Binding patterns and dynamics of double-stranded DNA on the phosphorene surface

Nanoscale ◽  
2020 ◽  
Vol 12 (17) ◽  
pp. 9430-9439 ◽  
Author(s):  
Baoyu Li ◽  
Xuejie Xie ◽  
Guangxin Duan ◽  
Serena H. Chen ◽  
Xuan-Yu Meng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Base Pairs ◽  
Upright Orientation ◽  
Double Stranded Dna ◽  
Dynamics Simulations

Molecular dynamics simulations and electrophoresis experiments show that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations.

scholarly journals Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations

2021 ◽  
Vol 49 (7) ◽  
pp. 3735-3747
Author(s):  
Rodrigo Galindo-Murillo ◽  
Thomas E Cheatham
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ethidium Bromide ◽  
Base Pair ◽  
Force Fields ◽  
Ligand Complex ◽  
Base Pairs ◽  
Duplex System ◽  
Double Stranded Dna ◽  
Dynamics Simulations

Abstract Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)2 also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.

scholarly journals Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

2019 ◽  
Vol 10 (43) ◽  
pp. 10010-10017 ◽  
Author(s):  
C. Lorena Manzanares-Palenzuela ◽  
Amir M. Pourrahimi ◽  
J. Gonzalez-Julian ◽  
Zdenek Sofer ◽  
Martin Pykal ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Double Stranded Dna ◽  
Fluorescent Biosensing ◽  
Dynamics Simulations ◽  
Differential Affinity

MXenes show differential affinity towards single- and double-stranded DNA, with unique kinetics and potential for fluorescent biosensing.

scholarly journals Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA

2015 ◽  
Vol 44 (5) ◽  
pp. 2085-2092 ◽  
Author(s):  
Spencer Carson ◽  
James Wilson ◽  
Aleksei Aksimentiev ◽  
Peter R. Weigele ◽  
Meni Wanunu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Properties ◽  
Double Stranded Dna ◽  
Physico Chemical ◽  
Translocation Experiments ◽  
Dynamics Simulations ◽  
Regulatory Dna ◽  
The Impact ◽  
Insight Into

Abstract Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.

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