Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations

2017 ◽  
Vol 36 (6) ◽  
pp. 1369-1401 ◽  
Author(s):  
R. Radhika ◽  
R. Shankar ◽  
S. Vijayakumar ◽  
P. Kolandaivel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Base Pairs ◽  
Quadruplex Dna ◽  
Dna Base ◽  
Dna Base Pairs ◽  
G Quadruplex ◽  
Dynamics Simulations

scholarly journals Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

2021 ◽  
Author(s):  
Michael P. O'Hagan ◽  
Susanta Haldar ◽  
Juan C. Morales ◽  
Adrian J. Mulholland ◽  
M. Carmen Galan
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Solution Phase ◽  
Enhanced Sampling ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dynamics Simulations

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.

scholarly journals Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Samuel Bowerman ◽  
Jeff Wereszczynski ◽  
Karolin Luger
Keyword(s):  
Molecular Dynamics ◽  
Analytical Ultracentrifugation ◽  
Base Pairs ◽  
Solution Structures ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Out Of Plane ◽  
Crystal Contacts ◽  
Chromatin Packing ◽  
Dynamics Simulations

Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form ‘nucleosome-like’ complexes that continuously wind between 60 and 500 base pairs of DNA (‘archaeasomes’), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

2020 ◽  
Vol 22 (41) ◽  
pp. 23754-23765
Author(s):  
Karan Deep Sharma ◽  
Preetleen Kathuria ◽  
Stacey D. Wetmore ◽  
Purshotam Sharma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Modified Dna ◽  
Dna Base Pairs

A comprehesive computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one or two Watson–Crick hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s).

scholarly journals Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways

2020 ◽  
Author(s):  
Samuel Bowerman ◽  
Jeff Wereszczynski ◽  
Karolin Luger
Keyword(s):  
Molecular Dynamics ◽  
Analytical Ultracentrifugation ◽  
Base Pairs ◽  
Solution Structures ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Out Of Plane ◽  
Crystal Contacts ◽  
Chromatin Packing ◽  
Dynamics Simulations

AbstractEukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ∼147 DNA base pairs into nucleosomes, archaeal histones form “nucleosome-like” complexes that continuously wind between 60 - 500 base pairs of DNA (“archaeasomes”), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90° out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.

Sign in / Sign up

Export Citation Format

Share Document