Review
Chemistry, Multidisciplinary
Harshita Shet, Rajesh Sahu, Yogesh S. Sanghvi, Anant R. Kapdi
Summary: Fluorinated nucleosides and oligonucleotides are widely used as probes for studying nucleic acid interactions, structures, transformations, and biomedical applications. The unique properties of fluorine atoms, such as small size, electronegativity, lipophilicity, and stereochemical control, have attracted attention for the fluorination of preformed nucleosides and/or nucleotides. This review discusses the synthetic protocols for selective fluorination of sugar or base moieties in preformed nucleosides, nucleotides, and nucleic acids using specific fluorinating reagents.
Article
Chemistry, Multidisciplinary
Juri Eyberg, Mark Ringenberg, Clemens Richert
Summary: A new type of deoxynucleoside was reported in this study, which can control the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell. The deoxynucleoside exhibits reactivity towards soft nucleophiles, changes its fluorescence, and has potential applications in controlled release, chemical biology, sensing, and diagnostics.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Kehinde M. Taiwo, Owen B. Becette, Guanghui Zong, Bin Chen, Peter Y. Zavalij, Theodore Kwaku Dayie
Summary: Solution NMR using the magnetically active fluorine-19 (F-19) isotope is advantageous for studying RNA structure and conformational changes, but synthesizing fluorinated RNA building blocks poses challenges. The study presents a scalable and reliable method to produce labeled nucleotides for incorporation into biologically active RNAs.
MONATSHEFTE FUR CHEMIE
(2021)
Article
Chemistry, Inorganic & Nuclear
Joanna Skiba, Aleksandra Kowalczyk, Damian Trzybinski, Krzysztof Wozniak, Valerije Vrcek, Magdalena Gapinska, Konrad Kowalski
Summary: This paper reports a Yb(OTf)(3)-mediated etherification reaction to obtain R,R and S,R isomers of ferrocenyl glycol nucleic acid (Fc-GNA) nucleosides from their stereo-defined (S,R) precursor. The mechanism of the reaction is explained by density functional theory calculations, and the obtained compounds show reversible oxidation of the ferrocenyl portion. Anticancer activity studies reveal that the (S,R) nucleoside exhibits the highest activity against cancer cells HeLa and Ishikawa, inducing apoptosis in HeLa cells at a concentration of IC50=66.0 μM after 72 hours of treatment.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2021)
Review
Chemistry, Multidisciplinary
Joern Bargstedt, Martin Reinschmidt, Leon Tydecks, Theresa Kolmar, Christoph M. Hendrich, Andres Jaeschke
Summary: Photochromic nucleosides have emerged as a promising approach for manipulating and studying complex processes in living organisms. This review highlights recent advancements in this field, including design principles, synthetic strategies, analytical challenges, and applications. The incorporation of photoswitchable moieties into biological macromolecules allows for light-responsive behavior, offering advantages in cellular and tissue applications due to its non-invasive nature. This field holds great potential for precise control of gene expression and modulation of biomolecular structure and function.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Mathijs J. Pals, Willem A. Velema
Summary: Terminal deoxynucleotidyl Transferase (TdT) is a template-independent DNA polymerase that has gained interest as a leukemia biomarker and potential therapeutic target. A FRET-quenched fluorogenic probe based on a size-expanded deoxyadenosine was developed to directly report on TdT enzymatic activity. The probe showed selectivity over other enzymes and its activity could be monitored in human T-lymphocyte cell extract and Jurkat cells using a simple fluorescence assay. A non-nucleoside TdT inhibitor was identified using the probe in a high-throughput assay.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Misa Shoji, Yasufumi Fuchi, Takashi Osawa, Han Kim, Yuta Ito, Yoshiyuki Hari
Summary: In this study, a unique consecutive three-acetal-containing nucleic acid (TaNA) was designed and its methylated derivatives were synthesized. The modified oligonucleotides showed higher stability when forming duplexes or triplexes compared to natural and other modified oligonucleotides, and also exhibited enhanced nuclease resistance.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Review
Food Science & Technology
Ting Ding, Ge Song, Xinran Liu, Meihong Xu, Yong Li
Summary: Nucleotides are the basic units of nucleic acid macromolecules, playing important physiological and biochemical functions in organisms. Recent studies have shown that exogenous nucleotides are essential nutrients under specific physiological conditions, entering tissues, reducing the body's synthesis needs, and enhancing immune function and regulating intestinal flora.
