Review
Plant Sciences
Vivien Strotmann, Yvonne Stahl
Summary: This review provides a comprehensive and critical overview of techniques used to measure protein-protein interactions in living plants, with a focus on in vivo imaging techniques. By comparing different methods and discussing their benefits and potential pitfalls, it facilitates the selection of appropriate techniques and gives a comprehensive overview of how to measure in vivo protein-protein interactions in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Samara Martin-Alonso, Dongwei Kang, Javier Martinez del Rio, Joanna Luczkowiak, Estrella Frutos-Beltran, Lina Zhang, Xiqiang Cheng, Xinyong Liu, Peng Zhan, Luis Menendez-Arias
Summary: In retroviruses, strand displacement DNA-dependent DNA polymerization catalyzed by viral reverse transcriptase (RT) is crucial for synthesizing double-stranded proviral DNA. This study demonstrates that the loss of RNase H activity in HIV-1 RT does not significantly affect strand displacement during DNA template copying but has a major impact on DNA polymerization during reactions with RNA templates. The findings suggest potential applications in transcriptomics technologies and the development of novel antiretroviral agents.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Takane Tsuchii, Kazuki Kaneko, Kenta Morita, Takashi Nishino, Tatsuo Maruyama
Summary: Fluorous chemistry was used to achieve rewritable surface functionalization of plastic substrates, enabling the successful study of the effects of fluoropolymer and Rf-amine molecular structures on surface immobilization. This approach showed potential for diverse applications and could be used for micropatterning of biomolecules on plastic surfaces through microcontact printing.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Robert Eckenstaler, Ralf A. Benndorf
Summary: Protein-protein interaction studies provide insights into the formation of complexes, regulation of enzymatic activity, and information transfer within cells. FRET microscopy is a powerful tool for non-invasive investigation of these interactions, allowing for analysis of multiple interacting proteins simultaneously. By combining different FRET data acquisition and interpretation methods, it is possible to distinguish between different types of protein-protein interactions in living cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Saumya Jani, Maria Soledad Ramirez, Marcelo E. Tolmasky
Summary: Antisense technologies show promise in treating a diverse group of diseases by interfering with undesirable biological processes through inhibition of gene expression. However, there is still a lag in applying these technologies to prokaryotes, particularly in targeting bacterial infections.
Editorial Material
Biochemistry & Molecular Biology
Scott N. Lyons, Xiaolu A. Cambronne
Summary: The ChemoX platform has revolutionized biosensor development by eliminating the need for optimization with each new iteration and enabling versatile applications and optimized readouts through unique Forster resonance energy transfer pairings.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Plant Sciences
Junye Jiang, Will Feindel, Michael Harding, David Feindel, Stacey Bajema, Jie Feng
Summary: A rapid and accurate detection method for Ilyonectria pseudodestructans, a plant pathogen that causes root rot on fruit trees and tuber decay in potatoes, was developed using an RNase H-dependent PCR protocol and a modified probe-based rh-quantitative PCR protocol. The primers designed based on the histone H3 gene showed excellent specificity in differentiating between I. pseudodestructans and other Ilyonectria spp. The sensitivity test demonstrated the high sensitivity of the protocol with a detection limit of 2 pg of I. pseudodestructans genomic DNA.
Review
Chemistry, Analytical
Yi Qiao, Yuhan Luo, Naiyun Long, Yi Xing, Jing Tu
Summary: Single-molecule Forster resonance energy transfer (smFRET) inherits the measurement strategy from FRET, allowing observation of molecular behaviors at nanometer scale with high throughput. Despite its widespread application, smFRET continues to develop and researchers have explored novel studies using advanced platforms to further improve its performance on different biomolecules.
