Article
Multidisciplinary Sciences
Yi Wang, Zhuodong Tang, Hong-Yuan Chen, Wei Wang, Nongjian Tao, Hui Wang
Summary: A nanoparticle-based technique has been developed to probe the energetic contributions of single-molecule binding events, introducing a single-molecule calorimeter that uncovers the complexity of molecular interactions and provides a comprehensive thermodynamic profile.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Pharmacology & Pharmacy
Suppakan Sripetch, Alexey Ryzhakov, Thorsteinn Loftsson
Summary: Dovitinib has been investigated as an anti-tumor drug due to its ability to inhibit multiple receptor tyrosine kinases. Salts and lipid-based formulations have been used to improve its bioavailability. The presence of acidic counterions, buffer species, and cyclodextrin were found to influence the aqueous solubility, lipophilicity, and stability of dovitinib.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2022)
Article
Virology
Sudip Nepal, Erik D. Holmstrom
Summary: The highly conserved hepatitis C virus core protein (HCVcp) plays a crucial role in nucleocapsid assembly. Single-molecule FRET spectroscopy reveals distinct binding mechanisms between HCVcp and antiviral therapeutics.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Doris Xu, Yuhong Wang
Summary: Ribosomal protein synthesis is a crucial process in modern biology, and understanding the precursor and evolution of the ribosome is important. This study identified two fragments in the peptidyl transfer center that can synthesize a long poly-lysine peptide in the presence of Mg2+. The synthesis is believed to be carried out by a ribozyme and involves substrate proximity through dimerization. This research contributes to our knowledge of ribosome evolution and the mechanism of peptidyl transfer reactions.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Hsuan-Lei Sung, Abhigyan Sengupta, David Nesbitt
Summary: The crowded cellular environment has a significant impact on the stability and functionality of biomolecules, with smaller molecular weight crowders proving to be more effective in increasing the folding rate and decreasing the unfolding rate of RNA tertiary structures. Experimental verification of the entropic crowding effects can predict the stabilization of RNA tertiary structures in the cellular environment under the influence of small molecular weight crowders.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Sung Hyun Kim, Hyunwoo Kim, Hawoong Jeong, Tae-Young Yoon
Summary: The study demonstrates the use of single-molecule FRET technology to encode virtual signals in DNA barcodes, allowing for precise measurement of FRET efficiency for each binding event and differentiation of six DNA barcodes.
Review
Cell Biology
Muwen Kong, Eric C. Greene
Summary: DNA double strand breaks are highly deleterious forms of DNA damage that, if left unrepaired, can lead to a high risk of cancer. Homologous recombination and nonhomologous end joining are the two major mechanisms responsible for repairing DSBs, and single-molecule studies have provided detailed insights into the repair processes at each step.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Debayan Purkait, Farhana Islam, Padmaja P. Mishra
Summary: The study reveals the important role of DrRecD2, an ATP-driven helicase, in DNA replication, nucleotide excision repair, and homologous recombination. Single-molecule studies show that DrRecD2 prefers binding at the 5' terminal end of single-stranded DNA and exhibits faster unwinding activity in the presence of ATP.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Mike Filius, Sung Hyun Kim, Ivo Severins, Chirlmin Joo
Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.
Article
Chemistry, Analytical
Daniel F. Kienle, Daniel K. Schwartz
Summary: In this study, the diffusion of small charged molecules in anisotropic polyelectrolyte multilayers was tracked in three dimensions using single-molecule fluorescence localization and Forster resonance energy transfer. The results showed a significantly slower diffusion in the surface-normal direction compared to lateral diffusion, which was hypothesized to be related to the periodic distribution of charge in the multilayer.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Ikenna C. Okafor, Janice Choi, Taekjip Ha
Summary: CRISPR proteins like Cas9 and Cas12a unwinds DNA without using ATP, by utilizing binding energy and basepairing with guide (g) RNA. Cas9 forms a complex with gRNA to bind and cause double strand breaks in DNA. Single-molecule FRET can be used to probe the unwinding state of DNA and the position of Cas9's HNH domain before and after cleavage.
Article
Chemistry, Physical
Carey Phelps, Tao Huang, Jing Wang, Xiaolin Nan
Summary: Forster resonance energy transfer (FRET) is a powerful tool for studying molecular interactions. However, its application in studying interactions involving multiple molecules has been limited by spectral crosstalk. In this study, multispectral FRET (msFRET) was developed to image multiple pairs of interactions simultaneously by spectrally resolving single fluorescent molecules. Using a dual channel and wide-field imaging configuration, close emission maxima as small as 6-10 nm could be reliably distinguished. The feasibility of msFRET was demonstrated by continuously monitoring the hybridization dynamics of multiple pairs of DNA oligos. Additionally, msFRET can be applied to probe fluorophore photophysics during FRET and in multiplexed superresolution imaging.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemical Research Methods
Subhra K. Das, Mai T. Huynh, Jia Gao, Bhaswati Sengupta, Satya P. Yadav, Tae -Hee Lee
Summary: The nucleosome is the basic unit of chromatin and plays a crucial role in chromatin transactions with enzymes and factors, which are regulated by chromatin modifications. Monitoring nucleosomal changes is challenging due to their stochastic, unsynchronized, and heterogeneous nature. Single-molecule fluorescence techniques have been used to investigate the structure and interactions of the nucleosome with various enzymes, and to elucidate the kinetics and implications of chromatin modifications in these processes.
