AI Article Synopsis
- The study examines how pH levels influence the formation of the i-motif structure in a specific nucleotide sequence, utilizing spectroscopic techniques, such as UV absorption and circular dichroism, at various pH levels (3.3-8.9) and 25°C.
- Two chemometric approaches—soft modelling (MCR-ALS) and hard modelling (matrix method)—were used to analyze experimental data, with soft modelling showing good reproduction of spectral variations using two or three spectral species.
- The research also determined key parameters like the intrinsic protonation constant and cooperativity, indicating that the folding process of the structure is cooperative, enhancing stability as protons are added.
Article Abstract
In the present study, the experimental data on the pH-induced formation of the i-motif structure in the nucleotide sequence 5'-CCTTTCCTTTTCCTTTCC-3' (25oC, pH 3.3-8.9) obtained by spectroscopic techniques, such as UV molecular absorption and circular dichroism, has been analysed using the chemometric soft modelling-based MCR-ALS approach and the hard modelling-based matrix method. Soft modelling using 2 or 3 spectral species correctly reproduced spectral variations observed experimentally. The use of hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant Kin, and the cooperativity parameter w have been calculated from the fitting procedure of the circular dichroism as well as molecular absorption spectra. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation.
Download full-text PDF |
Source |
|---|
Publication Analysis
Top Keywords
Similar Publications
Inhibition of amyloid-beta aggregation by phenyl butyric acid analogs and bile acids: a comprehensive in silico study.
Mol Divers
January 2025
Department of Biophysics, Panjab University, Chandigarh, 160014, India.
Alzheimer's disease (AD) is a degenerative neurological disorder defined by the formation of β-amyloid (Aβ) plaques and neurofibrillary tangles within the brain. Current pharmacological treatments for AD only provide symptomatic relief, and there is a lack of definitive disease-modifying therapies. Chemical chaperones, such as 4-Phenylbutyric acid (4PBA) and Tauroursodeoxycholic acid, have shown neuroprotective effects in animal and cell culture models.
View Article and Find Full Text PDFPreparation and Adsorption Properties of Sodium Trimetaphosphate Crosslinked Porous Corn Starch.
Biopolymers
March 2025
Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China.
The crosslinked porous corn starch was prepared by two steps: the native corn starch was hydrolyzed by α-amylase and glucoamylase, then the porous corn was crosslinked by sodium trimetaphosphate (STMP). The morphology and size of granules, spherulites, crystal type, molecular structure, swelling properties, thermal stability and adsorption properties of the crosslinked porous starch were investigated. The results indicated that a lot of holes formed in the porous starch, and the particle size of starch granules decreased.
View Article and Find Full Text PDFCore-Excited States for Open-Shell Systems in Similarity-Transformed Equation-of-Motion Theory.
J Chem Theory Comput
January 2025
Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
X-ray absorption spectroscopy (XAS) is a powerful method for exploring molecular electronic structure by exciting core electrons into higher unoccupied molecular orbitals. In this study, we present the first integration of the spin-unrestricted similarity-transformed equation-of-motion coupled cluster method (CVS-USTEOM-CCSD) for core-excited and core-ionized states into the ORCA quantum chemistry package. Using the core-valence separation (CVS) approach, we evaluate the accuracy of CVS-USTEOM-CCSD across 13 open-shell organic systems, covering over 20 core excitations with diverse spin multiplicities (doublet, triplet, and quartet).
View Article and Find Full Text PDFSubventricular Accumulation of Cu in the Aging Mouse Brain Does Not Associate with Anticipated Increases in Markers of Oxidative Stress.
ACS Chem Neurosci
January 2025
School of Molecular and Life Sciences, Faculty of Science and Engineering, Curtin University, Bentley, WA 6845, Australia.
Natural aging is associated with mild memory loss and cognitive decline, and age is the greatest risk factor for neurodegenerative diseases, such as Alzheimer's disease. There is substantial evidence that oxidative stress is a major contributor to both natural aging and neurodegenerative disease, and coincidently, levels of redox active metals such as Fe and Cu are known to be elevated later in life. Recently, a pronounced age-related increase in Cu content has been reported to occur in mice and rats around a vital regulatory brain region, the subventricular zone of lateral ventricles.
View Article and Find Full Text PDFCholesin, a new hormone bridges intestinal cholesterol absorption and hepatic synthesis.
Life Metab
August 2024
Department of Pediatrics, Group on the Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, AB T6G 2S2, Canada.
Want 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!