Article
Chemistry, Multidisciplinary
Kun Dai, Chen Gong, Yang Xu, Fei Ding, Xiaodong Qi, Xinyi Tu, Lu Yu, Xiaoguo Liu, Jiang Li, Chunhai Fan, Hao Yan, Guangbao Yao
Summary: This study presents a transcription-based approach to quantitatively integrate nucleoside analogue molecules into RNA nanostructures. The integrated RNA origami not only maintains its morphology and biostability, but also gains new biomedical functions, such as innate immune recognition after integrating epigenetic nucleoside analogues, and synergistic effects on tumor cell killing after integrating therapeutic nucleoside analogues. This research provides a promising method for the quantitative integration of functional nucleoside analogues into RNA nanostructures, offering valuable insights for the development of multifunctional RNA origamis.
Article
Chemistry, Multidisciplinary
Chaoming Gu, Zhoubin Yu, Xiaojie Li, Xin Zhu, Chuanhong Jin, Zhen Cao, Shurong Dong, Jikui Luo, Zhi Ye, Yang Liu
Summary: Solid-state nanopores are crucial in sensing single-biomolecules, but their ultra-short translocation time limits the acquisition of detailed information and further applications. Combining MoS2 and graphene, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores that slowed down the passage of biomolecules. By testing dsDNA and BSA at the single-molecule level, we observed special signals indicating the shape change of BSA during the slow translocation process. These findings suggest the potential of MoS2-graphene heterostructure nanopores in slowing down translocation and acquiring more detailed information about biomolecules.
Article
Chemistry, Analytical
Xueping Yang, Jingyun Li, Suixin Zhang, Chao Li, Jiehua Ma
Summary: CRISPR/Cas-based systems have intrinsic merits for developing diagnostic technologies, but nucleic acid amplification is still required for high sensitivity. This study presents a one-step and amplification-free detection method using Cas12a-based assay and a single-microbead detection platform, which allows single-molecule level detection of DNA. The method has been successfully applied for specific identification in real samples without extra nucleic acid amplification.
ANALYTICAL CHEMISTRY
(2022)
Letter
Biotechnology & Applied Microbiology
Long-Can Mei, Ge-Fei Hao, Guang-Fu Yang
Summary: This article reviews the existing thermodynamic databases for protein-nucleic acid interactions and provides general comments to enhance browsing and exploration.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Lingxiao Wang, Haodong Li, Xinyan Wang, Xichu Yang, Changlin Tian, Demeng Sun, Lei Liu, Jinghong Li
Summary: Solid-binding peptides are a versatile tool for non-covalent modification of solid material surfaces, and a novel bicyclic peptide targeting polypropylene has been discovered through phage display and next-generation sequencing. These bicyclic peptides display distinct enrichment properties compared to linear peptides, with specific amino acid abundance, negative net charges, and high hydrophobicity. The selected bicyclic peptide shows higher binding affinity for polypropylene than the previously reported linear peptide, enabling more effective enhancement of the hydrophilic and adhesive properties of polypropylene. This work paves the way for exploring and utilizing conformationally-restricted cyclic peptides as a new family of functionally evolvable agents for material surface modification.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Electrochemistry
Jose M. Gisbert-Gonzalez, Maria Oliver-Pardo, Francisco J. Sarabia, Victor Climent, Juan M. Feliu, Enrique Herrero
Summary: This study investigated the adsorption behavior of CTAB and CTAOH on gold single crystal electrodes in solutions with different pH values. The stability and composition of the adsorbed adlayer were found to vary with changes in surface charge.
ELECTROCHIMICA ACTA
(2021)
Letter
Biotechnology & Applied Microbiology
M. Michael Gromiha, Kannan Harini
Summary: Mei and colleagues introduced PNATDB, a thermodynamic database for protein-nucleic acid interactions with 12,635 experimentally determined parameters. They claimed that extracting data from existing databases is challenging. However, they did not discuss ProNAB, which contains over 20,000 experimental data points for binding affinities of protein-nucleic acid complexes and other information.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Ahsen Ozcan, Rohan Krajeski, Eleonora Ioannidi, Brennan Lee, Apolonia Gardner, Kira S. Makarova, Eugene Koonin, Omar O. Abudayyeh, Jonathan S. Gootenberg
Summary: The study revealed that Cas7-11 from class 1 CRISPR-Cas systems is a single-protein effector with RNA interference capability. It can process pre-CRISPR RNA into mature crRNA with high specificity, and has potential applications in RNA knockdown and editing in mammalian cells. The findings provide a basis for developing new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.
