Article
Chemistry, Analytical
Yike Huang, Yugao Xu, Min Wang, Xiaoya Fu, Ya Chen, Ting Hu, Gang Feng, Chao Yu, Zhining Xia
Summary: In this study, a strategy of selecting templates for class-selective molecular-imprinted polymers (MIPs) is proposed to improve the recognition ability. Computational simulation is used to compare the spatial size and binding energy of different genotoxic impurities (GTI). By shortening the width to increase similarity in binding energy and size, dual templates in two GTI families are successfully selected. The prepared dual-template MIPs show higher recognition efficiency and can simultaneously recognize all the GTIs in their respective families compared to single-template MIPs.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Elena Lenci, Lorenzo Baldini, Andrea Trabocchi
Summary: DNA-encoded libraries (DEL) are a powerful technology for drug discovery, but their exploration of chemical space is limited by DNA-compatible chemistry and synthetic methodologies, while the application of Diversity-Oriented Synthesis can significantly broaden this space.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Ryan M. Williams, Shi Chen, Rachel E. Langenbacher, Thomas V. Galassi, Jackson D. Harvey, Prakrit V. Jena, Januka Budhathoki-Uprety, Minkui Luo, Daniel A. Heller
Summary: Although nanotechnology is often utilized in the biomedical field, it can also aid in broad biological discoveries. There is currently opportunity for collaboration between chemical biologists and nanotechnologists, with nanotechnology expanding the utility of chemical tools and chemical biologists working with nanotechnologists to tackle challenging biological questions.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Antonie J. van der Zouwen, Martin D. Witte
Summary: Combining combinatorial and modular methods to synthesize small molecule modulators of protein activity has proven to be a powerful tool in developing new drug-like molecules. These methodologies have been adapted for the development of chemical probes and chemoproteomic profiling, providing new ways to screen novel chemical probes against proteins of interest.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemical Research Methods
Li Fu, Zi-Yi Yang, Zhi-Jiang Yang, Ming-Zhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Ting-Jun Hou, Dong-Sheng Cao
Summary: The research team developed a new strategy (QSAR-assisted-MMPA) to expand the number of chemical transformations in matched molecular pairs analysis by establishing a reliable prediction model and strict data screening. They found that the method is useful for deriving more chemical rules, and has the potential to enrich rule types or even identify completely novel rules.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Basem Al-Shayeb, Marie C. Schoelmerich, Jacob West-Roberts, Luis E. Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J. Wilkins, Kenneth H. Williams, Jennifer A. Doudna, Jillian F. Banfield
Summary: Anaerobic methane oxidation is controlled by large, diverse DNA sequences called 'Borgs' that provide Methanoperedens archaea with access to key genes involved in redox reactions and energy conservation. These Borgs play a crucial role in the metabolism of Methanoperedens archaea, which could impact greenhouse gas emissions, highlighting the need for further research to establish their functional relevance.
Review
Biotechnology & Applied Microbiology
Chiara Guidi, Xevi Biarnes, Antoni Planas, Marjan De Mey
Summary: Glycosyltransferases (GT) catalyze the biosynthesis of complex carbohydrates, playing important roles in many cellular mechanisms. Understanding the mechanism of GTs is valuable for studying the structure-function relationships and improving enzyme engineering for various applications. This review focuses on the recent advances in understanding processive enzymes and their engineering strategies, as well as the chain length-controlling mechanisms in both eukaryotic and prokaryotic enzymes.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Chemistry, Multidisciplinary
Ruiqi Liang, Qingliang Song, Ruipeng Li, An N. Le, Xiaowei Fu, Yazhen Xue, Xiaoyu Ji, Weihua Li, Mingjiang Zhong
Summary: In this study, a scalable and diversity-oriented synthetic approach is reported for the fabrication of hierarchically structured nanomaterials. By arranging and combining the same set of building blocks in different ways, diverse morphologies in the resultant structures can be achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Polymer Science
Xinxin Tan, Jie Du, Yiliu Liu, Jingwen Ba, Xiaoyu Yang, Xiwen Yang, Meifang Liu, Wenhua Luo
Summary: In this study, the concept of supramolecular polymers is introduced to develop new deuterated materials for applications in inertial confinement fusion. Supramolecular deuterated polymers are formed through hydrogen-bonding mediated supramolecular polymerization, and uniform polymer shells are prepared for ICF experiments.
