Article
Chemistry, Multidisciplinary
Caixia X. Liu, Bin Wang, Weiping P. Zhu, Yufang F. Xu, Yangyang Y. Yang, Xuhong H. Qian
Summary: This article describes a DNA nanodevice that has ER targeting capacity and undergoes new intracellular degradation via autophagy-dependent pathway. The DNA nanostructure functionalized with specific ligands is used to selectively catch ER-localized proteins and transport them to the lysosome for degradation. Through this technique, efficient degradation of both exogenous ER-resident protein (ER-eGFP) and endogenous overexpressed molecular chaperone (glucose-regulated protein 78) in cancer cells has been successfully achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Lorenzo Talamanca, Cedric Gobet, Felix Naef
Summary: The study revealed that the circadian clock regulates human physiology, but the specific gene expression rhythms and their dependence on age and sex in humans were not well-defined. By combining data from the GTEx project and an algorithm, the researchers identified mRNA rhythms in 46 tissues and found that they varied in breadth and were affected by sex and age. The overall gene expression rhythms were more sustained in females, while rhythmic programs generally dampened with age.
Article
Chemistry, Physical
Xun Gong, Nicholas Renegar, Retsef Levi, Michael S. Strano
Summary: Nanoparticle corona phase design allows for molecular recognition for sensing applications. In this study, the largest DNA-SWCNT PL response library was generated and machine learning techniques were utilized to understand the dependence of molecular recognition and DNA sequence.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Chemistry, Physical
Danfeng Wang, Min Liu, Yushu Wu, Tianxin Weng, Lu Wang, Yongfang Zhang, Yanna Zhao, Jun Han
Summary: The co-loading of chemotherapy-phototherapy (CTPT) combination drugs by aptamer-targeted DNA nanostructures has significant advantages in improving anticancer effects and overcoming the multidrug resistance of cancer cells. The binding modes of drugs to DNA nanostructures impact CTPT therapy.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biology
Robert T. Young, Luke Czapla, Zoe O. Wefers, Benjamin M. Cohen, Wilma K. Olson
Summary: DNA carries not only a list of biochemical ingredients but also a multitude of structural and energetic signals that determine its movement and response to proteins and other molecules. By analyzing protein-DNA crystal structures, we can estimate the natural structure and deformability of DNA. Updating the knowledge-based elastic potentials allows for a better understanding of the equilibrium structures and fluctuations of DNA.
Article
Multidisciplinary Sciences
Maria Arroyo, Florian D. Hastert, Andreas Zhadan, Florian Schelter, Susanne Zimbelmann, Cathia Rausch, Anne K. Ludwig, Thomas Carell, M. Cristina Cardoso
Summary: This study reveals that Tet1 and its short isoform Tet1s have different localization during DNA replication, affecting cytosine modification levels. Tet1s interacts with CRL4(VprBP), ubiquitinated, and recruited to late replicating heterochromatin by Uhrf1, leading to 5-methylcytosine oxidation and chromatin decondensation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Migle Tomkuvien, Markus Meier, Diana Ikasalaite, Julia Wildenauer, Visvaldas Kairys, Saulius Klimasauskas, Laura Manelyt
Summary: Methylation of cytosine is an important epigenetic mark that can alter DNA and chromatin structure. This study investigates how larger chemical variations in DNA affect chromatin structure and nucleosome formation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Sundararajan Ponkarpagam, Govindaraj Mahalakshmi, Kailasam N. Vennila, Kuppanagounder P. Elango
Summary: The study found that the antihistaminic drug oxatomide interacts with calf-thymus DNA through intercalation or groove binding, primarily driven by hydrophobic interactions. Voltammetric experiments and molecular modeling studies confirmed the concentration-dependent mode of binding, with metadynamics simulations revealing two major binding forces at the all-atom level.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Cell Biology
Sebastian Eustermann, Avinash B. Patel, Karl-Peter Hopfner, Yuan He, Philipp Korber
Summary: ATP-dependent chromatin remodellers regulate chromatin transactions by re-arranging nucleosomes. Recent studies have elucidated the organization of remodeller complexes, their ATPase activity, their regulation and their pathological dysregulation.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Masaki Hagihara
Summary: Our study reveals that an RNA template with eight GGG repeat sequences forms a tandem G-quadruplex structure, which effectively inhibits protein synthesis by aligning two individual G-quadruplexes in close proximity in the coding region of mRNA chains.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Yafu Wang, Huiyu Niu, Kui Wang, Ge Wang, Junwei Liu, Tony D. James, Hua Zhang
Summary: This study developed a near-infrared fluorescent probe YON that can specifically and in real-time monitor and evaluate the health of mitochondrial DNA. YON exhibits ultra-sensitive detection ability and is suitable for interference-free imaging.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Applied
Ivona Cipor, Atanas Kurutos, Georgi M. Dobrikov, Fadhil S. Kamounah, Dragomira Majhen, Davor Nestic, Ivo Piantanida
Summary: A series of monocationic styryl dyes were synthesized and characterized in this study. These dyes exhibited significant spectral shift and fluorescence enhancement, and showed strong affinity to DNA/RNA binding. The positioning and electronic properties of the dyes within the DNA/RNA binding site were found to play a crucial role in their fluorescence response selectivity.
