Single-stranded DNA adsorption on chiral molecule coated Au surface: a molecular dynamics study

2010 ◽  
Vol 12 (17) ◽  
pp. 4431 ◽  
Author(s):  
Haiqing Liang ◽  
Zhenyu Li ◽  
Jinlong Yang
Keyword(s):  
Molecular Dynamics ◽  
Chiral Molecule ◽  
Dna Adsorption ◽  
Single Stranded Dna

A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double- and single-stranded DNA

Biopolymers ◽  
1983 ◽  
Vol 22 (12) ◽  
pp. 2703-2726 ◽  
Author(s):  
George C. Levy ◽  
David J. Craik ◽  
Anil Kumar ◽  
Robert E. London
Keyword(s):  
Molecular Dynamics ◽  
Critical Evaluation ◽  
Nmr Studies ◽  
Single Stranded Dna

scholarly journals Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach

2015 ◽  
Vol 459 ◽  
pp. 137-147 ◽  
Author(s):  
Soumadwip Ghosh ◽  
Himanshu Dixit ◽  
Rajarshi Chakrabarti
Keyword(s):  
Molecular Dynamics ◽  
Structural Collapse ◽  
Single Stranded Dna

Probing the adsorption behavior and free energy landscape of single–stranded DNA oligonucleotides on single–layer MoS2 with molecular dynamics

2021 ◽  
Author(s):  
Nabanita Saikia
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transition Metal Dichalcogenides ◽  
Single Layer ◽  
Adsorption Behavior ◽  
Aqueous Environment ◽  
Stacking Interactions ◽  
Single Stranded Dna ◽  
Π Stacking ◽  
Functional Dna

Abstract Interfacing single–stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self–assembled hybrids is still not well understood. Here, atomistic Molecular Dynamics (MD) simulation is employed to study the distinct adsorption behavior of ssDNA on a single–layer MoS2 in aqueous environment. The ssDNA sequences [T10, G10, A10, C10, U10, (GT)5, and (AC)5] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waals π–stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly–purines demonstrate two concurrently competing π–stacking interactions: nucleobase–nucleobase (intramolecular) and nucleobase–MoS2 (intermolecular). The poly–pyrimidines, on the other hand, reveal enhanced π–stacking interactions, thereby maximizing the number of contacts. The results provide new molecular–level understanding of ssDNA adsorption on the MoS2 surface and facilitate future studies in design of functional DNA/MoS2 structure–based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

scholarly journals Site-specific interrogation of an ionic chiral fragment during photolysis using an X-ray free-electron laser

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Markus Ilchen ◽  
Philipp Schmidt ◽  
Nikolay M. Novikovskiy ◽  
Gregor Hartmann ◽  
Patrick Rupprecht ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Electron ◽  
Chiral Recognition ◽  
Ultrashort Pulses ◽  
Chiral Molecule ◽  
Site Specific ◽  
X Ray ◽  
Polarization Control ◽  
Trigger Event ◽  
Linearly Polarized

AbstractShort-wavelength free-electron lasers with their ultrashort pulses at high intensities have originated new approaches for tracking molecular dynamics from the vista of specific sites. X-ray pump X-ray probe schemes even allow to address individual atomic constituents with a ‘trigger’-event that preludes the subsequent molecular dynamics while being able to selectively probe the evolving structure with a time-delayed second X-ray pulse. Here, we use a linearly polarized X-ray photon to trigger the photolysis of a prototypical chiral molecule, namely trifluoromethyloxirane (C3H3F3O), at the fluorine K-edge at around 700 eV. The created fluorine-containing fragments are then probed by a second, circularly polarized X-ray pulse of higher photon energy in order to investigate the chemically shifted inner-shell electrons of the ionic mother-fragment for their stereochemical sensitivity. We experimentally demonstrate and theoretically support how two-color X-ray pump X-ray probe experiments with polarization control enable XFELs as tools for chiral recognition.

Experimental Evidence of Single-Stranded DNA Adsorption on Multiwalled Carbon Nanotubes

2020 ◽  
Vol 124 (12) ◽  
pp. 2514-2525
Author(s):  
Franco Tardani ◽  
Stefano Sarti ◽  
Simona Sennato ◽  
Manuela Leo ◽  
Patrizia Filetici ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Experimental Evidence ◽  
Multiwalled Carbon Nanotubes ◽  
Multiwalled Carbon ◽  
Dna Adsorption ◽  
Single Stranded Dna

scholarly journals Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

Coatings ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 289 ◽  
Author(s):  
Sebastian Muraru ◽  
Cosmin G. Samoila ◽  
Emil I. Slusanschi ◽  
Jorge S. Burns ◽  
Mariana Ionita
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Nucleic Acid ◽  
Reduced Graphene Oxide ◽  
Electrostatic Interactions ◽  
Nucleic Acid Hybridization ◽  
Stacking Interactions ◽  
Dna Adsorption ◽  
Reduced Graphene ◽  
Dynamics Simulations

Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.

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