Review
Biotechnology & Applied Microbiology
Ahmed Zayed, Hang Thi Thuy Cao, Vo Thi Dieu Trang, Roland Ulber
Summary: Fucoidans are sulfated, fucose-rich, and high molecular weight polysaccharides derived from brown seaweeds. Their applications are influenced by various chemical properties, and different strategies have been developed to modify native fucoidans for enhanced bioactivity and formulation efficiency.
JOURNAL OF APPLIED PHYCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Juntaek Oh, Ji Shin, Ilona Christy Unarta, Wei Wang, Aaron W. Feldman, Rebekah J. Karadeema, Liang Xu, Jun Xu, Jenny Chong, Ramanarayanan Krishnamurthy, Xuhui Huang, Floyd E. Romesberg, Dong Wang
Summary: The study found that eukaryotic RNA polymerase II is capable of selectively recognizing unnatural base pairs with high fidelity, especially when the template strand contains dTPT3. Additionally, a novel 3'-RNA binding site termed the swing state was identified after rNaM addition. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Claire Chung, Bert M. Verheijen, Zoe Navapanich, Eric G. McGann, Sarah Shemtov, Guan-Ju Lai, Payal Arora, Atif Towheed, Suraiya Haroon, Agnes Holczbauer, Sharon Chang, Zarko Manojlovic, Stephen Simpson, Kelley W. Thomas, Craig Kaplan, Peter van Hasselt, Marc Timmers, Dorothy Erie, Lin Chen, Jean-Francois Gout, Marc Vermulst
Summary: Accurate transcription is crucial for the faithful expression of genetic information. This study measured the error rate of transcription in five organisms and found variations in RNA polymerase II error rates among species. The research also identified genetic factors that affect transcription fidelity and provided insights into the co-evolution of transcription error rate and the genetic code.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Huasong Ai, Guo-Chao Chu, Qingyue Gong, Ze-Bin Tong, Zhiheng Deng, Xin Liu, Fan Yang, Ziyu Xu, Jia-Bin Li, Changlin Tian, Lei Liu
Summary: The chemical synthesis of homogeneously modified histones is a powerful approach to deciphering how post-translational modifications modulate epigenetic events. In this study, we developed a rapid method to synthesize phosphorylated and ubiquitinated H2AX proteins and found that H2AXS139 phosphorylation distorts the interaction interface between ubiquitin and the repair factor 53BP1. Our study revealed redundancy in the interplay of multiple histone PTMs, which is useful for controlling the dynamic distribution of effector proteins on nucleosomes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Patrick W. Kudella, Alexei Tkachenko, Annalena Salditt, Sergei Maslov, Dieter Braun
Summary: Through templated ligation reactions, the study found that linking short oligomers from a random sequence pool reduces the sequence space of product strands, resulting in long, highly structured sequences with low entropy. This self-selecting ligation reaction can be restarted by only a few majority sequences, providing a favorable starting point for Darwinian evolution in an RNA world scenario.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Chemistry, Medicinal
Rocio Garcia-Vazquez, Umberto Maria Battisti, Matthias M. Herth
Summary: Tetrazine ligation, as a bio-orthogonal chemistry tool, has gained interest in nuclear medicine for pretargeted approaches, with the potential to revolutionize theranostic strategies. Pretargeting can increase target-to-background ratios and reduce dose to healthy tissue. Combined with diagnostic imaging, pretargeting may be optimal for theranostic approaches.
Article
Biology
Alexandra Kuehnlein, Simon A. Lanzmich, Dieter Braun
Summary: The study demonstrated that replication and translation can emerge through a self-assembly mechanism; experiments showed how oligonucleotides spontaneously formed molecular assemblies and replicated information under thermal oscillations; thermal oscillations separated replicates from templates, driving cross-catalytic replication.
Article
Genetics & Heredity
MaryElizabeth Stein, Suzanne E. Hile, Matthias H. Weissensteiner, Marietta Lee, Sufang Zhang, Eduard Kejnovsky, Iva Kejnovska, Kateryna D. Makova, Kristin A. Eckert
Summary: G-quadruplex structures can influence the accuracy of DNA polymerase during synthesis, especially during the synthesis of stable G-quadruplexes. The errors made by polymerase are associated with the topology and stability of the G-quadruplex structures.
