scholarly journals Molecular Dynamics of Water-Mediated Interactions of a Linear Benzimidazole−Biphenyl Diamidine with the DNA Minor Groove

2009 ◽  
Vol 131 (22) ◽  
pp. 7618-7625 ◽  
Author(s):  
Prashanth Athri ◽  
W. David Wilson
Keyword(s):  
Molecular Dynamics ◽  
Minor Groove ◽  
Dna Minor Groove

Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin

2011 ◽  
Vol 17 (11) ◽  
pp. 2805-2816 ◽  
Author(s):  
Mathew Varghese Koonammackal ◽  
Unnikrishnan Viswambharan Nair Nellipparambil ◽  
Chellappanpillai Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Dynamics Simulations ◽  
Free Energy Analysis

scholarly journals Ligand-induced DNA conformational changes in proflavine minor groove-bound complexes studied by molecular dynamics simulation

2019 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Conformational Changes ◽  
Hydrophobic Interactions ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Dna Intercalation ◽  
Time Range ◽  
Dna Minor Groove ◽  
Dna Conformational Changes

Background: Minor groove binding is a rate-limiting step in proflavine-DNA intercalation reaction. This step is believed also to be responsible for the sequence-dependent kinetics of proflavine binding to DNA. At the same time, most studies are focused on the final stage of the reaction – the intercalation complex, and there is a lack of data concerning the structure and stability of proflavine-DNA minor groove-bound complexes. Objectives: The objective of this study was to investigate the stability of proflavine minor groove-bound complexes with DNA oligonucleotides of different sequence by molecular dynamics simulation and to analyze the DNA conformational changes caused by the proflavine binding. Materials and methods: The molecular dynamics simulations of proflavine minor groove-bound complexes with poly(dA)·poly(dT) and poly(dCG)·poly(dCG) oligonucleotides of 30 bp length were done in program package AMBER12 with explicit water (SPC/E) and ions (NaCl 0.15 M) using force fields FF14SB for DNA and GAFF for ligand. The starting configurations of complexes were obtained by docking method in AutoDock 3.05. After multi-stage equilibration protocol, each system was simulated at T=300 K and p=1 bar for a 50 ns production phase. Then trajectories were post-processed in AMBERTools17 and VMD-1.9.3 packages. Results: Our simulations confirm that proflavine-DNA minor groove-bound complexes are stable in the 50 ns time range but there are some structural rearrangements in them with respect to the initial structures. The narrowing of the DNA minor groove is observed in the proflavine binding site. In proflavine-poly(dCG)·poly(dCG) complex it is more pronounced and is accompanied by the BI/BII transitions in DNA and the reorientation of ligand. In proflavine-poly(dA)·poly(dT) complex the specific intermolecular hydrogen bonds are formed, which are optimized by the changes in opening and propeller twisting of involved AT-base pairs. Complexes are stabilized by the van der Waals and hydrophobic interactions, which are more favorable in the proflavine-poly(dA)·poly(dT) complex. Conclusions: Our results show that the binding of proflavine to a minor groove of DNA induces the conformational changes in the DNA that are important for the resulting complex stability.

scholarly journals Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d(CGCGAATTCGCG)2.

2000 ◽  
Vol 47 (3) ◽  
pp. 855-866 ◽  
Author(s):  
K Bielawski ◽  
A Bielawska ◽  
D Bartulewicz ◽  
A Rózański
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Complex Formation ◽  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Minor Groove ◽  
Model Complexes ◽  
Dna Minor Groove ◽  
Energetic Analysis ◽  
Effective Penetration

A molecular mechanics and molecular dynamics approach was used to examine the structure of complexes formed between the d(CGCGAATTCGCG)2 duplex and netropsin, distamycin, and four carbocyclic analogues of netropsin and distamycin (1-4). The resulting structures of the ligand-DNA model complexes and their energetics were examined. It is predicted that the compounds 1-4 should have a decreased affinity for the minor groove of AT-rich regions in comparison to netropsin and distamycin. From the energetic analysis it appears that van der Waals and electrostatic interactions are more important than specific hydrogen bonds in stabilizing the ligand-duplex complexes. We predict that compounds 1 and 2 are effectively isohelical with the DNA minor groove. The superior DNA-binding afforded by 1 and 2 in comparison to 3 and 4 results from their more effective penetration into the minor groove and smaller perturbation of molecular structure upon complex formation.

scholarly journals Cellular pharmacology of novel C8-linked anthramycin-based sequence-selective DNA minor groove cross-linking agents

1994 ◽  
Vol 70 (1) ◽  
pp. 48-53 ◽  
Author(s):  
M Smellie ◽  
LR Kelland ◽  
DE Thurston ◽  
RL Souhami ◽  
JA Hartley
Keyword(s):  
Minor Groove ◽  
Cross Linking ◽  
Dna Minor Groove ◽  
Cellular Pharmacology
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