Article
Biology
Sarah R. Hansen, David S. White, Mark Scalf, Ivan R. Correa, Lloyd M. Smith, Aaron A. Hoskins, Jonathan P. Staley
Summary: This study investigated the pathway of 5' SS selection by purified yeast U1 snRNP using colocalization single-molecule spectroscopy. The results revealed a sequence-dependent, two-step mechanism for U1 to reversibly select 5' SS, providing a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS.
Article
Chemistry, Physical
Ikenna C. Okafor, Taekjip Ha
Summary: CRISPR Cas9 is an RNA-guided endonuclease that is a part of bacterial adaptive immune system. By developing a single molecule FRET assay, the study investigated the conformational changes of sgRNA and the binding of Cas9 to sgRNA, providing insights into the assembly dynamics of Cas9 RNA ribonucleoprotein complex. This research could contribute to the rational design of sgRNAs and improve the editing outcomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
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)
Article
Multidisciplinary Sciences
Adrien Chauvier, Patrick St-Pierre, Jean-Francois Nadon, Elsa D. M. Hien, Cibran Perez-Gonzalez, Sebastien H. Eschbach, Anne-Marie Lamontagne, J. Carlos Penedo, Daniel A. Lafontaine
Summary: The researchers presented a new approach for site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes, revealing the relationship between RNA folding and gene regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christin Fuks, Sebastian Falkner, Nadine Schwierz, Martin Hengesbach
Summary: Riboswitch RNAs regulate gene expression through conformational changes induced by environmental conditions and specific ligand binding, which is of great significance for understanding the mechanism of RNA regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
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.
Article
Multidisciplinary Sciences
David Scheerer, Bharat V. Adkar, Sanchari Bhattacharyya, Dorit Levy, Marija Iljina, Inbal Riven, Orly Dym, Gilad Haran, Eugene I. Shakhnovich
Summary: Enzymes have a crucial role in controlling chemical reactions and achieving high catalytic efficiency and selectivity. The three-domain enzyme adenylate kinase (AK) catalyzes phosphotransfer between ATP and AMP. Our study using single-molecule FRET spectroscopy reveals that AMP inhibits AK by promoting faster and more cooperative domain closure by ATP, leading to an increased population of the closed state. We developed a model based on experimentally observed opening and closing rates, explaining the complex activity of AK, particularly substrate inhibition, and highlighting the importance of protein motions in enzymatic activity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Anoja Megalathan, Kalani M. Wijesinghe, Soma Dhakal
Summary: The article presents a background-free ultrasensitive detection sensor on a simple platform for p53 tumor suppressor gene, showing continuous dynamic switching between low- and high-FRET states in the presence of a target and detecting down to low femtomolar (fM) concentration. The sensor is also highly effective in discriminating against single-nucleotide polymorphisms (SNPs), offering a wide range of nucleic acid sequences detection for early disease diagnosis and genetic disorder screening.
Article
Chemistry, Physical
Maximilian Topel, Ayesha Ejaz, Allison Squires, Andrew L. Ferguson
Summary: Single-molecule Fo''rster resonance energy transfer (smFRET) is used to track the real-time dynamics of molecules. The Takens' Delay Embedding Theorem guarantees that the atomistic dynamics of a system can be represented by a time-delayed embedding of scalar observables. A method called Single-molecule TAkens Reconstruction (STAR) is used to learn the transformation between atomic coordinates and delay-embedded distances accessible to smFRET. STAR has been applied to reconstruct molecular configurations with high accuracy. In this work, the role of signal-to-noise ratio, data volume, and time resolution in simulated smFRET data is investigated to assess the performance of STAR under experimental conditions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Xinshuo Jia, Yanan Li, Teng Wang, Lulu Bi, Lijuan Guo, Ziting Chen, Xia Zhang, Shasha Ye, Jia Chen, Bei Yang, Bo Sun
Summary: EXD2 is a newly discovered exonuclease that has limited activity in cleaving double-stranded DNA, but displays both exoribonuclease and exodeoxyribonuclease activities towards RNA-DNA hybrids with a preference for RNA. The cleavage of hybrids by EXD2 proceeds in a discrete stepwise pattern, with a sudden duplex unwinding increment and subsequent dwell constituting a complete hydrolysis cycle.
