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

Isil Dilek; Marcela Madrid; Rojendra Singh; Christian P. Urrea; Bruce A. Armitage

doi:10.1021/ja045145a

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

Understanding the Population, Coordination, and Orientation of Water Species Contributing to the Nonlinear Optical Spectroscopy of the Vapor−Water Interface through Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp063063y ◽

2006 ◽

Vol 110 (41) ◽

pp. 20451-20459 ◽

Cited By ~ 69

Author(s):

Dave S. Walker ◽

Dennis K. Hore ◽

Geraldine L. Richmond

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Optical Spectroscopy ◽

Nonlinear Optical ◽

Water Interface ◽

Nonlinear Optical Spectroscopy ◽

Dynamics Simulations ◽

Water Species

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

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

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

Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp4005696 ◽

2013 ◽

Vol 117 (19) ◽

pp. 5857-5867 ◽

Cited By ~ 11

Author(s):

Frank Haverkort ◽

Anna Stradomska ◽

Alex H. de Vries ◽

Jasper Knoester

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Cyanine Dye ◽

Dynamics Simulations ◽

Structure Of Aggregates

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

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

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

Characterization of diadzein–hemoglobin binding using optical spectroscopy and molecular dynamics simulations

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2012.05.013 ◽

2012 ◽

Vol 51 (3) ◽

pp. 250-258 ◽

Cited By ~ 18

Author(s):

Bidisha Sengupta ◽

Sandipan Chakraborty ◽

Maurice Crawford ◽

Jasmine M. Taylor ◽

Laura E. Blackmon ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Optical Spectroscopy ◽

Hemoglobin Binding ◽

Dynamics Simulations

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