AI Article Synopsis
- The cytidine analog Çmf serves as a specific reporter for studying RNA dynamics, showing varying fluorescence properties based on the RNA's structure and surrounding nucleobases.
- Çmf was inserted at four different positions in the neomycin-binding aptamer N1 to analyze binding dynamics, revealing rapid binding kinetics through stopped-flow measurements.
- The study found that neomycin binding occurs primarily via a two-step mechanism, with conformational selection being the main pathway for this process.
Article Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326822 | PMC |
| http://dx.doi.org/10.1093/nar/gky1110 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Causal relationships between immune cells, inflammatory factors, and preeclampsia: A two-step, two-sample mendelian randomization study.
J Reprod Immunol
January 2025
Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China. Electronic address:
Background: Preeclampsia (PE) is a complex hypertensive disorder that occurs during pregnancy, with the immune system playing a key role. Although immune modulation is implicated in PE progression, the roles of specific immune cells and inflammatory mediators remain unclear.
Methods: We conducted a two-sample, two-step Mendelian randomization (MR) analysis, primarily using the inverse-variance weighted method, to investigate the causal effect of immune cell traits on PE.
Introducing Pyridone[α]-Fused BOPHYs as Red-Shifted Bright Fluorophore Potentially Useful as Non-fullerene Acceptors in Donor-Acceptor Dyads.
Inorg Chem
January 2025
Department of Chemistry University of Tennessee, Knoxville, Tennessee 37996-1600, United States.
A series of 2-pyridone[α]-fused BOPHYs - were prepared via a two-step procedure involving the preparation of enamine, followed by an intramolecular heterocyclization reaction. In addition to being fully conjugated with the BOPHY core pyridone fragment, BOPHYs and have a pyridine group connected to the BOPHY core via one- or two -CH- groups. New BOPHYs were characterized by spectroscopy as well as X-ray diffraction.
View Article and Find Full Text PDFDesign of pH-responsive and amphiphilic pullulan-based biological macromolecule for gene delivery.
Int J Biol Macromol
January 2025
Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, D-07743 Jena, Germany; Jena Center for Soft Matters (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, D-07743 Jena, Germany. Electronic address:
Nanomedicine, particularly gene delivery, holds immense potential and offers promising therapeutic options. Non-viral systems gained attention due to their binding capacity, stability and scalability. Among these, natural polysaccharides, such as pullulan, are advantageous in terms of sustainability, biocompatibility and potential degradability.
View Article and Find Full Text PDFEffects of vitamin B supply on cellular processes of the facultative vitamin B consumer .
Appl Environ Microbiol
January 2025
Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
Vitamin B (cobalamin, herein B) is a key cofactor for most organisms being involved in essential metabolic processes. In microbial communities, B is often scarce, largely because only few prokaryotes can synthesize B and are thus considered B-prototrophs. B-auxotrophy is mostly manifested by the absence of the B-independent methionine synthase, MetE.
View Article and Find Full Text PDFQuantitative Analysis of Phosphorothioate Isomers in CRISPR sgRNA at Single-Residue Resolution Using Endonuclease Digestion Coupled with Liquid Chromatography Cyclic Ion Mobility Mass Spectrometry (LC/cIMS).
Anal Chem
January 2025
Analytical Chemistry Group, ‡VI-NEXT Group, Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591-6706, United States.
Phosphorothioate (PS) modifications in single-guided RNA (sgRNA) are crucial for genome editing applications using the CRISPR/Cas9 system. These modifications may enhance sgRNA stability, pharmacokinetics, and binding to targets, thereby facilitating the desired genetic alterations. Incorporating multiple PS groups at varying positions may introduce chiral centers into the sgRNA backbone, resulting in a complex mixture of constitutional- and stereoisomers that challenges current analytical capabilities for reliable identification and quantification.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!