Simulation of DNA catenanes

Literature Information

Publication Date 2009-10-23
DOI 10.1039/B910812B
Impact Factor 3.676
Authors

Valentin V. Rybenkov


View Original

Abstract

DNA catenanes are important objects in biology, foremost as they appear during replication of circular DNA molecules. In this review we analyze how conformational properties of DNA catenanes can be studied by computer simulation. We consider classification of catenanes, their topological invariants and the methods of calculation of these invariants. We briefly analyze the DNA model and the simulation procedure used to sample the equilibrium conformational ensemble of catenanes with a particular topology. We consider how to avoid direct simulation of many DNA molecules when we need to account for the linking–unlinking process. The simulation methods and their comparisons with experiments are illustrated by some examples. We also describe an approach that allows simulating the steady state fraction of DNA catenanes created by type II topoisomerases.

Related Literature

Metal nanoinks as chemically stable surface enhanced scattering (SERS) probes for the analysis of blue BIC ballpoint pens

A. Alyami, D. Saviello, M. A. P. McAuliffe, A. Mirabile, D. Iacopino

2017-05-10 Paper

DOI: 10.1039/C7CP01983A

Photoelectrical properties of CdS/CdSe core/shell QDs modified anatase TiO2 nanowires and their application for solar cells

Qingqing Qiu, Ping Wang, Lingling Xu, Yanhong Lin, Tengfeng Xie

2017-05-23 Paper

DOI: 10.1039/C7CP02358H

Stoichiometric network analysis of spontaneous mirror symmetry breaking in chemical reactions

David Hochberg, Rubén D. Bourdon García, Jesús A. Ágreda Bastidas, Josep M. Ribó

2017-06-08 Paper

DOI: 10.1039/C7CP02159C

Improved magnetic and magnetoelectric properties in BaFe12O19 nanostructures

Xingyu Xu, Ye Shao, Min Zhou, Xianming Ren

2017-06-15 Paper

DOI: 10.1039/C7CP02276J

Predictive models of gas sorption in a metal–organic framework with open-metal sites and small pore sizes

Tony Pham, Katherine A. Forrest, Douglas M. Franz, Zhiyong Guo, Banglin Chen, Brian Space

2017-06-20 Paper

DOI: 10.1039/C7CP02767B

Method to determine radiative and non-radiative defects applied to AgInS2–ZnS luminescent nanocrystals

G. Le Blevennec, F. Chandezon

2016-12-22 Paper

DOI: 10.1039/C6CP06509K

You might also like

Compound Q&A

What is Ethyl 3-cyclohexylpropanoate (CAS: 10094-36-7)?

Ethyl 3-cyclohexylpropanoate is a clear, colorless to light yellow liquid with a...

10094-36-7Ethyl 3-cyclohexylpr...
Compound Q&A

How should waste containing 2-(Hydroxymethyl)-5-(methoxycarbonyl)-6-methyl-4-(2-nitrophenyl)nicotinic acid (CAS: 34783-31-8) be handled?

Waste containing 2-(Hydroxymethyl)-5-(methoxycarbonyl)-6-methyl-4-(2-nitrophenyl...

34783-31-82-(Hydroxymethyl)-5-...
Compound Q&A

How should waste containing 2,4,6-Tris(pentafluoroethyl)-1,3,5-triazine (CAS: 858-46-8) be handled?

Waste containing 2,4,6-Tris(pentafluoroethyl)-1,3,5-triazine (CAS: 858-46-8) sho...

858-46-82,4,6-Tris(pentafluo...
Compound Q&A

What precautions should be taken when handling Chloroac-nle-oh (CAS: 56787-36-1)?

When handling Chloroac-nle-oh (CAS: 56787-36-1), it is essential to wear appropr...

56787-36-1Chloroac-nle-oh
Compound Q&A

What industries use Ethyl 6-phenylimidazo[2,1-b][1,3]thiazole-3-carboxylate (CAS: 752244-05-6)?

Ethyl 6-phenylimidazo[2,1-b][1,3]thiazole-3-carboxylate is primarily used in the...

752244-05-6Ethyl 6-phenylimidaz...
Compound Q&A

Are there alternatives to alpha-(2-Bromophenyl)benzylamine (CAS: 55095-15-3) in synthesis?

Alternatives to alpha-(2-Bromophenyl)benzylamine (CAS: 55095-15-3) in synthesis ...

55095-15-3alpha-(2-Bromophenyl...
Compound Q&A

How should waste containing 2-Chloro-5-methoxypyridine (CAS: 139585-48-1) be handled?

Waste containing 2-Chloro-5-methoxypyridine (CAS: 139585-48-1) should be managed...

139585-48-12-Chloro-5-methoxypy...
Compound Q&A

What industries use 1-(4-Methoxyphenyl)-2,5-dimethyl-1H-pyrrole (CAS: 5044-27-9)?

1-(4-Methoxyphenyl)-2,5-dimethyl-1H-pyrrole (CAS: 5044-27-9) is used in various ...

5044-27-91-(4-Methoxyphenyl)-...
Compound Q&A

Are there alternatives to 3-Bromo-5-(N-Boc)aminomethylisoxazole (CAS: 903131-45-3) in synthesis?

There are alternative reagents and compounds that can be used in the synthesis o...

903131-45-33-Bromo-5-(N-Boc)ami...
Compound Q&A

What is Tungsten(IV) oxide (CAS: 12036-22-5)?

Tungsten(IV) oxide, also known as tungsten dioxide, is a chemical compound with ...

12036-22-5Tungsten(IV) oxide

Source Journal

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
Articles per Year: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

Recommended Compounds

Recommended Suppliers

Disclaimer
This page provides academic journal information for reference and research purposes only. We are not affiliated with any journal publishers and do not handle publication submissions. For publication-related inquiries, please contact the respective journal publishers directly.
If you notice any inaccuracies in the information displayed, please contact us at support@chemtradehub.com. We will promptly review and address your concerns.