Article
Biochemical Research Methods
Lessandro De Paepe, Enrico Cadoni, Alex Manicardi, Annemieke Madder
Summary: This study focuses on the utilization of furan-PNAs as pro-reactive probe systems and their applications to DNA and RNA targeting. Furans-PNAs provide practical insights into the design, synthesis, and application of furan-containing PNA probes for achieving efficient PNA-DNA and PNA-RNA interstrand crosslinking (ICL), as well as ON-templated PNA-PNA ligation systems. The applications of these probes in targeting DNA secondary structures, such as G-quadruplexes and i-motifs, target pull-down assays, and on-surface detection are discussed.
Article
Chemistry, Analytical
Yichen Han, Jie Zhou, Fang Liu, Yu Ouyang, Ruo Yuan, Ya-Qin Chai
Summary: In this study, a pH-stimulated self-locked DNA nanostructure (SLDN) was developed to selectively distinguish and detect cancer cells by unlocking in the acidic environment, allowing for high-resolution imaging of miRNAs in tumor cells. The unlocked-SLDN could simultaneously recognize and detect miRNA-21 and miRNA-155 by triggering the hybridization chain reaction (HCR) amplification. The proposed strategy eliminates interference from normal cells and achieves sensitive biomarker detection and precise cancer diagnosis.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Huiling Wang, Mingfang Wang, Zefeng Nie, Shuang Qiu, Xiaoping Huang, Xiang Li, Yanfang Cui, Chunrong Liu, Changlin Liu
Summary: Cu/Zn superoxide dismutase (SOD1) plays a key role as an antioxidant enzyme in maintaining cellular reactive oxygen species (ROS) homeostasis and regulating gene expression. We found that SOD1 is involved in gene expression regulation in response to changes in cellular ROS levels through its binding to DNA and the binding is redox-dependent.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Walaa Abdallah, Vanessa Chirino, Ian Wheeldon, Scott Banta
Article
Biochemistry & Molecular Biology
Sarah Thorwall, Cory Schwartz, Justin W. Chartron, Ian Wheeldon
NATURE CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Physical
Scott Banta, Ian Wheeldon
Article
Biotechnology & Applied Microbiology
Xuye Lang, Xiao Hong, Cetara A. Baker, Tamara C. Otto, Ian Wheeldon
BIOTECHNOLOGY AND BIOENGINEERING
(2020)
Article
Biochemical Research Methods
Adithya Ramesh, Thomas Ong, Jaime A. Garcia, Jessica Adams, Ian Wheeldon
ACS SYNTHETIC BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Mengwan Li, Xuye Lang, Marcos Moran Cabrera, Sawyer De Keyser, Xiyan Sun, Nancy Da Silva, Ian Wheeldon
Summary: The study focuses on engineering the Shikimate and Ehrlich pathways in yeast Kluyveromyces marxianus for the biosynthesis of 2-phenylethanol (2-PE). A CRISPR-mediated multigene integration system was developed to integrate multiple gene expression cassettes efficiently, leading to an increase in 2-PE production. The best strain achieved 1943 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures, demonstrating the potential of this approach for sustainable and economical production.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Biochemical Research Methods
Walaa Abdallah, Xiao Hong, Scott Banta, Ian Wheeldon
Summary: Natural cascades often use spatial organization to introduce beneficial substrate channeling mechanisms, which has been widely adopted in engineered multienzyme cascades. Utilizing new molecular scaffolds now allows testing the effects of spatial organization on cascade kinetics, but these scaffolds can also change the microenvironment experienced by the assembled enzymes, complicating kinetic analysis.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Dipankar Baisya, Adithya Ramesh, Cory Schwartz, Stefano Lonardi, Ian Wheeldon
Summary: In this paper, the authors propose a neural network-based architecture called DeepGuide, which learns from genome-wide CRISPR activity profiles to accurately design high activity sgRNAs. The experimental validation confirms the effectiveness of DeepGuide in predicting high activity sgRNAs in the oleaginous yeast Yarrowia lipolytica.