Article
Biochemistry & Molecular Biology
Bo Zhao, Xin Hu, Yuning Zhou, Yueru Shi, Rui Qian, Youzhong Wan
Summary: SF3B1, an essential component of the U2 snRNP, is frequently mutated in cancers, leading to aberrant RNA splicing at 3' splice sites. Mutated SF3B1 prefers alternative branchpoint sequences with higher affinity to U2 snRNA for splicing, affecting the splicing of DVL2. The selection of branchpoint sequences for splicing is influenced by the affinity to U2 snRNA and the distance to the 3'ss.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Rakesh Chatrikhi, Callen F. Feeney, Mary J. Pulvino, Georgios Alachouzos, Andrew J. MacRae, Zackary Falls, Sumit Rai, William W. Brennessel, Jermaine L. Jenkins, Matthew J. Walter, Timothy A. Graubert, Ram Samudrala, Melissa S. Jurica, Alison J. Frontier, Clara L. Kielkopf
Summary: This study identifies a compound that enhances RNA binding by the U2AF2 subunit and inhibits splicing of representative substrates, effectively killing cancer cells by stalling spliceosome assembly. The results suggest that trapping early spliceosome assembly could be an effective pharmacological approach for manipulating pre-mRNA splicing.
CELL CHEMICAL 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)
Review
Biochemistry & Molecular Biology
Kim Bartels, Tanya Lasitza-Male, Hagen Hofmann, Christian Loew
Summary: This review focuses on the recent progress in single molecule Forster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. It demonstrates the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins, highlighting the importance of membrane mimicking environments. These studies advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
Article
Biochemical Research Methods
Nathan Ponzar, Nicola Pozzi
Summary: Disulfide bonds are essential for protein folding and stability, and dysregulation of this process can lead to various disorders. Thiol-isomerases (TIs) are a family of enzymes that oversee this process in human cells. However, our understanding of how TIs select and interact with their substrates, as well as their response to changes in redox environment, remains limited.
Article
Mathematics, Applied
Amir Alwan, Zonglin Han, Jessica Lin, Zijian Tao, Andrej Zlatos
Review
Immunology
Lilly Stahl, Anna Duenkel, Nadja Hilger, Uta Sandy Tretbar, Stephan Fricke
FRONTIERS IN IMMUNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
David H. Beier, Tucker J. Carrocci, Clarisse van der Feltz, U. Sandy Tretbar, Joshua C. Paulson, Nikolai Grabowski, Aaron A. Hoskins
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Margaret L. Rodgers, Sarah A. Woodson
News Item
Biochemistry & Molecular Biology
Margaret L. Rodgers, Yumeng Hao, Sarah A. Woodson
NATURE CHEMICAL BIOLOGY
(2019)
Article
Immunology
Lia Walcher, Nadja Hilger, Anja K. Wege, Franziska Lange, U. Sandy Tretbar, Andre-Rene Blaudszun, Stephan Fricke
IMMUNITY INFLAMMATION AND DISEASE
(2020)
Article
Medicine, General & Internal
Maria-Filothei Lazaridou, Chiara Massa, Diana Handke, Anja Mueller, Michael Friedrich, Karthikeyan Subbarayan, Sandy Tretbar, Reinhard Dummer, Peter Koelblinger, Barbara Seliger
JOURNAL OF CLINICAL MEDICINE
(2020)
Review
Biochemistry & Molecular Biology
Margaret L. Rodgers, Sarah A. Woodson
Summary: RNP assembly starts during transcription with folding of RNA and recruitment of RNA-binding proteins. Early RNA-protein interactions are more dynamic than expected, until sufficient proteins are recruited to consolidate an entire domain of the RNP. This process competes against modification and processing of the RNA, with transcription setting the timeline for interactions that determine the fate of the nascent RNA.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Immunology
Lia Walcher, Ann-Kathrin Kistenmacher, Charline Sommer, Sebastian Boehlen, Christina Ziemann, Susann Dehmel, Armin Braun, Uta Sandy Tretbar, Stephan Kloess, Axel Schambach, Michael Morgan, Dennis Loeffler, Christoph Kaempf, Conny Blumert, Kristin Reiche, Jana Beckmann, Ulla Koenig, Bastian Standfest, Martin Thoma, Gustavo R. Makert, Sebastian Ulbert, Uta Kossatz-Boehlert, Ulrike Koehl, Anna Duenkel, Stephan Fricke
Summary: The study demonstrates that low energy electron irradiation (LEEI) efficiently inactivates (CAR-)NK-92 cells as gamma irradiation, with less impact on overall gene expression. LEEI might provide a superior alternative for the production of (CAR-)NK-92 cells for clinical application due to logistical advantages.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Lorenz Beckmann, Uta Sandy Tretbar, Reni Kitte, Maik Tretbar
Summary: Drimane and coloratane sesquiterpenoids are attracting attention as a potential source for new anticancer drugs. This review provides an overview of their known structures, activity against cancer cells, and potential modes of action. However, the mode of action and structure-activity relationships of these compounds have not been fully elucidated.