Article
Chemistry, Multidisciplinary
Jiao-Na Han, Caijun Zhong, Mingmin Ge, Shi Kuang, Zhou Nie
Summary: The NHCouI dual-emission chromophore is a G4-responsive probe with a red emission signal that specifically responds to parallel G4s and a green emission signal that acts as an internal reference signal. It can self-calibrate the signal and avoid viscosity disturbances during G4 imaging in living cells.
Article
Biology
Thomas J. Etheridge, Desiree Villahermosa, Eduard Campillo-Funollet, Alex David Herbert, Anja Irmisch, Adam T. Watson, Hung Q. Dang, Mark A. Osborne, Antony W. Oliver, Antony M. Carr, Johanne M. Murray
Summary: The Smc5/6 complex is associated with chromatin in unchallenged cells through the non-SMC protein Nse6, involving at least two Nse6-dependent sub-pathways. Mutations in core subunits of the Smc5/6 complex affect chromatin association, with disruption of single-stranded DNA binding activity leading to elevated levels of chromosomal rearrangements during replication restart.
Article
Multidisciplinary Sciences
Natalie Schindler, Matthias Tonn, Vanessa Kellner, Jia Jun Fung, Arianna Lockhart, Olga Vydzhak, Thomas Juretschke, Stefanie Moeckel, Petra Beli, Anton Khmelinskii, Brian Luke
Summary: The study reveals a genetic network involved in repairing the single ribonucleoside monophosphates (rNMPs) induced lesions and highlights its importance in human pathologies. This could potentially be utilized in the treatment of RNase H2-deficient pathologies.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Lavi S. Bigman, Harry M. Greenblatt, Yaakov Levy
Summary: This study investigates the minimal requirements for protein sliding along DNA, finding that coupling is not universal and some proteins transition from sliding to hopping at higher salt concentrations. Moreover, the sliding mechanism is found to be less dominant for certain DNA-binding proteins, even at low salt concentrations, with the toroidal PCNA protein displaying hopping rather than sliding.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Biology
Eman Zaffar, Pedro Ferreira, Luis Sanchez-Pulido, Dominik Boos
Summary: The initiation of DNA replication is a crucial step for the accurate inheritance of genetic information. Recent studies have revealed important insights into the molecular processes and cellular regulation of replication initiation in eukaryotic cells, with the identification of the MTBP protein as a key factor. MTBP plays a critical role in the initiation of replication and is regulated by kinases and controlled degradation.
Article
Chemistry, Multidisciplinary
Sunny Mukherjee, Sucharita Das, Navneeth Sriram, Sandipan Chakraborty, Mahesh Kumar Sah
Summary: This study aims to resolve the tertiary structure of MCM7 and repurpose FDA-approved drugs for cancer therapy by targeting MCM7 protein. The results reveal the potential of vitamin D and vitamin K as oncoprotein inhibitors for cancer therapy via inhibition of MCM7.
Article
Crystallography
Abigail R. Ward, Sara Dmytriw, Ananya Vajapayajula, Christopher D. Snow
Summary: By optimizing chemical DNA ligation, biomolecular co-crystals of DNA-binding proteins were made stable under harsh conditions without compromising crystal diffraction. This opens up possibilities for using crosslinked biomolecular co-crystals in biomedical applications.
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.
Correction
Chemistry, Multidisciplinary
Arun Shivalingam, Lapatrada Taemaitree, Afaf H. El-Sagheer, Tom Brown
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
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
Ysobel R. Baker, Liyiwen Yuan, Jinfeng Chen, Roman Belle, Robert Carlisle, Afaf H. El-Sagheer, Tom Brown
Summary: Rolling circle amplification (RCA) is a powerful tool for constructing DNA nanomaterials with potential therapeutic, imaging, and drug delivery applications. Orthogonal strategies can greatly expand the chemical functionalities of these materials, enabling the construction of DNFs with potential diagnostic and therapeutic applications.
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
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)