Article
Multidisciplinary Sciences
Qingdi Hu, Renjuan Qian, Yanjun Zhang, Xiaohua Ma, Youju Ye, Xule Zhang, Lin Lin, Hongjian Liu, Jian Zheng
Summary: This study analyzed the complete chloroplast genome of Sphaeropteris lepifera and compared it with previously published chloroplast genomes of Cyatheaceae family. The results showed that S. lepifera has a chloroplast genome with a length of 162,114 bp, encoding 129 genes, and differs from the genomes of other 7 Cyatheaceae plants. These findings provide a basis for species identification, biological studies, and understanding the endangerment mechanism of S. lepifera.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Sewon Oh, Erin E. Stache
Summary: This study reports a technique for the chemical upcycling of polystyrene into benzoyl products, primarily benzoic acid, through a catalyst-controlled photooxidative degradation method. The results demonstrate that this method is efficient in degrading polystyrene and producing targeted small molecule products.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Zhiyan Xi, Lloyd Davis, Kieran Baxter, Ailish Tynan, Angeliki Goutou, Sebastian Greiss
Summary: This article introduces a system that allows for genetic code expansion using quadruplet codons in multicellular organisms. The authors developed hybrid tRNA variants that can incorporate non-canonical amino acids in response to the quadruplet codon UAGA, and demonstrated the efficiency of the system.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Xinjia Li, Binbin Chen, Wanyi Chen, Zhongji Pu, Xin Qi, Lirong Yang, Jianping Wu, Haoran Yu
Summary: Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity is crucial for its wide applications. Multiple sequence alignment (MSA) is used to design TaqPol mutations and two double mutations are generated. Mutations targeted on coevolutionary residues are applied to rescue stability or activity loss, and a small-scale MSA is used to predict single variants with increased stability, activity, and sensitivity.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Bo Song, Dan Lu, Anjun Qin, Ben Zhong Tang
Summary: Scientists have developed a new method to synthesize sequence-defined macromolecules with high data storage density, offering new possibilities for applications in information encoding and encryption.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biotechnology & Applied Microbiology
Karen K. Gleason
Summary: This review focuses on the controlled release of pharmaceuticals and organic molecules using polymeric nanolayers grown by initiated chemical vapor deposition (iCVD). The technology allows for customization of reactors for various substrate geometries and can scale to large dimensions. iCVD layers can provide pinhole-free and ultrathin films, with rapid drug transport and mild conditions that avoid drug damage. Additionally, smart release is enabled by iCVD hydrogels responsive to pH, temperature, or light, and biodegradable iCVD layers have been demonstrated for drug release.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Qian Li, Jiemin Zhao, Longfei Liu, Sagun Jonchhe, Felix J. Rizzuto, Shankar Mandal, Huawei He, Sansen Wei, Hanadi F. Sleiman, Hanbin Mao, Chengde Mao
Review
Chemistry, Multidisciplinary
Aurelie Lacroix, Hanadi F. Sleiman
Summary: Despite the programmable assembly and precise control of size, shape, and function offered by DNA nanotechnology, challenges such as enzymatic hydrolysis, low cellular uptake, immune cell recognition and degradation, and unclear biodistribution profiles still need to be addressed before utilizing DNA particles in biological applications. Rigorous methodologies are necessary to study, understand, and control the fate of self-assembled DNA structures under physiological conditions. Achieving a detailed understanding of the fate of DNA nanostructures within living organisms through thorough characterization is crucial for driving the translation of DNA constructs toward preclinical design and clinical maturity.
Article
Chemistry, Multidisciplinary
Felix J. Rizzuto, Casey M. Platnich, Xin Luo, Yao Shen, Michael D. Dore, Christophe Lachance-Brais, Alba Guarne, Gonzalo Cosa, Hanadi F. Sleiman
Summary: The study demonstrates that slow proton dissipation can select for otherwise inaccessible morphologies of fibers built from DNA and cyanuric acid, influence the growth mechanism of supramolecular polymerization, and convert branched, interwoven networks into nanocable superstructures.
Article
Chemistry, Multidisciplinary
Christophe Lachance-Brais, Christopher D. Hennecker, Asem Alenaizan, Xin Luo, Violeta Toader, Monica Taing, C. David Sherrill, Anthony K. Mittermaier, Hanadi F. Sleiman
Summary: Nucleobase mimicking small molecules have been discovered as a strategy to reconfigure DNA, promising to extend the structural and functional diversity of nucleic acids. In this work, the addition of substituted cyanuric acid molecules successfully programmed polyadenine strands to assemble into supramolecular fibers, coating DNA triple helices with alkylamine or alcohol units. The study showed that small changes in the small molecule functional group can lead to large structural and energetic variations in the overall assembly, allowing for the controlled formation of hierarchical, hybrid DNA assemblies through the addition and variation of small, functionalized molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Daniel Saliba, Tuan Trinh, Christophe Lachance-Brais, Alexander L. Prinzen, Felix J. Rizzuto, Donatien de Rochambeau, Hanadi F. Sleiman
Summary: This research introduces a novel DNA nanotweezer that achieves simultaneous, asymmetric elongation of the molecular core through PCR, enabling the DNA tweezer to have a wider range of motion and the ability to respond to complex stimuli. The DNA nanotweezer can wrap around multiple streptavidin units, providing site-specific streptavidin recognition capability.
