RSC Chemical Biology最新文献

Experimental identification of preQ₁-binding RNAs in the pathogenic bacterium Listeria monocytogenes. 单核增生李斯特菌中前体q1结合rna的实验鉴定。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-14 DOI: 10.1039/d5cb00102a

Malou Hanisch, Laurin Flemmich, Christoph Mitteregger, Ingo Bauer, Cristian A Velandia-Huerto, Ivo Hofacker, Ronald Micura, Alexandra Lusser

{"title":"Experimental identification of preQ1-binding RNAs in the pathogenic bacterium Listeria monocytogenes.","authors":"Malou Hanisch, Laurin Flemmich, Christoph Mitteregger, Ingo Bauer, Cristian A Velandia-Huerto, Ivo Hofacker, Ronald Micura, Alexandra Lusser","doi":"10.1039/d5cb00102a","DOIUrl":"10.1039/d5cb00102a","url":null,"abstract":"Riboswitches are widespread regulatory RNA modules in bacteria, with many different classes already identified and even more yet to be discovered. Traditionally, the identification of riboswitches has relied on bioinformatic analyses and genetic screens. In this work, we explored the possibility of identifying and characterizing predicted and novel riboswitches using an affinity purification-based approach with a functionalized preQ1 ligand. We successfully enriched a predicted preQ1 riboswitch from L. monocytogenes total RNA. Biophysical characterization revealed that this riboswitch can simultaneously bind two ligand molecules and functions as a regulator of translation in vivo. Furthermore, a transcriptome-wide pull-down experiment resulted in strong preQ1-dependent enrichment of several candidate sequences. Characterization of the lmo2684 candidate mRNA revealed a preQ1 riboswitch-like sequence in its 5' untranslated region. Notably, preQ1 allowed translation of an upstream open reading frame in this region by promoting stop codon readthrough. Our findings highlight the utility of ligand-based pull-down strategies for enriching mRNAs with aptamers that elude computational detection and may possess undiscovered functions.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12519234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145303960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New insights into the structure and dynamics of the epigenetic modifications on DNA. 对DNA表观遗传修饰的结构和动力学的新见解。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-13 DOI: 10.1039/d5cb00207a

Dineshbabu Takkella, Javier Cerezo, Lara Martinez-Fernandez, Krishna Gavvala

{"title":"New insights into the structure and dynamics of the epigenetic modifications on DNA.","authors":"Dineshbabu Takkella, Javier Cerezo, Lara Martinez-Fernandez, Krishna Gavvala","doi":"10.1039/d5cb00207a","DOIUrl":"10.1039/d5cb00207a","url":null,"abstract":"DNA methylation is a key epigenetic modification involved in genomic imprinting, X-chromosome inactivation, and repression of repetitive element transcription and transposition. Despite its biological significance, the impact of epigenetic modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) on the structural and UV-induced dynamics of DNA remains poorly understood. Here, we employed the fluorescent nucleobase analogue 2-aminopurine (2Ap) in combination with steady-state and time-resolved spectroscopy, molecular dynamics, and quantum mechanical calculations to investigate these effects. Our findings reveal distinct differences in base stacking and helical stability between mC and hmC-modified DNA. mC-modified DNA predominantly adopts a stacked conformation, promoting efficient fluorescence quenching of 2Ap. In contrast, hmC-modified DNA displays both stacked and non-stacked conformations, leading to reduced base stacking and a more hydrophobic local environment, as indicated by blue-shifted emission spectra. Furthermore, although charge-transfer quenching occurs in all systems, hmC shows weaker charge-transfer character, resulting in higher fluorescence quantum yields and longer lifetimes. These results highlight the subtle but crucial role of hmC in modulating local DNA conformation and stability. Moreover, they demonstrate the effectiveness of 2Ap as a sensitive probe for detecting epigenetic modifications, offering deeper insights into the molecular mechanisms of DNA methylation and demethylation pathways.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12539948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145348947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alkyne-tagged ribitol-5-phosphate derivatives for metabolic labelling of alpha-dystroglycan. 烷基标记的利比醇-5-磷酸衍生物代谢标记α -三磷酸糖酐。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-10 DOI: 10.1039/d5cb00187k

Lloyd D Murphy, Saeed Akkad, Angelo Lopez, Morgan E Batiste-Simms, Greg L McNeil, Eva W Wan, Kathryn E Huxley, Luke Julyan, Mia Shandell, Lianne I Willems

引用次数: 0

Chemically inducible antisense oligonucleotides for cell-specific gene silencing. 用于细胞特异性基因沉默的化学诱导反义寡核苷酸。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-09 DOI: 10.1039/d5cb00186b

