A5075828988- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- DNA and Nucleic Acid Chemistry
- Chemical Synthesis and Analysis
- Sirtuins and Resveratrol in Medicine
- Peptidase Inhibition and Analysis
- Calcium signaling and nucleotide metabolism
- Radioactive element chemistry and processing
- Bacterial Genetics and Biotechnology
- interferon and immune responses
- Copper Interconnects and Reliability
- Biochemical and Molecular Research
- Chemical Synthesis and Characterization
- Genomics and Chromatin Dynamics
- Glycosylation and Glycoproteins Research
- Inorganic Fluorides and Related Compounds
- Analytical chemistry methods development
- Bacteriophages and microbial interactions
- Porphyrin and Phthalocyanine Chemistry
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Monoclonal and Polyclonal Antibodies Research
Second Affiliated Hospital of Zhejiang University
2023-2025
Shenyang Pharmaceutical University
2025
Nanjing Normal University
2025
Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application
2025
Zhejiang University
2016-2024
Xinyang Normal University
2024
Institute of Life Sciences
2023
Chongqing University of Posts and Telecommunications
2019
Memorial Sloan Kettering Cancer Center
2012-2017
Fudan University
2017
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures riboswitch aptamers and puzzle 7, ribozyme structure, are included this the experiment. The include biological binding sites for small molecules ( S -adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5′-triphosphate, glutamine) proteins (YbxF), one set describes large conformational...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
We recently reported that Drosophila Insensitive (Insv) promotes sensory organ development and has activity as a nuclear corepressor for the Notch transcription factor Suppressor of Hairless [Su(H)]. Insv lacks domains known biochemical function but contains single BEN domain (i.e., “BEN-solo” protein). Our chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) analysis confirmed binding to Su(H) target genes in Enhancer split gene complex [ E(spl) -C]; however, de novo motif revealed...
Cyclic dinucleotides are second messengers that target the adaptor STING and stimulate innate immune response in mammals. Besides protein receptors, there bacterial riboswitches selectively recognize cyclic dinucleotides. We recently discovered a natural riboswitch targets 3′,3′-cGAMP, which is distinguished from endogenous mammalian signal 2′,3′-cGAMP by its backbone connectivity. Here, we report on structures of aptamer domain 3′,3′-cGAMP Geobacter c-di-GMP bound states. The adopts tuning...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version the twister ribozyme is reported that lacks phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed nitrogen atoms N1 and N3 adenine-6 at site are indispensable for cleavage. By NMR spectroscopy, a pKa value 5.1 was determined (13) C2-labeled adenine this position in ribozyme, which significantly shifted compared to same substrate alone. This...
Recently, the BEN (BANP, E5R, and NAC1) domain was recognized as a new class of conserved DNA-binding domain. The fly genome encodes three proteins that bear only single (“BEN-solo” factors); namely, Insensitive (Insv), Bsg25A (Elba1), CG9883 (Elba2). Insv homodimers preferentially bind CCAATTGG palindromes throughout to mediate transcriptional repression, whereas Elba2 heterotrimerize with their obligate adaptor, Elba3 (i.e., ELBA complex), recognize CCAATAAG motif in Fab-7 insulator. While...
Abstract Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that central to regulation gene expression. Here we report the first three-dimensional structure recently discovered S -adenosyl-L-methionine responsive SAM-VI riboswitch. adopts a unique fold and ligand pocket distinct from all other known SAM riboswitch classes. The binds junctional region with its adenine tightly intercalated Hoogsteen base-paired. Furthermore, reveal discrimination mode...
Abstract Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at ribozyme core through long-range interactions mediated by hydrated Mg 2+ cations. The C62–A63 step site adopts splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is inwards anchored stacking hydrogen-bonding interactions. Structure-guided...
Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity scissile phosphate. Strikingly, catalytic pocket contains...
Abstract Pistol ribozymes constitute a new class of small self‐cleaving RNAs. Crystal structures have been solved, providing three‐dimensional snapshots along the reaction coordinate pistol phosphodiester cleavage, corresponding to pre‐catalytic state, vanadate mimic transition and product. The results led proposed underlying chemical mechanism. Importantly, hydrated Mg 2+ ion remains innersphere‐coordinated N7 G33 in all three states, is consistent with its likely role as acid general base...
The BEN domain is a recently recognized DNA binding module that present in diverse metazoans and certain viruses. Several factors are known as transcriptional repressors, but, overall, relatively little of how identify their targets humans. In particular, X-ray structures domain:DNA complexes only for Drosophila bearing single domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian (BD) factors, including from two NACC family BTB-BEN proteins BEND3, has four...
Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according phylogenetic analysis. To reveal three-dimensional architecture and ligand-binding mode this riboswitch, we solved crystal structure NAD+-II riboswitch complex NAD+....