A biotin-binding RNA pseudoknot developed through in vitro selection has been crystallized using the hanging-drop vapor-phase diffusion method. The X-ray diffraction data indicate that the crystals belong to the space group P4222 with unit-cell parameters a = b = 55.2, c = 62.7 A and alpha = beta = gamma = 90 degrees. The crystals are 120 x 80 x 40 microm and VM = 2.17 A3 Da-1. The crystals diffract to 2.8 A.
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http://dx.doi.org/10.1107/S0907444998004934 | DOI Listing |
RNA Biol
December 2025
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
We show that a small biotin-binding RNA aptamer that folds into a pseudoknot structure acts as a substrate for bacterial RNase P RNA (RPR) with and without the RNase P C5 protein. Cleavage in the single-stranded region in loop 1 was shown to depend on the presence of a RCCA-motif at the 3' end of the substrate. The nucleobase and the 2'hydroxyl at the position immediately 5' of the cleavage site contribute to both cleavage efficiency and site selection, where C at this position induces significant cleavage at an alternative site, one base upstream of the main cleavage site.
View Article and Find Full Text PDFSensors (Basel)
September 2024
School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
Direct detection of miRNA is currently limited by the complex amplification and reverse transcription processes of existing methods, leading to low sensitivity and high operational demands. Herein, we developed a CRISPR/Cas13a-mediated photoelectrochemical (PEC) biosensing platform for direct and sensitive detection of miRNA-21. The direct and specific recognition of target miRNA-21 by crRNA-21 eliminates the need for pre-amplification and reverse transcription of miRNA-21, thereby preventing signal distortion and enhancing the sensitivity and precision of target detection.
View Article and Find Full Text PDFViruses
June 2023
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.
We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target selection was achieved through panning with elution by infection.
View Article and Find Full Text PDFTalanta
November 2021
College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, 410083, People's Republic of China. Electronic address:
The hybridization and enzymolysis reactions for nucleic acid detection were carried out on the chip surface in the traditional surface plasmon resonance (SPR) biosensors. Herein, we proposed an innovative method for microRNA (miRNA) detection in which the hybridization-enzymolysis recycling reactions were performed in solution. Duplex-specific nuclease (DSN) and streptavidin-modified gold nanoparticles (SA-AuNPs) were employed for enhancing the assay sensitivity.
View Article and Find Full Text PDFTwo-channel fluorogenic RNA aptamer-based imaging is currently challenging. While we have previously characterized the Mango series of aptamers that bind tightly and specifically to the green fluorophore TO1-Biotin, the next aim was to identify an effective fluorogenic aptamer partner for two-color imaging. A competitive in vitro selection for TO3-Biotin binding aptamers was performed resulting in the Peach I and II aptamers.
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