Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.
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http://dx.doi.org/10.1093/nar/gku743 | DOI Listing |
J Control Release
January 2025
Department of Orthopedics, Sichuan Provincial People's Hospital, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, PR China; TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Chengdu 610072, Sichuan, PR China; Chongqing Engineering Laboratory of Nano/Micro Biomedical Detection Technology, Chongqing University of Science and Technology, Chongqing 401331, PR China; Department of Urology, Deyang People's Hospital, Deyang 618099, Sichuan, PR China. Electronic address:
Developing effective nanoplatforms for chemo-immunotherapy to achieve enhanced tumor suppression and systemic antitumor immunity has recently received extensive attention. Herein, we formulated a multifunctional DNA sandwich nanodevice, DSWAC/siPD-L1, based on triangular DNA origami, to implement enhanced cancer chemo-immunotherapy. Taking advantage of the tumor-targeting ability of the AS1411 aptamer, DSWAC/siPD-L1 efficiently delivered doxorubicin (DOX), CpG, and siPD-L1 into tumor cells.
View Article and Find Full Text PDFComput Biol Med
January 2025
Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh.
The ERBB2 is one of the most studied genes in oncology for its significant role in human malignancies. The metastasis-associated properties that facilitate cancer metastasis can be enhanced by activating the ERBB2 receptor signaling pathways. Additionally, therapeutic resistance is conferred by ERBB2 overexpression via receptor-mediated antiapoptotic signals.
View Article and Find Full Text PDFMikrochim Acta
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Electroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran.
A novel electrochemical aptasensor based on bimetallic zirconium and copper oxides embedded within mesoporous carbon (denoted as ZrOCuO@mC) was constructed to detect miRNA. The porous ZrOCuO@mC was created through the pyrolysis of bimetallic zirconium/copper-based metal-organic framework (ZrCu-MOF). The substantial surface area and high porosity of ZrOCuO@mC nanocomposite along with its robust affinity toward aptamer strands, facilitated the effective anchoring of aptamer strands on the ZrOCuO@mC-modified electrode surface.
View Article and Find Full Text PDFMikrochim Acta
January 2025
Department of General Surgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, Shandong, 266035, P.R. China.
A self-powered dual-electrode aptasensor was developed for the detection of tumor marker carcinoembryonic antigen (CEA). The composite BiVO/ZnInS, which is capable of forming a Z-scheme heterojunction, was chosen as the photoanode, and the AuNP/CuBiO complex was chosen as the photocathode in photoelectrochemical (PEC) detection. The experiments showed that the constructed self-powered dual-electrode system had a good photoelectric response to white light, and the photocurrent signal of the photocathode was significantly enhanced under the influence of the photoanode.
View Article and Find Full Text PDFMikrochim Acta
January 2025
School of Public Health, Jilin University, Changchun, Jilin, 130021, P. R. China.
A spherical nucleic acid (SNA, AuNPs-aptamer) into CRISPR/Cas12a system combined with poly T-template copper nanoparticles as fluorescence reporter was fabricated to establish an amplification-free sensitive method for Staphylococcus aureus (S. aureus) detection. This method, named PTCas12a, utilizes the concept that the bifunction of SNA recognizes the S.
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