Article
Chemistry, Physical
Mengjiao Wu, Yingying Huang, Li Yang, Yongshun Song, Xiaoling Lei
Summary: In this study, the dynamic process of single-strand DNA molecules moving from hydrophilic to hydrophobic regions on graphene oxide surface under heating was theoretically studied. It was found that heating facilitated the breaking/formation of hydrogen bonds and enhanced the flexibility of DNA molecules, enabling their movement from hydrophilic to hydrophobic regions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Jingtao Huang, Jingteng Xue, Mingwei Li, Jiaying Chen, Yuan Cheng, Zhonghong Lai, Jin Hu, Fei Zhou, Nan Qu, Yong Liu, Jingchuan Zhu
Summary: During the preparation or processing of graphene, structural flaws inevitably occur, leading to detrimental effects on mechanical properties. This paper uses first-principles computation to study single-atom adsorption on single vacancy graphene and creates a dataset for machine learning. Comparative analysis demonstrates that the BPNN model is best suited for the dataset. By adjusting its node parameters using genetic algorithm, the enhanced GA-BPNN model accurately predicts adsorption behavior on graphene surfaces, accelerating the atomic modification process. This research provides valuable insights into atom adsorption on graphene surfaces and highlights the potential of machine learning in accelerating first principle computations in material science.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Analytical
Huimin Hao, Ye Li, Bin Yang, Shuyan Lou, Zihua Guo, Weiyi Lu
Summary: In this study, a unique DNA probe with Hill-type cooperativity was developed based on toehold-mediated strand displacement processes, enabling accurate discrimination of single-nucleotide variants. The probe exhibited thermodynamic advantages for specificity, forming mismatch bubbles in the presence of single-nucleotide variants. The probe's feasibility was successfully demonstrated and its design allowed accurate discrimination of single-nucleotide variants, including insertions, mutations, and deletions, with Hill-type cooperativity serving as a novel strategy for DNA probe design.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Xiaoli Zhao, Qianyi Wan, Jian Zhang, Yake Duan, Yong Li, Jingrong Ma, Chao Shi, Cuiping Ma
Summary: Here, we developed an ultra-fast and visual single-tube nucleic acid detection approach that combines the self-settling characteristics of chitosan-functionalized diatomaceous earth (CDE) and accelerated PCR (AC-PCR). This method not only improves the sensitivity and specificity of detection, but also allows for the completion of the entire process in a short period of time, with results visible to the naked eyes.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Rolf David, Revati Kumar
Summary: Graphene oxide displays interesting reactive behavior at its interface with water, influenced by the level of oxidation. Fully oxidized sheets make the interfacial water acidic and negatively charged, while reduced sheets can form long-lived carbocations.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Haonan Fan, Yui Sasaki, Qi Zhou, Wei Tang, Yuta Nishina, Tsuyoshi Minami
Summary: We present an organic transistor that combines a phenylboronic acid derivative and graphene oxide to measure plasma glucose levels. This device minimizes interference from protein adsorption on the detection electrode.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Izaac Sit, Mark A. Young, James D. Kubicki, Vicki H. Grassian
Summary: This study investigates the surface chemistry of nucleotides adsorbed on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. The results show preferential adsorption of the phosphate group to either surface. The experimental absorption frequencies were compared to DFT calculations, revealing differences in the binding modes of nucleotides to the two mineral surfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Nidhi Nandu, Mustafa Salih Hizir, Neil M. Roberston, Birol Ozturk, Mehmet V. Yigit
Article
Biochemistry & Molecular Biology
Sophie Belin, Francesca Ornaghi, Ghjuvan Ghjacumu Shackleford, Jie Wang, Cristina Scapin, Camila Lopez-Anido, Nicholas Silvestri, Neil Robertson, Courtney Williamson, Akihiro Ishii, Carla Taveggia, John Svaren, Rashmi Bansal, Markus H. Schwab, Klaus Nave, Pietro Fratta, Maurizio D'Antonio, Yannick Poitelon, M. Laura Feltri, Lawrence Wrabetz
HUMAN MOLECULAR GENETICS
(2019)
Article
Chemistry, Physical
Christopher A. Myers, Rebecca J. D'Esposito, Daniele Fabris, Srivathsan Ranganathan, Alan A. Chen
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Review
