Molecular dynamics simulations of PNA–PNA and PNA–DNA duplexes by the use of new parameters implemented in the GROMACS package: a conformational and dynamics study

Ida Autiero; Michele Saviano; Emma Langella

doi:10.1039/c3cp54284j

Molecular dynamics simulations of PNA–PNA and PNA–DNA duplexes by the use of new parameters implemented in the GROMACS package: a conformational and dynamics study

Physical Chemistry Chemical Physics ◽

10.1039/c3cp54284j ◽

2014 ◽

Vol 16 (5) ◽

pp. 1868-1874 ◽

Cited By ~ 22

Author(s):

Ida Autiero ◽

Michele Saviano ◽

Emma Langella

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Duplexes ◽

Dynamics Simulations

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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

Journal of the American Chemical Society ◽

10.1021/ja963909j ◽

1997 ◽

Vol 119 (29) ◽

pp. 6722-6730 ◽

Cited By ~ 44

Author(s):

Piotr Cieplak ◽

T. E. Cheatham ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Duplexes ◽

Modified Dna ◽

Dynamics Simulations

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Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations

Chemistry - A European Journal ◽

10.1002/chem.200501126 ◽

2006 ◽

Vol 12 (13) ◽

pp. 3587-3595 ◽

Cited By ~ 18

Author(s):

David Řeha ◽

Michal Hocek ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Ab Initio Calculations ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Thermodynamic Stability ◽

Stacking Interactions ◽

Dna Duplexes ◽

Dynamics Simulations

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

Journal of Molecular Modeling ◽

10.1007/s00894-005-0085-8 ◽

2006 ◽

Vol 12 (6) ◽

pp. 781-791 ◽

Cited By ~ 6

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

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

Journal of the American Chemical Society ◽

10.1021/ja025660d ◽

2003 ◽

Vol 125 (7) ◽

pp. 1759-1769 ◽

Cited By ~ 102

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

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

Journal of the Chemical Society Faraday Transactions ◽

10.1039/ft9949001415 ◽

1994 ◽

Vol 90 (10) ◽

pp. 1415 ◽

Cited By ~ 3

Author(s):

Leonor Cruzeiro-Hansson ◽

Julia M. Goodfellow

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Duplexes ◽

Dynamics Simulations

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

Journal of the American Chemical Society ◽

10.1021/ja045145a ◽

2005 ◽

Vol 127 (10) ◽

pp. 3339-3345 ◽

Cited By ~ 31

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

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Molecular Dynamics Simulations of Mismatched DNA Duplexes Associated with the Major C8-Linked 2′-Deoxyguanosine Adduct of the Food Mutagen Ochratoxin A: Influence of Opposing Base, Adduct Ionization State, and Sequence on the Structure of Damaged DNA

Chemical Research in Toxicology ◽

10.1021/acs.chemrestox.8b00064 ◽

2018 ◽

Vol 31 (8) ◽

pp. 712-720 ◽

Cited By ~ 1

Author(s):

Preetleen Kathuria ◽

Purshotam Sharma ◽

Richard A. Manderville ◽

Stacey D. Wetmore

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Ochratoxin A ◽

Dna Duplexes ◽

Ionization State ◽

Mismatched Dna ◽

Dynamics Simulations ◽

Food Mutagen ◽

Damaged Dna

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

Molecular Physics ◽

10.1080/002689700162045 ◽

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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Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

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ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

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