Article
Biochemistry & Molecular Biology
Haritha Asha, Petr Stadlbauer, Lara Martinez-Fernandez, Pavel Banas, Jiri Sponer, Roberto Improta, Luciana Esposito
Summary: The study investigates the structural behavior of a quadruplex helix sequence in human telomeres when one of the G bases is ionized to G(center dot+). It is found that the position of G(center dot+) influences structural rearrangements, electrostatic repulsion, and solvent exposure, providing new insights into guanine reactions. The research suggests structural determinants of reactivity and implications for understanding reactivity in other G-quadruplex topologies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Cell Biology
Elisa Balzano, Franca Pelliccia, Simona Giunta
Summary: Repeated sequences make up more than half of the human genome and play a significant role in various physiological and pathological conditions. Tandem repeats, a major category of repetitive DNA in the human genome, have a higher mutation rate and are prone to aberrant recombination, leading to associations with a variety of diseases.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lydia Olejko, Anushree Dutta, Kosar Shahsavar, Ilko Bald
Summary: In this study, specific G-quadruplex structures formed by reversed human telomeric DNA in the presence of different cations were analyzed using circular dichroism spectroscopy and Forster resonance energy transfer. The results provide important insights into the formation of G-quadruplexes in different environments and the rational design of G-quadruplex-based applications in sensing and nanotechnology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Alexa M. Salsbury, Haley M. Michel, Justin A. Lemkul
Summary: This study used polarizable simulations to investigate telomeric DNA structures, including G-quadruplexes and G-hairpins. The presence of specific motifs, such as the G-triad, in the telomeric G-quadruplex suggests potential druggable sites. In addition, the simulations showed the unbiased formation of G-triad and G-tetrad in the G-hairpin, and the involvement of cations in their formation. Furthermore, the study demonstrated the specific interactions between K+ ions and guanine bases, providing new insights into the influence of ions on telomeric DNA structures.
Article
Chemistry, Inorganic & Nuclear
Jiafan Lin, Jishuai Zhang, Ziqi Ma, Xiaoqin Wu, Fuyi Wang, Yao Zhao, Kui Wu, Yi Liu
Summary: The interaction between a photoactivatable Pt(iv) prodrug and human telomeric DNA was studied. Two major mono-platinated DNA adducts were detected, with trans-[Pt-II(N-3)(py)(2)](+) and trans-[Pt-II(py)(2)](2+) as the bound Pt moieties. The platination sites were found to be G(6) and A(3) in one adduct, and a potential intrastrand crosslink was speculated after G(4) and G(6) in the other adduct. Minor platinated adducts and oxidized DNA adducts were also observed. These results provide valuable chemical information about the photoreaction between photoactivatable Pt(iv) anticancer prodrugs and human telomeric DNA.
DALTON TRANSACTIONS
(2023)
Article
Chemistry, Physical
Chensheng Ma, Joshua Chiu-Lok Chow, Allen Ka-Wa Wong, Qingwu Xiong, Jacob Chomchoei, Wai-Ming Kwok
Summary: This study reports the first direct probe of excitation dynamics for a bimolecular GQ from human telomeric repeat-containing RNA, revealing the existence of an unusual high-energy excimer in the core region with rapid proton transfer and an unprecedented exciplex with massively red-shifted fluorescence in the loop region, resulting from charge transfer.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Matko Gluncic, Ines Vlahovic, Marija Rosandic, Vladimir Paar
Summary: This study reveals the presence of corresponding NBPF 3mer HOR arrays in the Neanderthal genome, with slight differences in monomer structures and numbers of HOR copies compared to humans. Additionally, two novel tandem arrays of NBPF 3mer HOR repeats were identified, suggesting the existence of new NBPF genes.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Aghil Soman, Sook Yi Wong, Nikolay Korolev, Wahyu Surya, Simon Lattmann, Vinod K. Vogirala, Qinming Chen, Nikolay Berezhnoy, John van Noort, Daniela Rhodes, Lars Nordenskiold
Summary: This study reveals the molecular-level structure of telomeric chromatin, including telomeric chromatin fibres and the structure of telomeric tetranucleosome. The research found that columnar arrangement of nucleosomes with a short DNA repeat length is stabilized by specific histone tails synergistically, potentially making DNA susceptible to damage.
