A coarse-grained model for DNA that is intended to function realistically at the level of individual bases is reported. The model is composed of residues with up to eight coarse-grained beads each, which is sufficient for DNA-like base stacking and base-base recognition by hydrogen bonding. The beads interact by means of short-ranged pair potentials and a simple implicit solvent model. Movement is simulated by Brownian dynamics without hydrodynamic coupling. The main stabilizing forces are base stacking and hydrogen bonding, as modified by the effects of solvation. Complementary double-stranded chains of such residues form stable double helices over long runs (~10 μs) at or near room temperature, with structural parameters close to those of B-form DNA. Most mismatched chains or mismatched regions within a complementary molecule melt and become disordered. Long-range fluctuations and elastic properties, as measured by bending and twisting persistence lengths, are close to experimental values. Single-stranded chains are flexible, with transient stretches of free bases in equilibrium with globules stabilized by intrastrand stacking and hydrogen bonding. Model DNAs in covalently closed loops form right- or left-handed supercoils, depending on the sign of overtwist or undertwist. Short stem-loop structures melt at elevated temperatures and reanneal when the temperature is carefully lowered. Overall, most qualitative properties of real DNA arise naturally in the model from local interactions at the base-pair level.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/jp3009095 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Molecular Characterization and Potential Inhibitors Prediction of Protein Arginine Methyltransferase-2 in Carcinoma: An Insight from Molecular Docking, ADMET Profiling and Molecular Dynamics Simulation Studies.
Euroasian J Hepatogastroenterol
December 2024
Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Ehime, Japan.
Objectives: To predict and characterize the three-dimensional (3D) structure of protein arginine methyltransferase 2 (PRMT2) using homology modeling, besides, the identification of potent inhibitors for enhanced comprehension of the biological function of this protein arginine methyltransferase (PRMT) family protein in carcinogenesis.
Materials And Methods: An method was employed to predict and characterize the three-dimensional structure. The bulk of PRMTs in the PDB shares just a structurally conserved catalytic core domain.
Supramolecular Ionic Gels for Stretchable Electronics and Future Directions.
ACS Mater Au
January 2025
Department of Electrical and Electronic Engineering, Kyushu Institute of Technology, 1-1 Sensuicho, Tobataku, Kitakyushu, Fukuoka 804-8550, Japan.
Ionic gels (IGs), ionic liquids (ILs) dispersed in polymers, exhibit extremely low vapor pressure, electrochemical and thermal stability, and excellent mechanical characteristics; therefore, they are used for fabricating stretchable sensors, electrochemical transistors, and energy storage devices. Although such characteristics are promising for flexible and stretchable electronics, the mechanical stress-induced ruptured covalent bonds forming polymer networks cannot recover owing to the irreversible interaction between the bonds. Physical cross-linking via noncovalent bonds enables the interaction of polymers and ILs to form supramolecular IGs (SIGs), which exhibit favorable characteristics for wearable devices that conventional IGs with noncovalent bonds cannot achieve.
View Article and Find Full Text PDFExploring the Vibrational Coherences in the Ultrafast Electronic Relaxation of Pyrimidine Nucleobases and Nucleosides.
J Am Chem Soc
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
We studied the vibrational coherences during the ultrafast internal conversions (ICs) of pyrimidine nucleobases and -sides in aqueous solutions and the gas phase with an instrumental resolution of 14 fs. The coherence of the same ring-breathing vibrational mode with a frequency of 750 cm was observed. In the gas phase, the vibrational coherence was transferred during IC from the ππ* to the nπ* state, and it survived for approximately 1 ps.
View Article and Find Full Text PDF1.5D Chiral Perovskites Mediated by Hydrogen-Bonding Network with Remarkable Spin-Polarized Property.
Angew Chem Int Ed Engl
January 2025
Tianjin University, School of Chemical Engineering and Technology, Yaguan Road #135, Jinnan District, Tianjin 300354, P. R. China, CHINA.
In this study, we developed new chiral hybrid perovskites, (R/S-MBA)(GA)PbI4, by incorporating achiral guanidinium (GA+) and chiral R/S-methylbenzylammonium (R/S-MBA+) into the perovskite framework. The resulting materials possess a distinctive structural configuration, positioned between 1D and 2D perovskites, which we describe as 1.5D.
View Article and Find Full Text PDFMicroporous carbon derived from waste plastics for efficient adsorption of tetracycline: Adsorption mechanism and application potentials.
Environ Res
January 2025
MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.
In recent years, the accumulation of waste plastics and emergence plastic-derived pollutants such as microplastics have driven significantly the development and updating of waste plastic utilization technology. This study prepared the porous carbon (PC-1-KOH) material directly from polyethylene terephthalate (PET) in waste plastic bottles using KOH activation and molten salt strategy for efficient removal of antibiotic tetracycline (TC). The maximum removal efficiency of TC was 100.
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!