JOURNAL OF FUNCTIONAL FOODS
(2021)
Article
Chemistry, Organic
Takayuki Kanagawa, Shigetoshi Tachibana, Yoshiaki Masaki, Kohji Seio
Summary: A cyclic nucleoside has been designed and synthesized to introduce specific conformations into functional nucleic acids by fixing the rotation, base orientation, and sugar structure.
Article
Chemistry, Multidisciplinary
Qiang Li, Marko Trajkovski, Chaochao Fan, Jialiang Chen, Yifei Zhou, Kuan Lu, Hongjun Li, Xuncheng Su, Zhen Xi, Janez Plavec, Chuanzheng Zhou
Summary: Fluorinated nucleotides are crucial for F-19 NMR studies of nucleic acid structure and function. The synthesized 4'-SCF3-thymidine exhibits high adaptability and sensitivity, making it valuable for distinguishing diverse DNA structures with single-nucleotide resolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Physics, Fluids & Plasmas
Qiujin Wang, Shuo Lin, Xuan Liu, Wen Xu, Yiming Xiao, Changneng Liang, Lan Ding, F. M. Peeters
Summary: This study experimentally investigated the photoluminescence properties of DNA under different optical excitations, revealing that the behavior of ssDNA can be classified into two categories depending on the excitation wavelength. Different transition channels exist for different excitation wavelengths, while the strand length and base type also have an impact on the photoluminescence properties.
Article
Chemistry, Multidisciplinary
Hui Yang, Elena Eremeeva, Mikhail Abramov, Piet Herdewijn
Summary: The study demonstrates that modified nucleic acid fragments can be transcribed into natural or modified RNA and serve as genetic templates in vivo for encoding target proteins, showcasing the potential of synthetic materials in genetics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Hoai Nguyen, Mikhail Abramov, Jef Rozenski, Elena Eremeeva, Piet Herdewijn
Summary: Chemically modified nucleic acids are of great interest in synthetic biology for creating a regulatable and sophisticated synthetic system. Researchers have successfully synthesized modified DNA sequences and introduced them into eukaryotic cells, which is important for scientists working in the field of xenobiology in yeast.
Review
Chemistry, Analytical
Jadera Talap, Jing Zhao, Minzhe Shen, Zihan Song, Hui Zhou, Yu Kang, Lianli Sun, Lushan Yu, Su Zeng, Sheng Cai
Summary: Therapeutic nucleic acids, chemically modified RNA or DNA, target pathogenic genes accurately and have wide application prospects. 17 nucleic acid based therapeutics have been approved by FDA or EMA, raising higher requirements for analytical methods. This review introduces different classes of therapeutic nucleic acids, commercialized therapeutics, and analytical methods for nucleic acid based therapeutics.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Chemistry, Organic
Yasufumi Fuchi, Kouki Watanabe, Misa Shoji, Yuta Ito, Yoshiyuki Hari
Summary: The pyrimidine derivatives of methylated 2'-O,4'-C-methyleneoxy-bridged nucleic acid (Me-TaNA), a unique consecutive three-acetal-containing nucleic acid, have been shown to be promising building blocks for chemically modified oligonucleotides. In this study, purine derivatives of Me-TaNA (Me-TaNA-A and -G) were synthesized and introduced into oligonucleotides. The modified oligonucleotides, including purine derivatives of Me-TaNA, exhibited increased duplex stability compared to natural oligonucleotides when forming duplexes with single-stranded RNA.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Review