Article
Biochemistry & Molecular Biology
Javier Martinez del Rio, Nerea Lopez-Carrobles, Jesus I. Mendieta-Moreno, Oscar Herrera-Chacon, Adrian Sanchez-Ibanez, Jesus Mendieta, Luis Menendez-Arias
Summary: The combination of PCR and RTs has been widely used in RNA detection and gene expression analysis. Improving thermostability and nucleic acid binding affinity of RTs is crucial for enhancing the efficiency of these applications. This study investigated the effects of amino acid substitutions in the RT RNase H domain on its properties. It was found that specific substitutions resulted in loss of activity and mutations that improved cDNA synthesis efficiency also affected RNase H activity. This discovery provides evidence for a novel mechanism of RNase H inactivation.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Yuanming Wang, Zepeng Kang, Lingling Zhang, Zhiguang Zhu
Summary: This study investigates the interactions between PfSHI and carbon nanotubes, revealing that electrostatic and hydrophobic interactions play a crucial role in the interaction between PfSHI and electrodes. Based on these findings, a high-performance biofuel cell was constructed, demonstrating an improved power output.
Article
Biology
George L. Hamilton, Nabanita Saikia, Sujit Basak, Franceine S. Welcome, Fang Wu, Jakub Kubiak, Changcheng Zhang, Yan Hao, Claus A. M. Seidel, Feng Ding, Hugo Sanabria, Mark E. Bowen
Summary: PSD-95 is a scaffold protein that links postsynaptic receptors to presynaptic neurotransmitter release sites. The study combines discrete molecular dynamics and single molecule FRET to characterize the supertertiary structure of PSD-95. The results reveal the conformational changes of PDZ3 and its binding ability to neuroligin.
Article
Biochemistry & Molecular Biology
Paymaan Jafar-nejad, Berit Powers, Armand Soriano, Hien Zhao, Daniel A. Norris, John Matson, Beatrice DeBrosse-Serra, Jamie Watson, Padmakumar Narayanan, Seung J. Chun, Curt Mazur, Holly Kordasiewicz, Eric E. Swayze, Frank Rigo
Summary: ASO drugs have been shown to distribute widely in the central nervous system and reduce target RNA in various types of neurons, making them suitable for treating a wide range of neurological diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Isabell Schencking, Eva M. Schaefer, J. H. William Scanlan, Benjamin M. Wenzel, Rolf E. Emmerich, Torsten Steinmetzer, Wibke E. Diederich, Martin Schlitzer, Roland K. Hartmann
Summary: RNase P is an essential enzyme for tRNA maturation, and studies have shown that small-molecule inhibitors targeting bacterial RNase P may induce RnpA aggregation instead of specific inhibition. High-throughput screenings for bacterial RNase P inhibitors are prone to identifying false positives termed pan-assay interference compounds (PAINS).
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Chemistry, Multidisciplinary
Dongyang Zhang, Luping Liu, Shuaijiang Jin, Ember Tota, Zijie Li, Xijun Piao, Xuan Zhang, Xiang-Dong Fu, Neal K. Devaraj
Summary: In this study, we developed a RNA-CLAMP technique that allows site-specific and enzymatic cross-linking of two selected guanine residues within an RNA. The clamping disrupts RNA function, but can be restored by photocleavage of the cross-linker. We successfully clamped two stem loops within the sgRNA of the CRISPR-Cas9 gene editing system, completely inhibiting gene editing. Visible light irradiation cleaved the cross-linker and restored gene editing with high spatiotemporal resolution.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Chemistry, Multidisciplinary
Roberto El-Khoury, Masad J. Damha
Summary: FANA is an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions, showing high binding affinity and implications in therapeutics. It also holds promise in stabilizing noncanonical DNA structures and playing a role in biological research.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Murat Sunbul, Jens Lackner, Annabell Martin, Daniel Englert, Benjamin Hacene, Franziska Grun, Karin Nienhaus, G. Ulrich Nienhaus, Andres Jaschke
Summary: A newly developed light-up RNA aptamer, RhoBAST, enables super-resolution imaging with single-molecule localization microscopy, surpassing the limitation of photobleaching. The intermittent fluorescence emission of RhoBAST allows for high-resolution imaging of RNA subcellular structures in live and fixed cells with precise localization and high signal-to-noise ratio.