Article
Oncology
Christoforos K. Vaxevanis, Michael Friedrich, Sandy Uta Tretbar, Diana Handke, Yuan Wang, Juliane Bluemke, Reinhard Dummer, Chiara Massa, Barbara Seliger
Summary: This study revealed a novel mechanism in which miRNAs targeting the coding sequence of immune checkpoint genes are functional and have prognostic relevance. It also has the potential for the development of novel miRNA-based therapies.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Margaret L. Rodgers, Brett O'Brien, Sarah A. Woodson
Summary: sRNPs play key roles in guiding the folding, modification, and splicing of nascent precursor RNAs during transcription. However, the rapid co-transcriptional folding of RNA can hinder the recognition and regulation of sRNP binding sites. In this study, the binding of Hfq•DsrA sRNPs to rpoS transcripts was examined using the single-molecule co-localization co-transcriptional assembly (smCoCoA) technique. It was found that Hfq•DsrA samples the mRNA before the transcription of the target site, preparing it for base pairing with DsrA. Furthermore, it was observed that Hfq•DsrA often binds to the mRNA close to RNA polymerase (RNAP) during the synthesis of the target site. This suggests that targeting transcripts near RNAP allows sRNPs to capture the site before the RNA folds, providing a kinetic advantage in recognition and regulation.
Article
Biochemistry & Molecular Biology
Margaret L. Rodgers, Yunsheng Sun, Sarah A. Woodson
Summary: During transcription, ribosomal subunits begin assembly by folding rRNA and associating it with ribosomal proteins (RPs). The initial recognition of properly folded rRNA by primary assembly proteins, like S4, is delayed due to the variable folding of rRNA during transcription. Late-binding RP S12 promotes the association of S4 with pre-16S rRNA, accelerating ribosome assembly.
Proceedings Paper
Engineering, Biomedical
Peter Reinig, Hans-Georg Dallmann, Markus Schwarzenberg, Johannes Ziebarth, Jens Knobbe, Jiri Junek, Rudolf Herbst, Julian Rathert, Ruediger Gerlach, Ulrich Blache, Sandy Tretbar, Stephan Fricke
Summary: In this study, we present a novel MEMS-based confocal laser scanning microscope, named LSC-Onco, for tumor demarcation in oncological surgery. This microscope provides precise in situ tumor demarcation and is easy to use, making it highly demanded in surgical guidance.
ADVANCED BIOMEDICAL AND CLINICAL DIAGNOSTIC AND SURGICAL GUIDANCE SYSTEMS XX
(2022)
Article
Law
Jason M. Chin, Alexander C. DeHaven, Tobias Heycke, Alexander O. Holcombe, David T. Mellor, Justin T. Pickett, Crystal N. Steltenpohl, Simine Vazire, Kathryn Zeiler
Summary: Fields closely related to empirical legal research are improving their methods to enhance the credibility of their findings by making data and analysis codes openly available. However, ELR appears to be lagging behind cognate fields due to a lack of field-specific meta-research and guidance. The article provides practical guidance for empirical legal researchers, with recommendations for improving the regulation of ELR in law journals.
LAW TECHNOLOGY AND HUMANS
(2021)