Article
Multidisciplinary Sciences
Yanyan Xue, Jun Li, Dian Chen, Xizhu Zhao, Liang Hong, Yu Liu
Summary: This study develops a method to monitor the conformational change of riboSAM during transcription, and observes five co-existing states in riboSAM. A bifurcated helix structure is identified in one of the states and is found to be responsible for translation inhibition. This strategy enables the precise mapping of RNA conformational landscape during transcription.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Shashank Dadsena, Andreas Jenner, Ana J. Garcia-Saez
Summary: Apoptotic cell death plays a crucial role in development and tissue homeostasis, and MOMP is a central event in this process. Researchers focus on the interaction network of Bcl-2 family proteins and other regulatory elements, emphasizing the importance of single-molecule techniques in uncovering apoptosis regulation mechanisms.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemical Research Methods
Manuel Huepfel, Manuel Fernandez Merino, Johannes Bennemann, Masanari Takamiya, Sepand Rastegar, Anja Tursch, Thomas W. Holstein, G. Ulrich Nienhaus
Summary: This study proposes a fast approximation of three-dimensional multi-view deconvolution and demonstrates its advantages in image processing. The method is capable of handling large amounts of image data and performs well in time-critical applications.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Biology
Giulia Ambrosi, Oksana Voloshanenko, Antonia F. Eckert, Dominique Kranz, G. Ulrich Nienhaus, Michael Boutros
Summary: Wnt signaling is important in various biological processes, and mutations in beta-catenin can activate this signaling pathway. In this study, fluorescently tagged alleles of wild-type and mutant beta-catenin were engineered and analyzed to understand their properties. The results revealed distinct biophysical properties between the two alleles, and the wild-type allele could be manipulated to mimic the properties of the mutant allele through specific treatments.
Article
Chemistry, Multidisciplinary
Larissa Bessler, Lea-Marie Vogt, Marc Lander, Christina Dal Magro, Patrick Keller, Jonas Kuehlborn, Christopher J. Kampf, Till Opatz, Mark Helm
Summary: Both RNA modification and RNA damage involve non-canonical nucleoside structures. While RNA modifications improve function, RNA damage has detrimental effects. This study identified and characterized a new structure, 2-methylthio-1,N6-ethenoadenosine (ms(2)epsilon A), related to a lesion resulting from exposure to alkylating chemicals. The formation of ms(2)epsilon A involves cleavage of a prenyl moiety in a known transfer RNA modification.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Alexey Sudakov, Bozana Knezic, Martin Hengesbach, Boris Fuertig, Elke Stirnal, Harald Schwalbe
Summary: More than 170 post-transcriptional modifications of RNAs have been identified. However, the detailed investigation of these modifications is limited due to the difficulty in producing large RNAs containing these modifications. This study reports the chemo-enzymatic synthesis of RNA modifications and fluorine-modified analogs, allowing the synthesis of large RNAs. The incorporation of labeled nucleotides in the riboswitch demonstrated the applicability of the modified large RNAs in characterizing RNA fold and dynamics.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Florian Pichot, Marion C. Hogg, Virginie Marchand, Valerie Bourguignon, Elisabeth Jirstrom, Cliona Farrell, Hesham A. Gibriel, Jochen H. M. Prehn, Yuri Motorin, Mark Helm
Summary: Modification of tRNA is crucial for generating RNA expression diversity. In this study, the stoichiometry of incompletely modified sites in human tRNAs was investigated, and it was found that up to 75% of sites can be incompletely modified. The modification patterns of tRNA populations can provide information to differentiate different cell lines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Editorial Material
Chemistry, Multidisciplinary
Elke Duchardt-Ferner, Jan Ferner, Boris Fuertig, Martin Hengesbach, Christian Richter, Andreas Schlundt, Sridhar Sreeramulu, Anna Wacker, Julia E. Weigand, Julia Wirmer-Bartoschek, Harald Schwalbe
Summary: The COVID-19 outbreak in December 2019 led to the establishment of international collaborations to understand and combat the virus. The NMR community has come together to study the genome and proteome of SARS-CoV-2 and test their interaction with low-molecular-weight binders. Due to the global pandemic and extended lockdowns, research has shifted from local collaborations to digital formats, allowing immediate discussion of unpublished results, data analysis, sample sharing, and coordinated research between more than 50 groups from 18 countries. Key lessons and challenges for post-pandemic research are discussed.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Karin Nienhaus, Gerd Ulrich Nienhaus
Summary: Although a variety of nanoparticles have been developed for medical use, their application in clinical settings is limited. The lack of understanding of nanoparticle interactions in the bio-environment, particularly the protein corona, is a major obstacle. This article critically reviews research on the protein corona, including its structure, reversibility, time dependence, and role in nanoparticle agglomeration, highlighting the need for further mechanistic studies. The article concludes with a discussion of future research directions to enhance the understanding of the protein corona and improve the design of nanomedicines.
