Article
Chemistry, Multidisciplinary
Nikita Brodyagin, Aubrey L. Maryniak, Ilze Kumpina, John M. Talbott, Martins Katkevics, Eriks Rozners, James A. MacKay
Summary: Peptide nucleic acids (PNA) with extended isoorotamides containing nucleobases (I-o) were designed to bind A-U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments showed improved affinity for A-U using the Io scaffold in PNA, with PNAs having four sequential Io extended nucleobases maintaining high binding affinity.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Multidisciplinary Sciences
Alla E. Sidorova, Ekaterina V. Malyshko, Aleksey O. Lutsenko, Denis K. Shpigun, Olga E. Bagrova
Summary: This paper proposes methods for quantitative analysis of the chirality of protein helical and superhelical structures, revealing common and specific features among different protein classes. The data obtained can likely reflect considerations about molecular machines as chiral formations.
Article
Chemistry, Applied
Hao Lu, Yaoqi Tian, Rongrong Ma
Summary: In this study, the long- and short-range order of retrograded starch was evaluated using FTIR, XRD, and Raman spectroscopy. It was found that the order of all helical structures increased during retrogradation, with the amylose double helix having the highest order and crystallization rate.
FOOD HYDROCOLLOIDS
(2023)
Article
Chemistry, Multidisciplinary
Chunmei Zhao, Zhiying Ma, Chunli Li, Li Xu, Hua Wang
Summary: A novel racemate and enantiomer of binaphthylcyclooctaterthiophene (BN-COTh) were synthesized and investigated for their crystal structures, spectroscopic behaviors, chiral resolution, and characteristics. The enantiomer of (R,R, R)-BN-COTh exhibited unique intermolecular interactions in crystal, forming a larger and extended assembly packing along the b-axis.
CHINESE CHEMICAL LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Ilze Kumpina, Vladislavs Baskevics, Khoi D. Nguyen, Martins Katkevics, Eriks Rozners
Summary: This study investigated the use of five-membered heterocycles and linkers to optimize the formation of X • C-G and Y • U-A triplets. Increasing the linker length by four atoms improved binding affinity and selectivity.
Article
Multidisciplinary Sciences
Haina Huang, Katrin Karbstein
Summary: This passage discusses the tendency of three-helix junctions to misfold during the assembly of small ribosomal subunits in cells, and reveals the pivotal role of ribosome assembly factors in facilitating their correct folding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Jiangbin Wu, Nan Wang, Ya-Ru Xie, Hefei Liu, Xinghao Huang, Xin Cong, Hung-Yu Chen, Jiahui Ma, Fanxin Liu, Hangbo Zhao, Jun Zhang, Ping-Heng Tan, Han Wang
Summary: This research reports the extraordinary mechanical properties of the newly discovered inorganic double helical semiconductor tin indium phosphate, which has the lowest Young's modulus and large elastic and plastic bending strains. These results are of great significance for understanding the mechanical properties of the material and its potential applications in flexible electronics and nanomedicine.
Article
Multidisciplinary Sciences
Juan P. Castillo, Alexander B. Tong, Sara Tafoya, Paul J. Jardine, Carlos Bustamante
Summary: Ring ATPase translocases operate by forming lock-washer architectures and using a hand-over-hand mechanism when transporting disordered substrates. When challenged with different DNA substrates, such as DNA-RNA hybrids, these motors adjust their power strokes to match the helical pitches, alternating between ATP loading and hydrolysis stages. The authors propose a helical inchworm translocation mechanism to explain the structural changes observed during the operation of the motor on different substrates.
NATURE COMMUNICATIONS
(2021)
Article
Mechanics
Peng Zhang, Zhenyu Han, Jiachen Gu, Shouzheng Sun, Hongya Fu
Summary: The research studied the influence of winding patterns on the grid intersections and the manufacturing process and strength analysis of a cylindrical grid structure. Additionally, the fiber morphologies at the intersections formed by different fiber paths were compared.
COMPOSITE STRUCTURES
(2021)
Article
Chemistry, Multidisciplinary
John M. Talbott, Brandon R. Tessier, Emily E. Harding, Grant D. Walby, Kyle J. Hess, Vladislavs Baskevics, Martins Katkevics, Eriks Rozners, James A. Mackay
Summary: Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. The experiments showed that these new PNA nucleobases have strong binding affinity, which will contribute to the future design of nucleobases capable of recognizing any sequence of double helical RNA.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Organic
Tanima Bhattacharyya, Deepanjan Panda, Jyotirmayee Dash
Summary: The use of G-B hydrogel as a template allows for the assembly of DNA G-quadruplex-selective 1,4-triazole ligands while stabilizing and strengthening the gel assembly.