NATURE BIOTECHNOLOGY
(2021)
Article
Optics
Peng Gao, G. Ulrich Nienhaus
Summary: The axial line-scanning stimulated emission depletion fluorescence correlation spectroscopy (axial ls-STED-FCS) technique offers higher time resolution through axial line scanning, sub-diffraction spatial resolution, and the ability to study samples with densely labeled membranes.
Article
Physics, Applied
Zachary A. VanOrman, Jens Lackner, Sarah Wieghold, Karin Nienhaus, G. Ulrich Nienhaus, Lea Nienhaus
Summary: Photon upconversion via triplet-triplet annihilation can potentially surpass the efficiency limit of single junction solar cells. The efficiency of perovskite-sensitized upconversion devices is greatly influenced by trap density, showing peak performance under continuous illumination.
APPLIED PHYSICS LETTERS
(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.
Review
Nanoscience & Nanotechnology
Karin Nienhaus, Yumeng Xue, Li Shang, Gerd Ulrich Nienhaus
Summary: This review summarizes the key role of biomolecule adsorption onto engineered nanomaterials in therapeutic and diagnostic applications. It discusses the recent shift towards gaining active control of nano-bio interactions to enhance the efficacy of nanomaterials in biomedical applications. The review provides an overview of fundamental knowledge about protein-nanomaterial interactions and explores ways to exploit these interactions in biomedical applications.
Article
Multidisciplinary Sciences
Nane C. Kuznik, Valeria Solozobova, Irene I. Lee, Nicole Jung, Linxiao Yang, Karin Nienhaus, Emmanuel A. Ntim, Jaice T. Rottenberg, Claudia Muhle-Goll, Amrish Rajendra Kumar, Ravindra Peravali, Simone Graessle, Victor Gourain, Celia Deville, Laura Cato, Antje Neeb, Marco Dilger, Christina A. Cramer von Clausbruch, Carsten Weiss, Bruno Kieffer, G. Ulrich Nienhaus, Myles Brown, Stefan Braese, Andrew C. B. Cato
Summary: BAG1 proteins, particularly the isoform BAG1L, play crucial roles in prostate cancer by regulating the androgen receptor (AR) and affecting gene expression related to oxidative stress and metabolism. A small molecule, A4B17, targeting the BAG domain, shows promising results in downregulating AR target genes and inhibiting prostate tumor development, outperforming the clinically approved antagonist enzalutamide. BAG1 inhibitors offer unique opportunities for antagonizing AR action and prostate cancer growth.
Article
Biochemistry & Molecular Biology
Karin Nienhaus, Vandna Sharma, Gerd Ulrich Nienhaus, Larissa M. Podust
Summary: This study investigated the interplay between enzyme activity and oligomerization state of CYP51 enzymes in Acanthamoeba castellanii and Naegleria fowleri. The results indicate that dimeric assembly is critical for stabilizing thiolate coordination to heme and sustaining enzyme activity.
Article
Chemistry, Multidisciplinary
Haixia Wang, Karin Nienhaus, Li Shang, Gerd Ulrich Nienhaus
Summary: In this study, we investigated the interactions between positively charged MUTAB-stabilized quantum dots (QDs) and proteins, serum, and live cells using various techniques. The results showed that MUTAB-QDs have affinity towards HSA and serum, and can bind to and perforate the cell membrane. Pre-adsorption of proteins on the QD surfaces can reduce this process.
CHINESE JOURNAL OF CHEMISTRY
(2022)
Review
Chemistry, Analytical
Karin Nienhaus, Gerd Ulrich Nienhaus
Summary: Optical fluorescence microscopy is crucial for studying biological structure and dynamics, and genetically encodable fluorescent proteins are invaluable markers for live specimens. Protein engineering has enabled the development of FP variants with specific photophysical properties for advanced imaging techniques.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2022)
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
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)
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
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)
