Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition

1997 ◽  
Vol 119 (29) ◽  
pp. 6722-6730 ◽  
Author(s):  
Piotr Cieplak ◽  
T. E. Cheatham ◽  
Peter A. Kollman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Duplexes ◽  
Modified Dna ◽  
Dynamics Simulations

scholarly journals Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

2006 ◽  
Vol 12 (6) ◽  
pp. 781-791 ◽  
Author(s):  
Hongwei Jin ◽  
Suxin Zheng ◽  
Zhanli Wang ◽  
Cheng Luo ◽  
Jianhua Shen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Duplexes ◽  
Dynamics Simulations ◽  
Structural Insights

Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

2003 ◽  
Vol 125 (7) ◽  
pp. 1759-1769 ◽  
Author(s):  
Nad'a Špačková ◽  
Thomas E. Cheatham ◽  
Filip Ryjáček ◽  
Filip Lankaš ◽  
Luc van Meervelt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Dna Duplexes ◽  
Groove Binding ◽  
Thermodynamics Analysis ◽  
Dynamics Simulations

Comparison of DNA duplexes with and without O 4-methylthymine: nanosecond molecular dynamics simulations

1994 ◽  
Vol 90 (10) ◽  
pp. 1415 ◽  
Author(s):  
Leonor Cruzeiro-Hansson ◽  
Julia M. Goodfellow
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Duplexes ◽  
Dynamics Simulations

Effect of PNA Backbone Modifications on Cyanine Dye Binding to PNA−DNA Duplexes Investigated by Optical Spectroscopy and Molecular Dynamics Simulations

2005 ◽  
Vol 127 (10) ◽  
pp. 3339-3345 ◽  
Author(s):  
Isil Dilek ◽  
Marcela Madrid ◽  
Rojendra Singh ◽  
Christian P. Urrea ◽  
Bruce A. Armitage
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Optical Spectroscopy ◽  
Cyanine Dye ◽  
Dna Duplexes ◽  
Dye Binding ◽  
Dynamics Simulations

scholarly journals Molecular-Dynamics Simulations of Insertion of Chemically Modified DNA Nanostructures into a Water-Chloroform Interface

2008 ◽  
Vol 95 (3) ◽  
pp. 1099-1107 ◽  
Author(s):  
Jianping Lin ◽  
Nadrian C. Seeman ◽  
Nagarajan Vaidehi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Nanostructures ◽  
Chemically Modified ◽  
Modified Dna ◽  
Dynamics Simulations

scholarly journals Controlling aggregation of cholesterol-modified DNA nanostructures

2019 ◽  
Vol 47 (21) ◽  
pp. 11441-11451 ◽  
Author(s):  
Alexander Ohmann ◽  
Kerstin Göpfrich ◽  
Himanshu Joshi ◽  
Rebecca F Thompson ◽  
Diana Sobota ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membranes ◽  
Structural Control ◽  
Polyacrylamide Gel Electrophoresis ◽  
Dna Nanotechnology ◽  
Dna Nanostructures ◽  
Hydrophobic Moiety ◽  
Modified Dna ◽  
Dynamics Simulations

Abstract DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure–function relationship of membrane-interfacing DNA constructs — a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

2000 ◽  
Vol 98 (11) ◽  
pp. 701-707
Author(s):  
Alessandro Sergi, Mauro Ferrario, Francesco Bu
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations
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