Article
Biochemistry & Molecular Biology
Simone Carrino, Christopher D. Hennecker, Ana C. Murrieta, Anthony Mittermaier
Summary: Human chromosomes have long, single-stranded DNA overhangs with repetitive sequences (TTAGGG)n at the termini, which can fold into guanine quadruplexes (GQ). The folding of GQs within these chains is influenced by folding frustration and negative cooperativity, leading to increased unfolding of TTAGGG repeats and potential binding sites for telomeric proteins. This phenomenon is particularly pronounced at the chain termini, suggesting a role in telomere extension by telomerase.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Tom Miclot, Camille Corbier, Alessio Terenzi, Cecilia Hognon, Stephanie Grandemange, Giampaolo Barone, Antonio Monari
Summary: This study demonstrated the crucial role of the stability of G-quadruplex in telomeric DNA in resisting oxidative stress and as an inhibitor of telomerase, an enzyme overexpressed in most cancers associated with oxidative stress. The combined experimental and computational investigation utilized circular dichroism, cellular immunofluorescence assays, and molecular dynamics simulations to identify these roles.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Diana Muller, Irene Bessi, Christian Richter, Harald Schwalbe
Summary: The folding kinetics of RNA G4 and DNA G4 differ significantly during K+-induced folding, mainly due to differences in their folded conformations, especially regarding the chi angle preferences. Modified DNA G4 can achieve faster folding kinetics and monomorphic conformations similar to RNA G4 by adjusting the chi angle.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Benedetta Petra Rosi, Valeria Libera, Luca Bertini, Andrea Orecchini, Silvia Corezzi, Giorgio Schiro, Petra Pernot, Ralf Biehl, Caterina Petrillo, Lucia Comez, Cristiano De Michele, Alessandro Paciaroni
Summary: We investigated the stacking interactions and structural features of telomeric G4 multimers using a low-resolution structural approach that combines small-angle X-ray scattering (SAXS) with extremely coarse-grained (ECG) simulations. The self-assembly of G4 multimers leads to significant polydispersity and exponential distribution of contour lengths. We found that the strength of the stacking interaction between G4 monomers increases with increasing DNA concentration, as well as the average number of units in the aggregates. The proposed methodology may aid in the selection and design of drugs that target G4s under physiological conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Genetics & Heredity
Yuzhe Liu, Jinhuan Li, Qiang Wu
Summary: Short tandem repeats (STRs) are abundant structural or functional elements in the human genome that exhibit polymorphic nature and are associated with neurological disorders. This study examined STR instability in cultured human cells and found that both Sanger sequencing and next-generation sequencing can accurately assess STR length. Additionally, the study revealed the intrinsic instability of STRs in cultured human cell populations and during single-cell cloning. These findings provide a reliable method for assessing STR length and have important implications for investigating the pathogenesis of STR expansion diseases.
Article
Biochemistry & Molecular Biology
Chih-Yi Gabriela Lin, Anna Christina Naeger, Thomas Lunardi, Aleksandra Vancevska, Gerald Lossaint, Joachim Lingner
Summary: Telomere shortening can lead to diseases and aging, often due to the lack of telomerase in cells. By developing a new isolation protocol, specific proteins associated with telomere replication can be purified, revealing their importance for maintaining telomere stability. This study provides a valuable resource for understanding the dynamic changes of the telomeric proteome during replication.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Junyeop Lee, Keewon Sung, So Young Joo, Jun-Hyeon Jeong, Seong Keun Kim, Hyunsook Lee
Summary: The dynamic interaction between BRCA2 and telomeric G-quadruplex (G4) plays a crucial role in telomere replication. Binding of BRCA2 remodels telomeric G4 structure, allowing the restart of stalled replication forks driven by G4 and preventing telomere breakdown.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Yihong Feng, Masayuki Endo, Hiroshi Sugiyama
Summary: Nucleosomes, as the fundamental building blocks of chromatin, are highly dynamic and play vital roles in the formation of higher-order chromatin structures and gene regulation. Recent advances in epigenetics research have gradually unraveled nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions. With the continuous development of research methods such as cryo-EM and next-generation sequencing, our understanding of nucleosomes is becoming broader and deeper.
Article
Chemistry, Multidisciplinary
Shubham Mishra, Soyoung Park, Tomoko Emura, Hidaka Kumi, Hiroshi Sugiyama, Masayuki Endo
Summary: Stimuli-responsive switching molecules such as arylazopyrazole (AAP) have shown promising potential in controlling photoinduced assembly and disassembly of DNA origami nanostructures. AAP can achieve repeated assembly and disassembly of DNA origami structures through alternating UV and visible-light irradiation, demonstrating its versatility as a photoswitching molecule.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Rina Maeda, Toshikazu Bando, Hiroshi Sugiyama
Summary: Pyrrole-imidazole (PI) polyamides, which target specific DNA sequences, have shown sequence-specific alkylating activities when conjugated with DNA-alkylating agents, making them potential candidates for developing new anticancer drugs.
Review
Biochemistry & Molecular Biology
Soumya Sethi, Hiroshi Sugiyama, Masayuki Endo
Summary: DNA nanotechnology is a promising toolkit for mimicking cell-cell and cell-matrix interactions, aiding in understanding and manipulating cellular functions. Future innovations in the field can be inspired by exploring the potentials of DNA-based nanostructures and addressing current challenges.