Article
Chemistry, Medicinal
Marvin Schwickert, Robert A. Zimmermann, Tanja Habeck, Sabrina N. Hoba, Zarina Nidoieva, Tim R. Fischer, Martin M. Stark, Christian Kersten, Frederik Lermyte, Mark Helm, Tanja Schirmeister
Summary: The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme that plays a role in various pathophysiological processes, including mental and metabolic disorders and cancer. In this study, covalent SAH-based DNMT2 inhibitors were developed and tested for their effectiveness. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) was found to be the most potent and selective inhibitor, with confirmed covalent reaction with the catalytically active cysteine-79.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Optics
Lan Yu, Yu Wang, Yang Wang, Kequn Zhuo, Min Liu, G. Ulrich Nienhaus, Peng Gao
Summary: We introduce a label-free technique called two-beam phase correlation spectroscopy (2B-ICS) to measure the dynamics of flowing particles, such as blood flow. This method combines phase imaging with correlation spectroscopy and uses the refractive index contrast of particles against the fluid background for analysis. 2B-ICS is a simple procedure that involves acquiring phase images of flowing particles and correlating the phase fluctuations to determine concentration and flow velocity.
PHOTONICS RESEARCH
(2023)
Review
Genetics & Heredity
Sylvain Delaunay, Mark Helm, Michaela Frye
Summary: Chemical modifications of nucleotides in RNA can alter its properties and are used for clinical purposes in stable artificial RNAs. These modifications also regulate cellular processes and their study has led to the understanding of disease mechanisms and innovative clinical approaches. The ability to manipulate RNA modifications offers therapeutic potential and has paved the way for novel clinical strategies.
NATURE REVIEWS GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Afaf Elkurdi, Gernot Guigas, Latifa Hourani-Alsharafat, Patrick Scheerer, Gerd Ulrich Nienhaus, Norbert Krauss, Tilman Lamparter
Summary: Phytochromes are photoreceptor proteins that can convert between two different forms, Pr and Pfr. The N-terminal photosensory chromophore module (PCM), composed of PAS, GAF, and PHY domains, and the C-terminus histidine kinase module play important roles in this process. By studying Agp1 mutants, researchers found a mechanical coupling between position 362 and the histidine kinase, and flexibility around position 308 in both Pr and Pfr forms.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Daniel Englert, Eva-Maria Burger, Franziska Gruen, Mrigank S. Verma, Jens Lackner, Marko Lampe, Bastian Buehler, Janin Schokolowski, G. Ulrich Nienhaus, Andres Jaeschke, Murat Sunbul
Summary: Spirocyclic rhodamine probes were designed for visualizing RNA in live or fixed cells using SMLM and STED microscopy modalities. A novel probe called SpyRho was developed, which tightly binds to the RhoBAST aptamer and exhibits high brightness and fluorogenicity. This system represents significant advances in live-cell RNA imaging.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Anna Wierczeiko, Stefan Pastore, Stefan Muendnich, Anne M. Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber
Summary: Oxford Nanopore Technologies' sequencing platform allows for real-time analysis, providing early insights and accelerating decision-making for further analysis. NanopoReaTA is introduced as a user-friendly toolbox for real-time analysis of RNA-sequencing data from ONT, offering visual snapshots and enabling interactive sequencing and rapid decision-making.
Article
Biochemistry & Molecular Biology
Mark Helm, Markus T. Bohnsack, Thomas Carell, Alexander Dalpke, Karl-Dieter Entian, Ann Ehrenhofer-Murray, Ralf Ficner, Christian Hammann, Claudia Ho''bartner, Andres Ja''schke, Albert Jeltsch, Stefanie Kaiser, Roland Klassen, Sebastian A. Leidel, Andreas Marx, Mario Mo''rl, Jochen C. Meier, Gunter Meister, Andrea Rentmeister, Marina Rodnina, Jean-Yves Roignant, Raffael Schaffrath, Peter Stadler, Thorsten Stafforst
Summary: This article describes the impact and subsequent effects of the DFG-funded priority program SPP1784 on the field of nucleic acid modifications. The program has facilitated interdisciplinary collaborations and contributed to the development of the nucleic acid chemistry community. The extension of funding during the COVID-19 pandemic has led to increased interest and research in the field of RNA and RNA modifications, particularly in the context of vaccination campaigns against SARS-CoV-2.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Physical
Rui Ma, Martin Stefl, Gerd Ulrich Nienhaus
Summary: This study used super-resolution microscopy to analyze the development of Clathrin-coated pits and caveolae on the plasma membrane of cells, and found that they have remarkably similar temporal evolution, suggesting the involvement of shared key accessory proteins in this process.
NANOSCALE HORIZONS
(2022)