Article
Chemistry, Physical
Zhuanfang Zhang, Qingfang Zhen, Chunjing Zhang, Xiao Liu, Yu Sun, Haijun Pang
Summary: A new polyoxometalate-based compound with helical and porous structural features was synthesized and investigated for its luminescent properties in the solid state at room temperature. The enhanced luminescent property of this compound is attributed to an internal heavy metal effect.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Engineering, Biomedical
Wei Zhou, Ge Shi, Peng Zhao, Gai Zhang, Peilang Yang, Bohan Li, Bowen Li, Xinhua Wan, Yijun Zheng
Summary: This study discovers that pyrrolidinium-pendant polyacetylenes (PAs) with dynamic helical conformations exhibit fast and efficient antimicrobial activity against a wide range of pathogens, with low toxicity to mammalian cells and minimal risk of antibiotic resistance. The full-thickness wound infection model in mice demonstrates the favorable biocompatibility and effective in vivo antibacterial capabilities of these PAs. The dynamic helical structure of these PAs allows them to adapt and form pores in the bacterial membrane upon interaction, leading to their potent antimicrobial activity.
ACTA BIOMATERIALIA
(2023)
Article
Materials Science, Multidisciplinary
Qianqian Shi, Dashen Dong, Gediminas Gervinskas, Han Lin, Debabrata Sikdar, Baohua Jia, Sumeet Walia, Sharath Sriram, Madhu Bhaskaran, Lim Wei Yap, Wenlong Cheng
Summary: This work presents a method for fabricating 3D helical plasmonic nanostructures from 2D plasmene nanosheets. By using a micro-spatula-based strategy inspired by the chocolate curls-making process, the plasmene nanosheets can be selectively scraped to free space, resulting in the spontaneous folding of the nanosheets into various complex helical nanostructures with controlled dimensions. This versatile fabrication route combines both bottom-up and top-down approaches and has potential applications in next-generation flexible nanophotonic devices.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Physical
Salah Eddine Ghellab, Xiaojun Han
Summary: Biomolecular self-assembly is crucial in the life system. In this study, double-helical phospholipid-modified carbon nanotube structures were created through the self-assembly of phospholipids on carbon nanotubes. These micrometer size spring structures may have potential applications in biocompatible microrobots.
Correction
Oncology
Kalle Gehring, Hiroaki Miki
BRITISH JOURNAL OF CANCER
(2021)
Review
Biochemistry & Molecular Biology
Kalle Gehring, Guennadi Kozlov, Meng Yang, Rayan Fakih
Summary: Phosphatases of regenerating liver (PRLs) are protein phosphatases involved in the control of cell growth and migration. Recent studies have shown that PRLs have dual functions as both catalytically active enzymes and pseudophosphatases, contributing to their unique properties.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Christopher Liczner, Cameron C. Hanna, Richard J. Payne, Christopher J. Wilds
Summary: This study presents an efficient method for synthesizing peptide-oligonucleotide conjugates using a diselenide-selenoester ligation strategy, which leads to stable amide linkages between the two biomolecules. The novel conjugation strategy increases synthesis efficiency and expands the applications of chemical modification.
Article
Biochemistry & Molecular Biology
Marta Vranas, Yang Lu, Shafqat Rasool, Nathalie Croteau, Jonathan D. Krett, Veronique Sauve, Kalle Gehring, Edward A. Fon, Thomas M. Durcan, Jean-Francois Trempe
Summary: Mutations in Parkin and PINK1 cause early-onset familial Parkinson's disease. The study found that His433 contributes to the catalysis of Parkin and its mutation impairs mitophagy. Mfn2 is a kinetically preferred substrate for Parkin, co-localizing with PINK1 and phospho-ubiquitin upon mitochondrial depolarization.
Article
Biochemistry & Molecular Biology
Veronique Sauve, George Sung, Emma J. MacDougall, Guennadi Kozlov, Anshu Saran, Rayan Fakih, Edward A. Fon, Kalle Gehring
Summary: PINK1 and parkin play a crucial role in mitochondrial quality control and are often mutated in Parkinson's disease. PINK1 phosphorylates ubiquitin and the Ubl domain of parkin to regulate the localization and activity of parkin. The study discovered that phospho-ubiquitin can bind to two different sites on parkin, controlling its localization and releasing its autoinhibition. Activation of parkin by phosphorylated ubiquitin plays a significant role in the PINK1-parkin pathway.
