists/antagonists have been discovered and [...] Read more.

Aptamers are artificial oligonucleotides with excellent molecule-targeting ability. Compared with monoclonal antibodies, aptamers have the advantages of low cost, no batch effect, and negligible immunogenicity, making them promising candidates for cancer immunotherapy. To date, a series of aptamer agonists/antagonists have been discovered and directly used to activate immune response, such as immune checkpoint blockade, immune costimulation, and cytokine regulation. By incorporating both tumor- and immune cell-targeting aptamers, multivalent bispecific aptamers were designed to pursue high tumor affinity and enhanced immune efficacy. More importantly, benefiting from feasible chemical modification and programmability, aptamers can be engineered with diverse nanomaterials (e.g., liposomes, hydrogels) and even living immune cells (e.g., NK cells, T cells). These aptamer-based assemblies exhibit powerful capabilities in targeted cargo delivery, regulation of cell–cell interactions, tumor immunogenicity activation, tumor microenvironment remodeling, etc., holding huge potential in boosting immunotherapeutic efficacy. In this review, we focus on the recent advances in aptamer-based immune drug systems (AptIDCs) and highlight their advantages in cancer immunotherapy. The current challenges and future prospects of this field are also pointed out in this paper. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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14 pages, 2346 KiB

Open AccessReview

DNA-Based Mechanical Sensors for Cell Applications

by Xiaoya Sun, Pengyan Hao and Na Wu

Chemistry 2023, 5(3), 1546-1559; https://doi.org/10.3390/chemistry5030106 - 19 Jul 2023

Cited by 2 | Viewed by 1268

Abstract

Cells constantly experience mechanical forces during growth and development. Increasing evidence suggests that mechanical forces can regulate cellular processes such as proliferation, migration, and differentiation. Therefore, developing new tools to measure and manipulate cellular mechanical forces is essential. DNA nanostructures, due to their [...] Read more.

Cells constantly experience mechanical forces during growth and development. Increasing evidence suggests that mechanical forces can regulate cellular processes such as proliferation, migration, and differentiation. Therefore, developing new tools to measure and manipulate cellular mechanical forces is essential. DNA nanostructures, due to their simple design and high programmability, have been utilized to create various mechanical sensors and have become a key tool for studying mechanical information in both cellular and non-cellular systems. In this article, we review the development of DNA-based mechanical sensors and their applications in measuring mechanical forces in the extracellular matrix and cell–cell interactions and summarize the latest advances in monitoring and manipulating cellular morphology and function. We hope that this review can provide insights for the development of new mechanical nanodevices. Full article

(This article belongs to the Special Issue Functional Biomolecule-Based Composites and Nanostructures: Current Developments and Applications—a Themed Issue in Honor of Prof. Dr. Itamar Willner)

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