AI Article Synopsis
- The study explores the topological properties of DNA, specifically focusing on the calculation of its twisting number as proposed by White's formula: L=W+T.
- It highlights the confusion surrounding the definition of torsion in differential geometry, suggesting that DNA twisting numbers should be calculated using the curve's geodesic torsion.
- The findings aim to clarify discrepancies in previously calculated twisting numbers and offer accurate methods for future research in DNA topology.
Article Abstract
The topological properties of DNA have long been a focal point in biophysics. In the 1970s, White proposed that the topology of closed DNA double helix follows White's formula: L=W+T. However, there has been controversy in the calculation of DNA twisting number, partly due to discrepancies in the definition of torsion in differential geometry. In this paper, we delved into a detailed study of torsion, revealing that the calculation of DNA twisting number should use the curve's geodesic torsion. Furthermore, we found that the discrepancy in DNA twisting numbers calculated using different torsion is N. This study elucidated the impact of torsion on the calculation of DNA twisting numbers, aiming to resolve controversies in the calculation of DNA topology and provided accurate computational methods and theoretical foundations for related research.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.bbrc.2024.149856 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Synthesis, biological activities, DFT calculations and molecular docking studies of O-methyl-inositols.
Chem Biodivers
January 2025
Ordu University: Ordu Universitesi, Department of Chemistry, Cumhuriyet Mah., Ordu, TURKEY.
The concise synthesis of O-methyled-inositol derivative and conduritol derivatives was obtained starting from p-benzoquinone. Spectroscopic methods have been performed for characterization of new synthesized compounds. Cyclitols are useful molecules with anticancer, antibiotic, antinutrient and antileukemic activity.
View Article and Find Full Text PDFsp. nov. and sp. nov., two bacteria isolated from marine sediment in the East China Sea.
Int J Syst Evol Microbiol
January 2025
Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, PR China.
Two Gram-stain-negative, curved-rod-shaped, non-motile and aerobic bacteria W6 and I13 were isolated from marine sediment samples collected from Meishan Island located in the East China Sea. Catalase and oxidase activities and hydrolysis of Tween 40, 60 and 80 were positive for both strains, while nitrate reduction, indole production, methyl red reaction and HS production were negative. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains W6 and I13 formed distinct phylogenetic lineages within the genera and , respectively.
View Article and Find Full Text PDFCharacterizing Conical Intersections of Nucleobases on Quantum Computers.
J Chem Theory Comput
January 2025
Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.
Hybrid quantum-classical computing algorithms offer significant potential for accelerating the calculation of the electronic structure of strongly correlated molecules. In this work, we present the first quantum simulation of conical intersections (CIs) in a biomolecule, cytosine, using a superconducting quantum computer. We apply the contracted quantum eigensolver (CQE)─with comparisons to conventional variational quantum deflation (VQD)─to compute the near-degenerate ground and excited states associated with the conical intersection, a key feature governing the photostability of DNA and RNA.
View Article and Find Full Text PDFSignatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador.
G3 (Bethesda)
January 2025
Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 94720, USA.
Atahualpa is a rural village located in coastal Ecuador, a region that has been inhabited by people as early as 10,000 years ago. The traditional diet of their indigenous inhabitants is rich in oily fish and they have, therefore, served as a model for investigating the beneficial effects of such a diet. However, the genetic background of this population has not been studied.
View Article and Find Full Text PDFDual recycling signal amplification strategy based on autocatalytic entropy-driven circuit and DNAzyme for colorimetric detection of platelet-derived growth factor-BB.
Anal Methods
January 2025
College of Chemistry, Sichuan University, Chengdu 610064, China.
Platelet-derived growth factor-BB (PDGF-BB), an important protein biomarker, is closely associated with tumorigenesis. Therefore, it is important to develop a simple and sensitive method to detect PDGF-BB. Herein, we developed a dual recycling signal amplification strategy for colorimetric and sensitive detection of PDGF-BB using a PDGF-BB specific aptamer.
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!