Article
Chemistry, Multidisciplinary
Chuan Jiang, Biao Lu, Wei Zhang, Yoel P. Ohayon, Feiyang Feng, Shijie Li, Nadrian C. Seeman, Shou-Jun Xiao
Summary: This study demonstrates the formation of planar 2D lattices and tubular structures in DNA nanostructures by designing different tile cores and varying inter-tile distances. By using streptavidin and biotin labeling techniques, the inside and outside surfaces of the tubes can be characterized to determine the tile conformation with addressable faces. Integration of the intrinsic curvature of the tiles with arm twist allows the generation of DNA tubes with right- or left-handed chirality.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Nanoscience & Nanotechnology
Muhammad Tayyab Raza, Suyoun Park, Anshula Tandon, Sungjin Lee, Thi Hong Nhung Vu, Thi Bich Ngoc Nguyen, Sung Ha Park
Summary: The construction of nanostructures with nanometre-scale precision through DNA building blocks relies on self-assembly, base-pair complementarity, and sequence programmability. Multi-step annealing and the use of boundaries allow for efficient and effective construction of target lattices. Atomic force microscopy (AFM) visualization confirms the successful formation of target DNA lattices within single crystals.
Article
Biochemistry & Molecular Biology
Paula Alonso-Ramos, David Alvarez-Melo, Katerina Strouhalova, Carolina Pascual-Silva, George B. Garside, Meret Arter, Teresa Bermejo, Rokas Grigaitis, Rahel Wettstein, Marta Fernandez-Diaz, Joao Matos, Marco Geymonat, Pedro A. San-Segundo, Jesus A. Carballo
Summary: This study reveals previously undescribed functions of the evolutionary conserved Cdc14 phosphatase in the regulation of meiotic recombination, including the regulation of crossover formation and the control of the activity of the Holliday Junction resolvase Yen1/GEN1.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Lin Dai, Lian Lu, Xu Zhang, Juhong Wu, Jinyu Li, Zhonghui Lin
Summary: The Holliday junction branch migrator RuvAB complex is a crucial factor in homologous recombination and DNA damage repair, and can be targeted for the treatment of bacterial pathogens. This study identified small-molecule inhibitors of PaRuvAB, including corilagin, bardoxolone methyl, and 10-(6 '-plastoquinonyl) decyltriphenylphosphonium, which efficiently inhibited the branch migration activity of PaRuvAB and increased the susceptibility of P. aeruginosa to UV-C irradiation.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Akanksha Singh, Ramesh Kumar Yadav, Ali Shati, Nitin Kumar Kamboj, Hesham Hasssan, Shiv Bharadwaj, Rashmi Rana, Umesh Yadava
Summary: In this study, we investigated the dynamic folding transitions of a unique DNA junction and its self-assembly into a four-way DNA junction form with sticky ends. Molecular dynamics simulations were conducted under various physiological conditions, and the post-dynamics structure parameters were compared with the crystal structure. It was found that the self-assembly dynamics of the DNA junction were temperature and pH sensitive, revealing peculiar structural properties over time. These findings have implications for the synthesis and development of DNA junctions for various applications, such as genetic biomarkers and drug-releasing nanomachines triggered by pH dis-regulation.
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
Multidisciplinary Sciences
Chiara Balbo Pogliano, Ilaria Ceppi, Sara Giovannini, Vasiliki Petroulaki, Nathan Palmer, Federico Uliana, Marco Gatti, Kristina Kasaciunaite, Raimundo Freire, Ralf Seidel, Matthias Altmeyer, Petr Cejka, Joao Matos
Summary: Bloom's syndrome is caused by the inactivation of the BLM helicase, which requires the activity of CDK1, PLK1, and TOPBP1 to avoid somatic crossing-over. CDK1 phosphorylates BLM and TOPBP1, promoting their interaction with PLK1. The CDK1-TOPBP1-PLK1 axis stimulates BTR-mediated dissolution of recombination intermediates late in the cell cycle, suppressing crossover recombination and reducing genomic instability.
Article
Chemistry, Multidisciplinary
Saber Mehrparvar, Christoph Woelper, Gebhard Haberhauer
Summary: Until now, there have been few cases of designing helical structures from planar building blocks via self-assembly. In this study, we demonstrate that the carbonyl-tellurium interaction motif can assemble small planar units into helical structures in solid phase. We discovered two different types of helices: single and double helices, depending on the substitution pattern. The carbonyl-tellurium chalcogen bond has the potential to generate complex three-dimensional patterns.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yun-Lan Li, Zhong-Ming Huang, Hai-Ling Wang, Zhong-Hong Zhu, Fu-Pei Liang, Hua-Hong Zou
Summary: This study synthesized two Dy-8 clusters with opposite framework structures and revealed their excellent molecular magnetic properties. The self-assembly process of the clusters was successfully tracked using HRESI-MS, and a possible self-assembly mechanism was proposed.