Article
Chemistry, Multidisciplinary
Felix J. Rizzuto, Michael D. Dore, Muhammad Ghufran Ra, Xin Luo, Hanadi F. Sleiman
Summary: The sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. Changing only the sequence of DNA can result in different structures, and the secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Tyler M. Brown, Hassan H. Fakih, Daniel Saliba, Jathavan Asohan, Hanadi F. Sleiman
Summary: A barrier for biological applications of DNA structures is their instability to nucleases. This study explores the use of UV-mediated thymine dimerization to crosslink and stabilize DNA nanostructures. The researchers compare different methods of DNA irradiation and show that all approaches can achieve nuclease protection, but with varying levels of off-target crosslinking and damage. They also demonstrate a mild irradiation condition that enhances serum stability while maintaining DNA function. This methodology has potential applications in nucleic acid therapy and nanotechnology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Muhammad Ghufran Rafique, Jacob M. M. Remington, Finley Clark, Haochen Bai, Violeta Toader, Dmytro F. F. Perepichka, Jianing Li, Hanadi F. F. Sleiman
Summary: The study focuses on the systematic research of polymer structure, pathway mechanism, and supramolecular morphology in order to assemble water-soluble block copolymers into two-dimensional structures. By using sequence-defined triblock DNA amphiphiles, the researchers successfully polymerized free-standing DNA nanosheets in water. They found that the alkyl chain core formed a cell membrane-like structure, and the distal pi-stacking chromophore block folded back to interact with the hydrophilic DNA block on the nanosheet surface. This interaction was crucial for sheet formation and showed sensitivity to DNA sequence. The findings open up possibilities for applications in cell sensing, nucleic acid therapeutic delivery, and enzyme arrays.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Christophe Lachance-Brais, Mostafa Rammal, Jathavan Asohan, Adam Katolik, Xin Luo, Daniel Saliba, Antranik Jonderian, Masad J. Damha, Matthew J. Harrington, Hanadi F. Sleiman
Summary: DNA hydrogels are programmable and biocompatible materials that can respond to complex stimuli, making them valuable in various applications. However, the existing DNA hydrogels are soft and lack functionality. In this study, a DNA/small-molecule motif is used to create stiff hydrogels, reaching high storage modulus. These hydrogels have tunable mechanical properties, self-healing ability, and respond to multiple stimuli. They can be used for delivering antisense oligonucleotides and enhancing gene silencing efficacy. This work extends the capabilities of DNA hydrogels and provides promising materials for various applications.
Article
Chemistry, Multidisciplinary
Sinan Faiad, Quentin Laurent, Alexander L. Prinzen, Jathavan Asohan, Daniel Saliba, Violeta Toader, Hanadi F. Sleiman
Summary: Nucleic acid therapeutics (NATs) are efficient tools for gene expression modulation and treating undruggable diseases. Spherical nucleic acids (SNAs) can effectively deliver small NATs to cells and protect them from degradation while improving biodistribution and reducing immune activation. Self-assembled SNAs, nanostructures made from a single DNA-polymer conjugate, have similar properties as small molecule encapsulation. A study on the factors that govern the fate of self-assembled SNAs reveals the importance of extracellular stability for recognition by membrane receptors and cellular uptake, as well as the requirement for intracellular dissociation for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic gene silencing therapeutics. These findings will aid in the translation of self-assembled structures for in vivo gene silencing applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Polymer Science
Donatien de Rochambeau, Maciej Barlog, Felix J. Rizzuto, Quentin Laurent, Xin Luo, Kai Lin Lau, Hassan S. Bazzi, Hanadi F. Sleiman
Summary: The research focuses on the impact of monomer sequence on the self-assembly behavior of supramolecular materials. By precisely controlling the monomer sequence, the researchers demonstrate how small differences in sequence can lead to significant morphological changes, such as the formation of spheres or nanosheets. The ability to explore these subtle variations in polymer sequence enables the systematic study of supramolecular chemistry and the rational design of functional polymers.
Article
Chemistry, Multidisciplinary
Daniel Saliba, Xin Luo, Felix J. Rizzuto, Hanadi F. Sleiman
Summary: DNA nanotubes, built with high aspect ratio and encapsulation potential, have potential for various biological and materials applications. A systematic investigation was conducted to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes through experimental and computational design. The design concepts enable fine-tuning of nanotube stiffness and may pave the way for the development of designer nanotubes for studying cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
Article
Chemistry, Multidisciplinary
Hassan H. Fakih, Adam Katolik, Elise Malek-Adamian, Johans J. Fakhoury, Sepideh Kaviani, Masad J. Damha, Hanadi F. Sleiman
Summary: Spherical nucleic acids (SNAs) show great potential as drug delivery vectors for nucleic acid therapeutics, with recent modifications enhancing stability and gene silencing potency. A cleavable DNA-based spacer is essential for maximum activity, and the modularity of FANA-SNA allows for versatile applications in gene silencing for various targets. Transfection-free delivery is superior for modified SNAs compared to free FANA oligonucleotides.
Review
Chemistry, Multidisciplinary
Casey M. Platnich, Felix J. Rizzuto, Gonzalo Cosa, Hanadi F. Sleiman
CHEMICAL SOCIETY REVIEWS
(2020)
Article
Chemistry, Multidisciplinary
Xin Luo, Christophe Lachance-Brais, Amy Bantle, Hanadi F. Sleiman