Article
Biochemistry & Molecular Biology
Yuki Hirose, Tomo Ohno, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: A cyclic pyrrole-imidazole polyamide (cPIP) was synthesized to bind to the abnormal expanded CAG/CTG repeat DNA sequences, showing high binding affinity and specificity for its target DNA sequence.
Article
Biochemistry & Molecular Biology
Ryu Tashiro, Ji Hye Yum, Soyoung Park, Hiroshi Sugiyama
Summary: The study showed that the photoreactivity of U-Br changes dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when U-Br was incorporated into the RNA strand and the pyrene was conjugated to the 5 ' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes.
Article
Biochemistry & Molecular Biology
Kai Yu, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Naturally occurring ribozymes with modular architecture are promising for designing and assembling three-dimensional RNA nanostructures with catalytic abilities. In this study, RNA nanostructures with polygonal-shaped ribozyme oligomers were constructed using unit RNAs from the Tetrahymena group I intron, and ribozyme trimers with a triangular shape were dimerized by introducing pillar units. The resulting double-decker nanostructures containing six ribozyme units showed higher catalytic activity than the parent ribozyme trimers.
Article
Biochemistry & Molecular Biology
Sagun Jonchhe, Shankar Pandey, Christian Beneze, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao
Summary: Researchers found that a DNA nanobowl significantly increased the stability of a human telomeric G-quadruplex and its binding with a ligand. By minimizing the proximity effect and attributing the increased affinity to the nanoconfinement effect, they provided insights into the mechanisms of binding events in nanocavities.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Satoru Ide, Asuka Sasaki, Yusuke Kawamoto, Toshikazu Bando, Hiroshi Sugiyama, Kazuhiro Maeshima
Summary: The new PI-PRICh method allows effective isolation of specific chromatin segments and identification of both protein and RNA components. This approach shows good reproducibility in identifying telomeric chromatin, providing a promising alternative for studying chromatin organization and functions within the cell.
EPIGENETICS & CHROMATIN
(2021)
Article
Chemistry, Multidisciplinary
Vinodh J. Sahayasheela, Zutao Yu, Yuki Hirose, Ganesh N. Pandian, Toshikazu Bando, Hiroshi Sugiyama
Summary: Research suggests that targeting Gli-mediated transcription to inhibit the proliferation of cancer stem cells may be a promising strategy.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2022)
Article
Biochemistry & Molecular Biology
Shingo Hirashima, Hiroshi Sugiyama, Soyoung Park
Summary: This study characterized 2FA-containing DNA molecules and found that they have similar structure and properties to native adenine due to their small size, but exhibit unique features due to their high electronegativity. This provides valuable information for future applications of 2FA-modified DNA.
Article
Biochemistry & Molecular Biology
Junnosuke Hatanaka, Yuki Hirose, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: In this study, we synthesized linear pyrrole-imidazole polyamides (PIPs) that can selectively bind to DNA. These linear PIPs have lower molecular weights compared to commonly used hairpin PIPs. The binding affinity of the PIPs to DNA was improved by modifying the N-terminus of the linear PIPs. These findings provide insights for the design of effective linear PIPs.
Article
Biochemistry & Molecular Biology
Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Ganesh N. Pandian, Hiroshi Sugiyama
Summary: This study constructed a class of compounds that can selectively alkylate mutant mitochondrial DNA, with the potential to treat mitochondrial diseases. These compounds have programmability and can be used to target pathogenic mutations associated with mitochondrial diseases in future studies.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Haruhiko Eki, Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo
Summary: This study used atomic force microscopy to directly observe the formation and degradation of tensegrity triangle DNA crystals at a molecular level, visualizing the dynamic process and characterizing them with nanoscale resolution.
CHEMICAL COMMUNICATIONS
(2021)
Article
Oncology
Tomoo Daifu, Masamitsu Mikami, Hidefumi Hiramatsu, Atsushi Iwai, Katsutsugu Umeda, Mina Noura, Hirohito Kubota, Tatsuya Masuda, Kana Furuichi, Saho Takasaki, Yuki Noguchi, Ken Morita, Toshikazu Bando, Masahiro Hirata, Tatsuki R. Kataoka, Tatsutoshi Nakahata, Yasumichi Kuwahara, Tomoko Iehara, Hajime Hosoi, Junko Takita, Hiroshi Sugiyama, Souichi Adachi, Yasuhiko Kamikubo
Summary: Malignant rhabdoid tumor (MRT) is a rare and highly aggressive pediatric malignancy with poor prognosis. Current therapies are not effective enough, making the inhibition of RUNX1 a potential novel strategy for MRT treatment.