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Biomedical
Wenguang Wang, Haiheng Xu, Qingsong Ye, Feng Tao, Ian Wheeldon, Ahu Yuan, Yiqiao Hu, Jinhui Wu
Summary: Flagellated bacteria coated with antigen-adsorbing polymer nanoparticles and injected into tumours in mice after radiotherapy elicit systemic antitumour effects by transporting antigens to the tumour's periphery. This finding highlights the potential of leveraging bacteria to enhance dendritic cell activation and improve in situ cancer vaccination strategies.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Brian Lupish, Jordan Hall, Cory Schwartz, Adithya Ramesh, Clifford Morrison, Ian Wheeldon
Summary: Yarrowia lipolytica is a yeast strain of interest for metabolic engineering due to its ability to metabolize various renewable carbon sources. Through a genome-wide CRISPR screen, we identified the Delta RAS2 mutant as the only one that inhibits hyphal formation without affecting lycopene production. This suggests that the Delta RAS2 mutant could be useful for engineering the production of carotenoids and other biochemicals.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Nanoscience & Nanotechnology
Arpita Iddya, Piotr Zarzycki, Ryan Kingsbury, Chia Miang Khor, Shengcun Ma, Jingbo Wang, Ian Wheeldon, Zhiyong Jason Ren, Eric M. Hoek, David Jassby
Summary: This study demonstrates a nanocomposite ion-exchange membrane material that enables a reverse-selective transport mechanism with high selectivity. By incorporating hydrous manganese oxide nanoparticles into the membrane, the phosphate flux is significantly increased and the selectivity for phosphate ions over other ions is greatly enhanced.
NATURE NANOTECHNOLOGY
(2022)
Article
Biology
Adithya Ramesh, Varun Trivedi, Sangcheon Lee, Aida Tafrishi, Cory Schwartz, Amirsadra Mohseni, Mengwan Li, Stefano Lonardi, Ian Wheeldon
Summary: acCRISPR is a method that corrects the inaccuracies in CRISPR screening results caused by variability in sgRNA cutting efficiency by computing a fitness score for each targeted gene. It is used to identify essential genes and their fitness effects in CRISPR screens. The study applied acCRISPR to identify essential genes for growth under glucose and salt tolerance conditions in the yeast Yarrowia lipolytica. This work presents an experimental-computational framework for CRISPR-based functional genomics studies in non-conventional organisms.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Sarah Thorwall, Varun Trivedi, Eva Ottum, Ian Wheeldon
Summary: The emergence of next-generation sequencing (NGS) technologies has enabled the identification of metabolic engineering targets in microbial populations. This study used NGS data and bioinformatics tools to identify genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. By sequencing and analyzing different Pseudomonas isolates, the study identified several genes that significantly influenced phenazine production. Overall, this work demonstrates the value of population genomics in identifying targets for metabolic engineering in bioproduction hosts.
METABOLIC ENGINEERING
(2023)
Review
Biotechnology & Applied Microbiology
Varun Trivedi, Adithya Ramesh, Ian Wheeldon
Summary: The multifaceted nature of CRISPR screens has driven advancements in functional genomics. However, the application of CRISPR screens in non-conventional yeasts and the lack of accurate bioinformatic algorithms for analyzing microbial screening data have been limitations. This mini-review explores the potential and methods for using CRISPR screens in non-conventional microbes and highlights the importance of developing accurate algorithms for data analysis.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Xiao Hong, Timothy Cholko, Chia-en A. Chang, Ian Wheeldon
Summary: Biopolymer scaffold modification is widely used to enhance enzyme catalysis. However, predicting the effects of scaffold position on enzyme properties is a central challenge. Researchers have developed a computational-experimental approach to model the effects of DNA scaffold position on enzyme kinetics and have found that the conjugation position is as important as the scaffold's chemistry and structure. They also discovered that there is a significant enhancement in enzyme kinetics when the scaffold is positioned at a suitable distance from the active site.