Zhen Xun, Yang Hai, Li-Juan Tang, Jian-Hui Jiang, Zhenkun Wu

{"title":"Chemically inducible antisense oligonucleotides for cell-specific gene silencing.","authors":"Zhen Xun, Yang Hai, Li-Juan Tang, Jian-Hui Jiang, Zhenkun Wu","doi":"10.1039/d5cb00186b","DOIUrl":"10.1039/d5cb00186b","url":null,"abstract":"Cell-specific control of the function of antisense oligonucleotides (ASOs) is highly desirable for precise gene therapy while minimizing adverse effects in normal cells. Herein, we report a novel class of chemically inducible ASOs (iASOs) that achieve tumor-cell-selective gene silencing through hydrogen peroxide (H2O2)-triggered activation. Through post-synthetic incorporation of phenylboronic acid (BO) caging groups at the backbone positions, we developed iASOs that remain functionally inactive until the H2O2-triggered removal of the BO groups caused activation. Using EGFP as a reporter system, we demonstrated that the optimal BO-modified iASO exhibited slight gene silencing activity in normal cells but achieved >80% knockdown of the target mRNA in tumor cells. The BO-modified iASO was further applied to target the endogenous Bcl2 gene, demonstrating its ability for controlling gene silencing and inducing cell death. This study establishes a simple and effective platform for conditional gene regulation and the development of cell-specific ASO therapeutics.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12538225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145349018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biocatalytic synthesis of phenyl benzoate esters using the amide ligase ClxA. 利用酰胺连接酶ClxA生物催化合成苯甲酸苯酯。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-08 DOI: 10.1039/d5cb00205b

Alexander Ascham, Qingyun Tang, Ian J S Fairlamb, Gideon Grogan

引用次数: 0

Glyco-functionalization of ECM mimics, influence in morphology and cell behaviour. ECM模拟物的糖功能化，对形态学和细胞行为的影响。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-03 DOI: 10.1039/d5cb00185d

Maddalena Bracchi, Francesco Nicotra, Laura Russo

{"title":"Glyco-functionalization of ECM mimics, influence in morphology and cell behaviour.","authors":"Maddalena Bracchi, Francesco Nicotra, Laura Russo","doi":"10.1039/d5cb00185d","DOIUrl":"10.1039/d5cb00185d","url":null,"abstract":"Current tissue engineering strategies primarily focus on replicating mechanical properties of the extracellular matrix (ECM); however, several studies have underscored the critical role of the ECM biochemical cues in developing functional tissue substitutes. Among these, glycans are known to play a key role in regulating cell fate. In this study we developed ECM mimics glyco-conjugated with two different glycans, α-d-glucopyranose (αGlc) and β-d-galactopyranose (βGal), to investigate their influence on morphology and cell behaviour. The ECM mimics were generated crosslinking glycosylated gelatin samples, functionalised with the glycans by reductive amination, and hyaluronic acid. The crosslinking was performed by previous functionalization of gelatin and hyaluronic acid with tyramine, to enable enzymatic phenol-phenol coupling via horseradish peroxidase (HRP) and hydrogen peroxide (H2O2). The glyco-conjugated hydrogels exhibited markedly different morphologies, characterized by increased fibrous content, smaller pore sizes, and more wrinkled surfaces. Bone marrow-derived mesenchymal stem cells (BM-MSCs) seeded in hydrogels functionalized αGlc and βGal exhibited a more elongated morphology and differential glycosignature compared to controls.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12522395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145309570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative aptamer profiling reveals cell surface remodeling and the emergence of a noncanonical cell surface protein under oncogenic signaling. 比较适体分析揭示了在致癌信号传导下细胞表面重塑和非典型细胞表面蛋白的出现。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-03 DOI: 10.1039/d5cb00110b

Jungo Kakuta, Kenji Ohba, Hideaki Ogasawara, Kyohei Okahara, Kazumi Emoto, Hiroaki Sako, Miho Sekai, Yasuyuki Fujita, Toshio Imai, Yogo Sakakibara

{"title":"Comparative aptamer profiling reveals cell surface remodeling and the emergence of a noncanonical cell surface protein under oncogenic signaling.","authors":"Jungo Kakuta, Kenji Ohba, Hideaki Ogasawara, Kyohei Okahara, Kazumi Emoto, Hiroaki Sako, Miho Sekai, Yasuyuki Fujita, Toshio Imai, Yogo Sakakibara","doi":"10.1039/d5cb00110b","DOIUrl":"https://doi.org/10.1039/d5cb00110b","url":null,"abstract":"Identifying cell type-specific molecular markers on the cancer cell surface is essential for understanding cancer progression and for discovering critical neoantigens relevant to immunotherapy. Nucleic acid aptamers serve as powerful tools for probing complex and dynamic cell surface characteristics. Here, we introduce a streamlined comparative aptamer profiling methodology that enables side-by-side analysis of cell surface remodeling. Using cell-SELEX (systematic evolution of ligands by exponential enrichment), we generated a modified base-incorporated aptamer library directly from cells, which was then employed to explore the surface states of normal and mutant protein-expressing cells. Differential analysis of aptamer enrichment using next-generation sequencing revealed distinct aptamer signatures that correlated with cell types. Our analysis demonstrated that mutant K-Ras expression dynamically altered cell surface composition. Individual aptamers showed specific binding to mutant K-Ras-expressing cells without requiring sequence optimization. Moreover, target identification of one aptamer revealed abnormal translocation of a mitochondrial matrix protein to the cell surface without detectable changes in mRNA or protein levels upon altered cellular signaling. These findings highlight the dynamic modulation of cell surface states by aberrant cellular signaling. Overall, we present a useful comparative strategy to investigate cell surface alterations. This approach may help uncover previously unrecognized cell surface markers associated with oncogenic signaling.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12541808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of ligands for E3 ligases with restricted expression using fragment-based methods. 基于片段的限制性表达E3连接酶配体鉴定方法。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-02 DOI: 10.1039/d5cb00198f