PEDIATRIC BLOOD & CANCER
(2021)
Review
Chemistry, Multidisciplinary
Dan He, Yawen Li, Fuwen Zhao, Yuze Lin
Summary: High trap density in organic solar cells leads to localized charge carriers and reduced carrier lifetime, limiting device efficiency. This feature article summarizes the recent advances of trap suppression by material design and device engineering.
CHEMICAL COMMUNICATIONS
(2024)
Review
Chemistry, Multidisciplinary
Olivier Monfort, Arshitha Madhusudhan, Martin Motola
Summary: This article presents the advantages of coupling photocatalysis and Fenton-based processes for environmental remediation and discusses their synergy. It critically examines the simultaneous triggering of these two processes and provides insights into research approaches. The study aims to enhance understanding of this complex process and highlight the potential integration of new catalysts in current wastewater treatment technology.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Manideepa Dhar, Chittaranjan Mishra, Avijit Das, Uttam Manna
Summary: An approach of 'polymerization of monomers in its aggregated form' has been introduced to tailor the water wettability of fibrous and porous substrates, achieving hydrophobicity to superhydrophobicity transition, as well as patterned wettability. This facile chemical method provides a durable coating with adjustable and patterned wettability for various potential applications.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Saswat Ranjan Bhoi, Chhanda Debnath, Shikha Gandhi
Summary: In this article, a novel catalytic reaction using Pd(0) and Bronsted acid is reported for the synthesis of biologically important imidazolidinone-fused N-heterocycles through redox-neutral intramolecular N-allylation of indoles and pyrroles with alkynes. This atom-economical method is applicable to a wide range of substrates and eliminates the need for leaving groups or oxidizing agents commonly used in traditional allylation reactions.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Longkun Chen, Mingshuai Zhang, Meichen Liu, Zhuoyuan Liu, Yuetong Qiu, Zhilai Zhang, Fuchao Yu, Jiuzhong Huang
Summary: In this study, an efficient Rh(III)-catalyzed selective mono- and dual-C-H bond functionalization/cyclization with iodonium ylide as the sole coupling partner was demonstrated. Fused benzodiazepine skeletons were obtained in excellent yields, providing an improved approach to dual C-H unsymmetrical functionalization.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Alice Kennett, Sven Epple, Gabriella van der Valk, Irene Georgiou, Evelyne Gout, Romain R. Vives, Angela J. Russell
Summary: This study presents the design and synthesis of sulfated disaccharide inhibitors based on IdoA(2S)-GlcNS(6S), which showed potent inhibition of Sulf-2. The results suggest that IdoA(2S)-GlcNS(6S) is the shortest fragment size required for effective inhibition of Sulfs, and a trisulfated disaccharide is identified as the minimal fragment size of heparan sulfate for effective endosulfatase inhibition.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Mauro Garbini, Andrea Brunetti, Riccardo Pedrazzani, Magda Monari, Massimo Marcaccio, Giulio Bertuzzi, Marco Bandini
Summary: The self-adaptability of galvanostatic electrolysis was found to be helpful in a multistage chemo- and diastereoselective electrochemically promoted cyclodimerization of chalcones. Through a series of reductive events, densely functionalized cyclopentanes with five contiguous stereocenters were obtained (25 examples, yields up to 95%, dr values up to >20:1). Further experimental and electrochemical investigations indicated the crucial role of dynamic kinetic resolution of the aldol intermediate in the reaction mechanism.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Dhananjay S. Nipate, Neha Meena, Prakash N. Swami, Krishnan Rangan, Anil Kumar
Summary: In this study, the synthesis of functionalized benzo[a]phenazines and indazolo[2,3-a]quinolines was achieved through Rh(III)-catalyzed oxidative annulation of 2-arylquinoxalines and 2-aryl-2H-indazoles with allyl alcohols. The method showed a wide substrate scope, excellent functional group tolerance, good to high yields of annulated products, and the capability for scaled-up synthesis. A tentative mechanism of the annulation reaction was proposed based on a preliminary mechanistic investigation.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Ruonan Zhang, Abudukadi Tudi, Xia Yang, Xuping Wang, Zhihua Yang, Shujuan Han, Shilie Pan
Summary: A new lead tellurium borate material with a unique fundamental building block [B4O10] was synthesized and found to exhibit high birefringence. The structure-property relationship was discussed using first-principles calculations.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Amresh Kumar Singh, Baishali Thakurta, Anupam Giri, Monalisa Pal
Summary: This study introduces three key concepts for the quick synthesis of large-scale high-quality 2D materials films and their utilization in device fabrication.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Reina Hagiwara, Shun Nishimura, Kosuke Okeyoshi
Summary: A copolymer-conjugated nanocatalytic system has been developed to improve electron transfer and enhance photoinduced H2 generation.
CHEMICAL COMMUNICATIONS
(2024)