Article
Multidisciplinary Sciences
Sharon Kaisari, Shirly Miniowitz-Shemtov, Danielle Sitry-Shevah, Pnina Shomer, Guennadi Kozlov, Kalle Gehring, Avram Hershko
Summary: The mitotic checkpoint system ensures accurate chromosome segregation in mitosis. UBR5 is a protein associated with mitotic checkpoint proteins and plays a role in regulating the inactivation of the mitotic checkpoint.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Cell Biology
Rayan Fakih, Veronique Sauve, Kalle Gehring
Summary: Parkinson's disease is a neurodegenerative disorder caused by the loss of dopaminergic neurons. Mutations in PRKN and PINK1 genes are responsible for early onset Parkinson's. Our research shows that PINK1 can activate PRKN to promote mitophagy. This signaling pathway offers potential for the development of therapeutics.
Article
Chemistry, Medicinal
Alexander Pontarelli, Christopher J. Wilds
Summary: This article describes the synthesis of a novel C5-propynyl-beta-Darabinouridine (araUP) phosphoramidite and its incorporation into oligonucleotides. The chemical modification of oligonucleotides can enhance their stability and improve their resistance to nucleases and serum, which shows potential for therapeutic gene silencing.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Rayan Fakih, Veronique Sauve, Kalle Gehring
Summary: Parkin and PINK1 regulate a mitochondrial quality control system that is mutated in some early onset forms of Parkinson's disease. Recently, an alternative feed-forward mechanism was identified that bypasses the need for parkin phosphorylation. This study reveals the structure of parkin activated through this feed-forward mechanism and provides insights into the differences in specificity and affinity of the binding sites.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Organic
Alexander Pontarelli, Jiang Tian Liu, Hourieh Movasat, Sarah Menard, Jung Kwon Oh, Christopher J. Wilds
Summary: The synthesis and incorporation of a tosylated phosphoramidite linker containing a disulfide bond is described. This linker was efficiently incorporated into short DNA and RNA oligomers using automated solid phase synthesis, allowing for the expansion of strategies for bifunctional modification of synthetic oligonucleotides for conjugation applications.
Article
Biochemistry & Molecular Biology
Guennadi Kozlov, Sandy Mattijssen, Jianning Jiang, Samuel Nyandwi, Tara Sprules, James R. Iben, Steven L. Coon, Sergei Gaidamakov, Anne M. Noronha, Christopher J. Wilds, Richard J. Maraia, Kalle Gehring
Summary: In this study, the La-module of LARP1 was characterized, and it was found that unlike other LARPs, the La-module of LARP1 does not contain an RRM domain. The La-module alone is capable of binding poly(A) RNA with high specificity for the RNA 3'-end. This study provides insights into the functional relevance of LARP1 RNA binding in cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Alexander Pontarelli, Christopher J. Wilds
Summary: Chemical modifications on nucleic acids have allowed for the development of ASOs in the clinic. In this study, the synthesis and incorporation of C5-propynyl arabinouridine and arabinocytidine into ASOs were reported. The modified ASOs showed improved stability with RNA but not with DNA. This suggests that C5-modified arabinonucleic acids could be a potential chemical modification for therapeutic ASOs.
Review
Biochemistry & Molecular Biology
Yu Seby Chen, Kalle Gehring
Summary: Magnesium (Mg2+) is a vital divalent cation in cells and has crucial roles in various biological processes. CNNMs, a class of Mg2+ transporters, were initially found in bacteria and are present in humans as four proteins, involved in divalent cation transport, genetic diseases, and cancer. Eukaryotic CNNMs consist of four domains, including an extracellular domain, a transmembrane domain, a CBS-pair domain, and a cyclic nucleotide-binding homology domain. This review focuses on the structural and functional studies of eukaryotic and prokaryotic CNNMs, which contribute to the understanding of their regulation and ion transport mechanism. Recent studies on prokaryotic CNNMs show that the transmembrane domain facilitates ion transport, while the CBS-pair domain may regulate the process through binding divalent cations. Moreover, studies on mammalian CNNMs have revealed new binding partners, leading to better comprehension of this widely conserved family of ion transporters.
Article
Biochemistry & Molecular Biology
Rayan Fakih, Robert H. Goldstein, Guennadi Kozlov, Kalle Gehring
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Alexander Pontarelli, Christopher J. Wilds
Summary: This study describes the synthesis of C5-propynyl-2'-fluoroarabinonucleic acids (FANAP) and reveals that these modifications enhance RNA binding and support RNase H mediated cleavage. These findings suggest that C5-propynyl ANA/FANA modifications have promising potential for the design of therapeutic ONs.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