Medical Laboratory Technology
Carmela Paolillo, Eric Londin, Paolo Fortina
CLINICAL CHEMISTRY
(2019)
Article
Biochemical Research Methods
Gaurav Kumar, Adam Ertel, George Feldman, Joan Kupper, Paolo Fortina
BMC BIOINFORMATICS
(2020)
Article
Medicine, Research & Experimental
Lauren K. Meyer, Benjamin J. Huang, Cristina Delgado-Martin, Ritu P. Roy, Aaron Hechmer, Anica M. Wandler, Tiffaney L. Vincent, Paolo Fortina, Adam B. Olshen, Brent L. Wood, Terzah M. Horton, Kevin M. Shannon, David T. Teachey, Michelle L. Hermiston
JOURNAL OF CLINICAL INVESTIGATION
(2020)
Article
Immunology
Jing Chen, Jennifer L. Martindale, Kotb Abdelmohsen, Gaurav Kumar, Paolo M. Fortina, Myriam Gorospe, Abdolmohamad Rostami, Shiguang Yu
JOURNAL OF IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Kristen Upton, Apexa Modi, Khushbu Patel, Nathan M. Kendsersky, Karina L. Conkrite, Robyn T. Sussman, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Paolo Fortina, Sharon J. Diskin, John M. Maris, Jo Lynne Rokita
Article
Immunology
Javad Rasouli, Giacomo Casella, Satoshi Yoshimura, Weifeng Zhang, Dan Xiao, James Garifallou, Michael Gonzalez, Alice Wiedeman, Anna Kus, Elisabeth R. Mari, Paolo Fortina, Hakon Hakonarson, S. Alice Long, Guang-Xian Zhang, Bogoljub Ciric, Abdolmohamad Rostami
SCIENCE IMMUNOLOGY
(2020)
Article
Medical Laboratory Technology
Leila Youssefian, Amir Hossein Saeidian, Fahimeh Palizban, Atefeh Bagherieh, Fahimeh Abdollahimajd, Soheila Sotoudeh, Nikoo Mozafari, Rahele A. Farahani, Hamidreza Mahmoudi, Sadegh Babashah, Masoud Zabihi, Sirous Zeinali, Paolo Fortina, Julio C. Salas-Alanis, Andrew P. South, Hassan Vahidnezhad, Jouni Uitto
Summary: This study analyzed the whole transcriptome of 40 families with Mendelian skin disorders and found that RNA-seq combined with other next-generation sequencing methods could successfully identify pathogenic mutations. They also proposed a novel pipeline to increase the yield of variant calling from RNA-seq by using genome and transcriptome references in parallel.
CLINICAL CHEMISTRY
(2021)
Article
Immunology
Javad Rasouli, Giacomo Casella, Larissa L. W. Ishikawa, Rodolfo Thome, Alexandra Boehm, Adam Ertel, Carolina R. Melo-Silva, Elisabeth R. Mari, Patrizia Porazzi, Weifeng Zhang, Dan Xiao, Luis J. Sigal, Paolo Fortina, Guang-Xian Zhang, Abdolmohamad Rostami, Bogoljub Ciric
Summary: The study reveals that IFN-beta therapy reduces GM-CSF production by Th cells indirectly through its effects on monocytes, and increases IL-10 expression in monocytes to suppress IL-1 beta secretion, thereby disrupting a proinflammatory loop involving several molecules derived from Th cells and monocytes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Patrizia Porazzi, Svetlana Petruk, Luca Pagliaroli, Marco De Dominici, David Deming, Matthew Puccetti, Saul Kushinsky, Gaurav Kumar, Valentina Minieri, Elisa Barbieri, Sandra Deliard, Alexis Grande, Marco Trizzino, Alessandro Gardini, Eli Canaani, Neil Palmisiano, Pierluigi Porcu, Adam Ertel, Paolo Fortina, Christine M. Eischen, Alexander Mazo, Bruno Calabretta
Summary: Inhibition of EZH2 can decondense H3K27me3-marked chromatin in AML cells, leading to enhanced chemotherapy-induced DNA damage, apoptosis, and leukemia suppression. Inducing cell cycle entry further promotes these effects. Combination treatment with EZH2 inhibitor and doxorubicin induces transcriptional reprogramming and increases the expression of cell death-promoting and growth-inhibitory genes.