Article
Biochemistry & Molecular Biology
Sebastian Sewerin, Jorg Piontek, Ria Schonauer, Sonja Grunewald, Angelika Rauch, Steffen Neuber, Carsten Bergmann, Dorothee Gunzel, Jan Halbritter
Summary: This study investigated the molecular basis and phenotypic consequences of a CLDN10 gene variant, which disrupts the assembly of tight junction (TJ) strands. The mutant proteins compromised the function of TJ and exhibited tissue-specific insertion into TJs.
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
Chemistry, Analytical
Haobo Sun, Lisheng Qian, Jinming Kong, Xueji Zhang
Summary: A novel electrochemical biosensor platform with triple helix structure switch and double signal amplification strategy was proposed for nucleic acid detection, achieving ultra-sensitivity and high selectivity. The biosensor showed a detection limit as low as 1.954 aM and a linear range of 7 orders of magnitude. Additionally, it demonstrated excellent anti-interference ability when analyzing DNA in serum samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Chemistry, Physical
Roaa Mahmoud, Soma Dhakal
Summary: This article systematically investigates the effects of cell-mimic solvent composition and crowding on DNA Holliday junctions (HJs) branch migration (BM) using single-molecule fluorescence analysis. The results show that BM is affected by cosolutes in a concentration-dependent manner, and it is significantly accelerated under crowding environments. The enhanced mobility of HJs in cell-like environments may provide new avenues for therapeutic interventions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Cell Biology
Aurore Sanchez, Giordano Reginato, Petr Cejka
Summary: This article reviews models explaining the processing of recombination intermediates in vegetative and meiotic cells and its regulation, focusing on MLH1-MLH3-dependent crossing-over during meiotic recombination. The summary emphasizes the importance of accurate recombination for genome stability in vegetative cells and the role of crossovers in promoting genetic diversity during meiosis.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2021)
Article
Materials Science, Characterization & Testing
Jordana K. Palacios, Rose Mary Michell, Alejandro J. Mueller
Summary: This review provides a comprehensive analysis of the crystallization behavior and self-assembly of block copolymers with up to four potentially crystallizable phases. It discusses the factors affecting the development of crystalline structures and highlights recent advances in block copolymer crystallization. The article also explores the influence of different molecular architectures, as well as the role of nanofillers and additives in the crystallization process.
Review
Chemistry, Multidisciplinary
Nicolo Zuin Fantoni, Afaf H. El-Sagheer, Tom Brown
Summary: Click chemistry, particularly azide-alkyne cycloadditions, is a powerful technique for the covalent conjugation of molecular entities. Its application in nucleic acid chemistry allows efficient and cost-effective labeling, ligation, and cyclization of oligonucleotides compared to traditional techniques. This review provides a guide to researchers approaching the field, discussing the chemistry and applications of AAC reactions in nucleic acids.
Article
Chemistry, Multidisciplinary
Miguel Xavier, Maria-Eleni Kyriazi, Stuart Lanham, Konstantina Alexaki, Elloise Matthews, Afaf H. El-Sagheer, Tom Brown, Antonios G. Kanaras, Richard O. C. Oreffo
Summary: Researchers have developed DNA-gold nanoparticles to identify and sort SSCs with specific mRNA signatures, significantly enriching these skeletal stem cells. This method has the potential to enhance our understanding of bone cell biology and translational applications.
Article
Chemistry, Multidisciplinary
Alisina Bazrafshan, Maria-Eleni Kyriazi, Brandon Alexander Holt, Wenxiao Deng, Selma Piranej, Hanquan Su, Yuesong Hu, Afaf H. El-Sagheer, Tom Brown, Gabriel A. Kwong, Antonios G. Kanaras, Khalid Salaita
Summary: Research has shown that optimizing DNA motor performance can be achieved by adjusting structural parameters and buffer conditions. Increasing DNA leg density can improve speed and processivity, while DNA leg span can increase processivity and directionality. Label-free imaging has also revealed the unique motion patterns of the motors.
Article
Biochemistry & Molecular Biology
Bengt Norden, Tom Brown, Bobo Feng
Summary: This study investigates the effect of a semi-hydrophobic environment represented by poly(ethylene glycol) on the strand exchange process of DNA, specifically focusing on the role of the concentration of the co-solute in accelerating the exchange from mismatched to matched strands. The results suggest that the semi-hydrophobic environment affects the process through various mechanisms, including weakening base stacking, strengthening base-pair hydrogen bonds, and stabilizing unstacked mismatched bases with intercalated hydrophobic co-solvent molecules.
