Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314182 | PMC |
| http://dx.doi.org/10.1039/c8cc09048c | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Environmental and genetic influence on the rate and spectrum of spontaneous mutations in .
Microbiology (Reading)
April 2024
Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK.
Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions.
View Article and Find Full Text PDFInfluence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17.
Int J Mol Sci
July 2023
Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia.
The influence of a single H/H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had.
View Article and Find Full Text PDFStability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions.
Langmuir
April 2023
Department of Physics, Kent State University, Kent, Ohio 44242, United States.
Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS).
View Article and Find Full Text PDFSingle nucleotide polymorphisms (rs3736228 and rs4988321) in low-density lipoprotein receptor-related protein-5 gene with predisposition to rheumatoid arthritis.
Gene
January 2023
The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan. Electronic address:
Background: LRP5 (Lipoprotein Receptor 5) is one of the representatives of the low-density lipoprotein receptors family that play a crucial role in the process of bone homeostasis and bone remodeling. The role of LRP5 single nucleotide polymorphisms (SNPs) rs3736228 and rs4988321 has been associated with the susceptibility to osteoporosis and bone fracture. The frequency of mentioned LRP5 SNPs is unknown among RA (Rheumatoid Arthritis) patients.
View Article and Find Full Text PDFHost translesion polymerases are required for viral genome integrity.
Proc Natl Acad Sci U S A
August 2022
BIO5 Institute, University of Arizona, Tucson, AZ 85721.
Human cells encode up to 15 DNA polymerases with specialized functions in chromosomal DNA synthesis and damage repair. In contrast, complex DNA viruses, such as those of the herpesviridae family, encode a single B-family DNA polymerase. This disparity raises the possibility that DNA viruses may rely on host polymerases for synthesis through complex DNA geometries.
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!