Article
Dermatology
Bahar Dasgeb, Sara Pajouhanfar, Ali Jazayeri, Elizabeth Schoenberg, Gaurav Kumar, Paolo Fortina, Adam C. Berger, Jouni Uitto
Summary: The study investigated genetic markers that may lead to early development of multiple BCCs, identifying oncogenic mutations in PTCH1 and TP53 in patients with numerous and postexcision recurring BCCs of large size. These mutations may explain the characteristics of the BCCs observed and could serve as genetic markers for high-risk patients.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Genetics & Heredity
Amir Hossein Saeidian, Leila Youssefian, Jianhe Huang, Andrew Touati, Hassan Vahidnezhad, Luke Kowal, Matthew Caffet, Tamara Wurst, Jagmohan Singh, Adam E. Snook, Ellen Ryu, Paolo Fortina, Sharon F. Terry, Jonathan G. Schoenecker, Jouni Uitto, Qiaoli Li
Summary: This study reports the genetic findings from an international cohort of patients with heritable ectopic mineralization. Multiple gene variants were identified, including 159 distinct variants in the ABCC6 gene. The functional assessment of these variants highlighted the importance of determining pathogenicity through appropriate experimental systems.
GENETICS IN MEDICINE
(2022)
Article
Immunology
Jennifer L. Hope, Manzhi Zhao, Christopher J. Stairiker, Caoimhe H. Kiernan, Alison J. Carey, Yvonne M. Mueller, Marjan van Meurs, Inge Brouwers-Haspels, Dennis C. Otero, Eun-Ah Bae, Hannah A. Faso, Alex Maas, Hans de Looper, Paolo M. Fortina, Isidore Rigoutsos, Linda M. Bradley, Stefan J. Erkeland, Peter D. Katsikis
Summary: This study characterized the expression profile of miRNAs in antiviral CD8(+) T cells and found that miR-139 was highly downregulated in effector CTLs. However, the deficiency or overexpression of miR-139 did not affect the development and response of immune cells.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Jeffrey A. Rappaport, Ariana A. Entezari, Adi Caspi, Signe Caksa, Aakash V. Jhaveri, Timothy J. Stanek, Adam Ertel, Joan Kupper, Paolo M. Fortina, Steven B. McMahon, James B. Jaynes, Adam E. Snook, Scott A. Waldman
Summary: The study revealed the corepression of GUCY2C ligand transcription by beta-catenin/TCF signaling and provided genomic strategies to reestablish hormone expression. This mechanism reflects a novel pathophysiological step in tumorigenesis.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Medicine, Research & Experimental
Amir Hossein Saeidian, Leila Youssefian, Charles Y. Huang, Fahimeh Palizban, Mahtab Naji, Zahra Saffarian, Hamidreza Mahmoudi, Azadeh Goodarzi, Soheila Sotoudeh, Fatemeh Vahidnezhad, Maliheh Amani, Narjes Tavakoli, Ali Ajami, Samaneh Mozafarpoor, Mehrdad Teimoorian, Saeed Dorgaleleh, Sima Shokri, Mohammad Shenagari, Nima Abedi, Sirous Zeinali, Paolo Fortina, Vivien Beziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, Jouni Uitto, Hassan Vahidnezhad
Summary: This study presents a whole-transcriptome sequencing-based method that can simultaneously identify the cutaneous virome and the underlying inborn errors of immunity (IEI) genes by RNA-Seq on a single skin biopsy. The method allows for rapid and accurate diagnosis of patients with viral skin infections and potential genetic defects, providing guidance for further treatment.
Article
Cell Biology
Fabio Quaglia, Shiv Ram Krishn, George G. Daaboul, Srawasti Sarker, Raffaella Pippa, Josep Domingo-Domenech, Gaurav Kumar, Paolo Fortina, Peter McCue, William K. Kelly, Himisha Beltran, Qin Liu, Lucia R. Languino
JOURNAL OF EXTRACELLULAR VESICLES
(2020)