Article
Biotechnology & Applied Microbiology
Martin Philpott, Jonathan Watson, Anjan Thakurta, Tom Brown, Tom Brown, Udo Oppermann, Adam P. Cribbs
Summary: scCOLOR-seq is a method for single-cell corrected long-read sequencing, allowing standalone cDNA nanopore sequencing of single cells. It corrects errors in barcode and unique molecular identifier sequences, and is used for evaluating the transcriptomic features of different cell lines.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
David A. Rusling
Summary: The introduction of the nucleobase 6-amino-5-nitropyridin-2-one (Z) enables stable and selective triplex formation of synthetic TFOs at neutral pH and above, overcoming the limitation of cytosine protonation at low pH. Furthermore, a universal strategy for enzymatic assembly of Z-containing TFOs using commercially available deoxyribonucleotide triphosphate has been demonstrated, aiming to improve the recognition properties of TFOs and reduce the cost and expertise associated with their chemical syntheses.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Cheng Jin, Afaf H. Ei-Sagheer, Siqi Li, Katherine A. Vallis, Weihong Tan, Tom Brown
Summary: Oligonucleotides containing cleavable linkers are versatile tools for stimulus-responsive and site-specific DNA cleavage, but their previous limitations have restricted their in vivo applications. Inspired by cathepsin B-sensitive dipeptide linkers in ADCs, we have developed phosphoramidites of Val-Ala-02 and Val-Ala-Chalcone for automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B efficiently digests these linkers, enabling cleavage of oligonucleotides or release of small-molecule payloads. We believe that these dipeptide linker phosphoramidites will expand the clinical applications of therapeutic oligonucleotides.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Maria-Eleni Kyriazi, Afaf H. El-Sagheer, Igor L. Medintz, Tom Brown, Antonios G. Kanaras
Summary: Researchers have overcome the limitation of enzymatic degradation of spherical nucleic acids by introducing a phosphorothioate bond modification on the oligonucleotide backbone, allowing for high selectivity and specificity in the detection of mRNA in cells.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Yue Zhao, Arun Richard Chandrasekaran, David A. Rusling, Karol Woloszyn, Yudong Hao, Carina Hernandez, Simon Vecchioni, Yoel P. Ohayon, Chengde Mao, Nadrian C. Seeman, Ruojie Sha
Summary: Reconfigurable DNA structures engineered through hybridization and self-assembly have potential applications in nanotechnology. This study demonstrates the creation of robust macroscopic DNA crystals through strand displacement of triplex-forming oligonucleotides (TFOs), which can be removed or replaced using different methods. X-ray diffraction analysis confirms the designed structure of the crystals in the presence of TFOs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Joseph Hennessy, Piotr Klimkowski, Daniel Singleton, Alex Gibney, Malou Coche, Nicholas P. Farrell, Afaf H. El-Sagheer, Tom Brown, Andrew Kellett
Summary: We report a new class of carboplatin-TFO hybrid that incorporates a bifunctional alkyne-amine nucleobase monomer called AP-C3-dT, enabling dual 'click' platinum(ii) drug conjugation and thiazole orange fluorophore coupling. These hybrids exhibit superior stability and crosslinking properties compared to previous Pt(ii)-TFOs, and show sequence-specific binding at neutral pH.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Chunsen Bai, Piotr Klimkowski, Cheng Jin, Jagannath Kuchlyan, Afaf H. El-Sagheer, Tom Brown
Summary: Oligonucleotides labelled with thiazole orange intercalator and a reporter dye on the same thymine base have been synthesized, enabling dual orthogonal labelling of the nucleobase. These combination probes show high duplex stability and fluorescence when bound to complementary DNA and RNA in their DNA and 2'-OMe RNA formats.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Konstantina Alexaki, Maria Eleni Kyriazi, Joshua Greening, Lapatrada Taemaitree, Afaf H. El-Sagheer, Tom Brown, Xunli Zhang, Otto L. Muskens, Antonios G. Kanaras
Summary: In this study, we successfully demonstrated the rapid and accurate detection of SARS-CoV-2 infection without the need for PCR amplification using UCNPs and GO.
Article
Biochemistry & Molecular Biology
Anna Dysko, Ysobel R. Baker, Graham McClorey, Matthew J. A. Wood, Sabine Fenner, Glynn Williams, Afaf El-Sagheer, Tom Brown
Summary: Oligonucleotides are powerful therapeutics for difficult diseases, but they require chemical modification. Substituting the phosphodiester backbone with a triazole linkage provides stability and improved cell penetration, but reduces RNA target binding. Attaching pyrene or anthraquinone to the ribose sugar of the triazole restores stability and splice switching ability.
RSC CHEMICAL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Angela F. De Fazio, Doxi Misatziou, Ysobel R. Baker, Otto L. Muskens, Tom Brown, Antonios G. Kanaras
Summary: The self-assembly of inorganic nanoparticles into larger structures allows for the fabrication of novel materials with collective properties; recently developed methods for controlling nanoparticle organization have enabled the fabrication of new materials; DNA modifications and molecular intercalators have been utilized as tools for manipulating DNA-nanoparticle structures.
CHEMICAL SOCIETY REVIEWS
(2021)