Alex G Waterson, Brian D Lehmann, Zhenwei Lu, John L Sensintaffar, Edward T Olejniczak, Bin Zhao, Tyson Rietz, William G Payne, Jason Phan, Stephen W Fesik

{"title":"Identification of ligands for E3 ligases with restricted expression using fragment-based methods.","authors":"Alex G Waterson, Brian D Lehmann, Zhenwei Lu, John L Sensintaffar, Edward T Olejniczak, Bin Zhao, Tyson Rietz, William G Payne, Jason Phan, Stephen W Fesik","doi":"10.1039/d5cb00198f","DOIUrl":"10.1039/d5cb00198f","url":null,"abstract":"Heterobifunctional molecules that induce targeted degradation have emerged as powerful tools in chemical biology, target validation, and drug discovery. Despite their promise, the field is constrained by the relative paucity of ligands available for E3 ligases. Expanding the ligand repertoire for E3 ligases and other components of ubiquitin-proteasome system could significantly broaden the scope of the targeted degradation field. In this study, we report the identification of ligands for non-essential E3 ligases that are preferentially expressed in cancer tissues relative to normal tissues. Using a protein-observed NMR-based fragment screen, an ideal technique for this purpose, we identified fragment ligands and characterized their binding modes by X-ray crystallography. These ligands represent promising starting points for further optimization toward the discovery of tumor-selective degraders that may enhance the therapeutic window targeting proteins for which inhibition or degradation is associated with systemic toxicity.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thiazole peptidomimetics as chemical modulators of KRAS gene expression via G-quadruplex stabilization. 噻唑类肽通过g -四重体稳定作为KRAS基因表达的化学调节剂。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-02 DOI: 10.1039/d5cb00046g

Debasmita Biswas, Ananta Gorai, Sandip Maiti, Ritapa Chaudhuri, Sayantan Pradhan, Jyotirmayee Dash

引用次数: 0

Selective labeling and visualization of viral and bacterial neuraminidases using ortho-quinone methide-based probes. 利用邻醌类探针对病毒和细菌神经氨酸酶进行选择性标记和可视化。

IF 3.1

RSC Chemical Biology Pub Date : 2025-10-01 DOI: 10.1039/d5cb00170f

Erianna I Alvarado-Melendez, Simon T Ruessink, Karin Strijbis, Tom Wennekes

{"title":"Selective labeling and visualization of viral and bacterial neuraminidases using ortho-quinone methide-based probes.","authors":"Erianna I Alvarado-Melendez, Simon T Ruessink, Karin Strijbis, Tom Wennekes","doi":"10.1039/d5cb00170f","DOIUrl":"10.1039/d5cb00170f","url":null,"abstract":"Neuraminidases (NAs) are critical virulence factors in pathogens. In viruses such as influenza A, neuraminidase facilitates the release of virions, thereby enabling infection propagation. In pathogenic bacteria, NA activity has been linked to the pathogenicity of species such as S. pneumoniae, P. aeruginosa, and V. cholerae. Studies suggest that bacterial NAs play roles in mucus degradation, exposing host epitopes to enhance bacterial adhesion, biofilm formation, and bacterial survival. However, the specific mechanisms by which bacterial NAs contribute to pathogenesis remain poorly understood and largely unknown. To gain a deeper understanding of the molecular mechanisms underlying this class of enzymes, highly selective and sensitive strategies are needed for screening, detecting, and studying active NAs in complex biological samples. Specifically, chemical tools that can covalently label NAs without interfering with their enzymatic activity offer a powerful approach to precisely label and visualize these enzymes in their native environments. In this work, we present the development of novel ortho-quinone methide-based probes featuring an azide and biotin tags for the labeling and detection of NAs. These probes exhibit high selectivity in labeling recombinantly expressed NAs from influenza A virus and pathogenic Gram-negative Prevotella strains at nanomolar concentrations. Moreover, we developed a strategy that significantly improves labeling specificity of NAs when using our probes in complex samples, addressing the common issue of nonspecific labeling associated with quinone methide-based probes. Additionally, we demonstrate the potential of these probes for imaging extracellular NAs on bacterial surfaces, highlighting their utility for studying NAs in their native environments.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12536644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145349071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0