Article
Chemistry, Organic
Toby Lewis-Atwell, Piers A. Townsend, Matthew N. Grayson
Summary: In this study, the relative performances of different force fields for conformational searching of hydrogen-bond-donating catalyst-like molecules were compared. MM3, MMFFs, and OPLS3e consistently showed strong performances and are recommended for conformationally searching molecules structurally similar to those in this study.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Review
Pharmacology & Pharmacy
Anas Ahmad, Mohammad Imran, Haseeb Ahsan
Summary: A biomarker is a measurable biological molecule that can serve as an index of normal or abnormal pathophysiology or the response to treatment. Different tissues in the body have distinct biomolecular make-ups called biomarkers, which include genes, proteins, and other biomolecules. Biomarkers can be objectively quantified through biochemical samples to evaluate an organism's exposure to normal or pathological processes or how it responds to drug interventions. Understanding the significance of biomarkers is crucial for efficient disease diagnosis and guiding treatment choices. Advances in omics technologies have allowed for the discovery of new biomarkers using various strategies like genomics, epigenetics, metabolomics, transcriptomics, lipid analysis, and protein studies. These biomarkers have been applied for screening normal and diseased tissue or serum samples and are valuable tools in pharmacology and therapeutics. This review summarizes various types of biomarkers, their classification, and monitoring and detection methods and strategies. It also discusses analytical techniques and clinically applicable biomarker sensing techniques, including recent developments in nanotechnology-based biomarker sensing and detection.
Article
Chemistry, Multidisciplinary
Jinqi Deng, Chao Liu, Jiashu Sun
Summary: Extracellular vesicles (EVs) are nanovesicles derived from cells, carrying various molecular cargos and playing important roles in intercellular communication and physiological and pathological processes. DNA-based nanomaterials, with their excellent programmability and modifiability, have emerged as promising tools for detecting molecular cargos carried by EVs. This perspective summarizes recent advancements in EV analysis using different types of DNA-based nanomaterials, including linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of these DNA nanomaterials, as well as their performance for detecting EVs, are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.
ADVANCED MATERIALS
(2023)
Review
Chemistry, Multidisciplinary
Yao-Hua Liu, Ying-Ming Zhang, Hua-Jiang Yu, Yu Liu
Summary: The use of cucurbiturils (CBs) in biomacromolecular assemblies has made significant progress in various applications, including biosensors, biochemical reaction regulation, and disease treatment. CBs have also shown the ability to promote subcellular bioimaging in different organelles, demonstrating diverse applications in the field of supramolecular chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Pengyu Wang, Xiaocui Fang, Rong Du, Jiali Wang, Mingpeng Liu, Peng Xu, Shiqi Li, Kaiyue Zhang, Siyuan Ye, Qing You, Yanlian Yang, Chen Wang
Summary: In this study, we determined the binding strengths between nucleotides of adenine, thymine, guanine, and cytosine in single stranded DNAs and homo-octapeptides consisting of 20 common amino acids. Using a bead-based fluorescence assay, we identified unique binding strength patterns for each DNA nucleotide and amino acid, which can be attributed to their chemical structures.
Review
Food Science & Technology
Simone Schefer, Marie Oest, Sascha Rohn
Summary: This article discusses the importance of interactions between proteins, carbohydrates, and phenolic compounds in influencing the functionality of foods, especially focusing on the potential ternary interactions involving ferulic acid as the most abundant phenolic acid, particularly in bread-making.
Review
Chemistry, Medicinal
Jiang Liu, Xin Ding, Yupeng Fu, Cen Xiang, Yuan Yuan, Yongmin Zhang, Peng Yu
Summary: Macro biomolecules like proteins and nucleic acids play a crucial role in drug delivery, and appropriate delivery systems are essential for protecting them from degradation.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Benedetta Carrozzini, Giovanni Luca Cascarano, Carmelo Giacovazzo
Summary: This article introduces a new molecular replacement program, REMO22, which is effective in model searching for proteins and nucleic acids by utilizing various types of prior information. The program has been validated through several test cases and is primarily developed as an automated tool for determining crystal structures of macromolecules. Experimental tests comparing REMO22 with leading MR programs indicate that REMO22, along with its pipeline REMO22 + SYNERGY + CAB, presents a viable alternative to currently used phasing tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Andres Rodriguez-Galvan, Flavio F. Contreras-Torres
Summary: Scanning tunneling microscopy (STM) is an important technique for directly observing individual biomolecules at near-molecular scale. It plays a crucial role in structural analysis, understanding imaging formation, and developing related techniques.
Article
Nanoscience & Nanotechnology
Fangfei Yin, Haipei Zhao, Shasha Lu, Juwen Shen, Min Li, Xiuhai Mao, Fan Li, Jiye Shi, Jiang Li, Baijun Dong, Wei Xue, Xiaolei Zuo, Xiurong Yang, Chunhai Fan
Summary: The article introduces a DNA-encoded molecular classifier that can classify multidimensional molecular clinical data and has been tested in prostate cancer patients.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Steven Doria, Jarad Yost, Zachary Gagnon
Summary: The ability to preconcentrate, separate, and purify biomolecules is important for portable diagnostic tools. A new technique called teichophoresis (TPE) is presented for the concentration and separation of proteins and nucleic acids. TPE does not require a leading electrolyte and allows for continuous biomolecular concentration. It is biocompatible, requires low voltage, and produces no significant pH changes.
Article
Chemistry, Analytical
Dongliu Xiang, Hui Wen, Hongmei Fang, Yuan Zhou, Lei Luo, Qing Wang, Xueting Yan, Jin Huang, Jianbo Liu, Xiaohai Yang, Kemin Wang
Summary: A versatile detection technique was developed using magnetic beads, barcoded DNA strands released from gold nanoparticles, and exonuclease III cyclic cleavage-assisted signal amplification. This technique was integrated into a microfluidic chip with multiple chambers and the mixing was achieved by acoustic vibration from a portable sonic toothbrush. The detection limits of three different targets were successfully demonstrated, and this platform is expected to be developed into an automatic sample-to-answer device.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Marltan O. Wilson, David M. M. Huang
Summary: We have developed a machine-learning method to coarse-grain condensed-phase molecular systems using anisotropic particles. This method extends the capabilities of high-dimensional neural network potentials by accounting for molecular anisotropy. By parameterizing single-site coarse-grained models of benzene and sexithiophene, we demonstrate the flexibility of the method in achieving structural accuracy comparable to all-atom models but at a lower computational cost. The method is proven to be straightforward and robust in capturing anisotropic interactions and many-body effects, as evidenced by reproducing the structural properties of the liquid phase and phase transitions of the molecules.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Yuanyuan Chen, Peng Gao, Wei Pan, Mingwan Shi, Shujie Liu, Na Li, Bo Tang
Summary: The research developed an X-ray-induced phenotypic transformation strategy through macrophage engineering for safe and efficient tumor immunotherapy. The engineered macrophages demonstrated high tumor recognition and X-ray-induced polarization effects, significantly inhibiting tumor growth in mice even with a reduced radiation dose compared to natural macrophages. The X-PT strategy opens a new avenue for clinical immune cell-based therapy.
Article
Chemistry, Multidisciplinary
Jasper W. Dittmar, Michelle H. Teplensky, Michael Evangelopoulos, Lei Qin, Bin Zhang, Chad A. Mirkin
Summary: The stability of the liposome core is crucial for the effectiveness of liposome-based drugs. This study explores the impact of anchor chemistry on immunotherapeutic function and demonstrates that a stable anchor can enhance immune stimulation and improve therapeutic efficacy.