Radiology, Nuclear Medicine & Medical Imaging
Nazanin Talebloo, Mithil Gudi, Neil Robertson, Ping Wang
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2020)
Article
Multidisciplinary Sciences
Lorenzo Baronti, Ileana Guzzetti, Parisa Ebrahimi, Sarah Friebe Sandoz, Emilie Steiner, Judith Schlagnitweit, Bastian Fromm, Luis Silva, Carolina Fontana, Alan A. Chen, Katja Petzold
Article
Multidisciplinary Sciences
Phensinee Haruehanroengra, Sweta Vangaveti, Srivathsan Ranganathan, Song Mao, Max Daniel Su, Alan A. Chen, Jia Sheng
Article
Biochemistry & Molecular Biology
Vibhav Valsangkar, Sweta Vangaveti, Goh Woon Lee, Walid M. Fahssi, Waqas S. Awan, Yicheng Huang, Alan A. Chen, Jia Sheng
Summary: Chemical modifications of the thrombin binding aptamer were studied for their effects on structure and thrombin binding affinity, with modifications found to maintain stability and binding patterns similar to the native form. Potential positions for modifications were identified without adverse effects, providing insights for the design and development of more functional TBA analogues.
Article
Genetics & Heredity
Rebecca J. D'Esposito, Christopher A. Myers, Alan A. Chen, Sweta Vangaveti
Summary: This review provides an overview of the current status and challenges of molecular dynamics simulations (MDS) of modified RNA, as well as the need for relevant reference experiments to study the effects of RNA modifications.
Article
Chemistry, Multidisciplinary
Mengwen Yan, Christopher A. Myers, Gregory M. John, Vincent E. Meyers, Alan A. Chen, Jeremy Feldblyum
Summary: The discovery of layered materials with unique electrical and chemical properties has been a major focus of materials research in the past decade. In this study, the authors investigated the stability of ZnSe-based layered hybrids (LHs) and found that it is related to the length and chemistry of the organic ligands on the LH surfaces. They also discovered that both H2O and O2 contribute to the degradation of ZnSe-LHs. The findings provide insights into protection strategies for layered materials and propose a degradation pathway that may apply to other layered materials.
ADVANCED MATERIALS INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Johnsi Mathivanan, Zhixue Bai, Alan Chen, Jia Sheng
Summary: By incorporating a 2'-5' linkage in an RNA aptamer, the binding affinity and energy with aminoglycosides can be increased. Molecular dynamics simulations reveal that this noncanonical linkage creates a narrower binding pocket, improving the ligand's fit. These findings provide new insights into the use of 2'-5' linkages to diversify RNA aptamers as noncovalent protective groups.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hiba Faheem, Johnsi Mathivanan, Hannah Talbot, Hana Zeghal, Sweta Vangaveti, Jia Sheng, Alan A. Chen, Arun Richard Chandrasekaran
Summary: In this study, the authors introduce a method of adding an extra layer of control to strand displacement reactions through a process called 'toehold clipping'. By designing DNA complexes with a photocleavable linker-containing toehold or an RNA toehold, they demonstrate the ability to prevent strand displacement reactions using light or enzymes. This work holds potential applications in biosensing, drug delivery or molecular computation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jibin Abraham Punnoose, Kevin J. Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan Chen, Thomas Banco, Ken Halvorsen
Summary: Stacking interactions between adjacent bases in DNA and RNA are important for biological processes and biotechnology applications. In this study, the authors used a centrifuge force microscope to measure stacking energies between individual bases. They found that stacking energies are strongest between purines (G|A) and weakest between pyrimidines (C|T). Phosphorylated, methylated, and RNA nucleotides had no effect on stacking energies, but a fluorophore modification reduced stacking energy.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Rafael G. Viegas, Murilo N. Sanches, Alan A. A. Chen, Fernando V. Paulovich, Angel E. Garcia, Vitor B. P. Leite
Summary: Molecular dynamics (MD) simulations are powerful tools for studying the folding pathways of biomolecules. In this study, we used MD simulations to investigate the folding of an RNA tetraloop and analyzed the dynamics using the energy landscape visualization method (ELViM). Our results provide insights into the folding process of the tetraloop and demonstrate the potential of ELViM for studying biomolecules.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)