Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Saikia, Nabanita; Taha, Mohamed; Pandey, Ravindra

doi:10.1039/d0cp05759b

Cited by 5 publications

(1 citation statement)

References 45 publications

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“…The water molecules were modeled using the TIP3P potential [68], with constraints applied to bond lengths and angles using the SETTLE algorithm. Based on earlier studies, simulations with such time scales were deemed sufficient for the system to equilibrate and obtain stabilized structures [56,69,70]. The long-range Coulomb interactions were computed using the particle-mesh Ewald full electrostatics while the vdW interactions between the atoms were calculated using a cutoff of 12 Å [71].…”

Section: Simulationmentioning

confidence: 99%

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

Saikia

2021

Nanotechnology

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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.

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Section: Simulationmentioning

confidence: 99%

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

Saikia

2021

Nanotechnology

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A comparative simulation study of piezoelectric properties in zigzag and armchair boron nitride nanotubes: by discovering a pioneering protocol

Adel,

Keyhanvar,

Zahmatkeshan

et al. 2024

J Math Chem

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Atomistic simulation of biological molecules interacting with nanomaterials

Saikia¹,

Pandey²

2023

Modeling, Characterization, and Production of Nanomaterials

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Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Abstract: The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

Cited by 5 publications

References 45 publications

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

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

A comparative simulation study of piezoelectric properties in zigzag and armchair boron nitride nanotubes: by discovering a pioneering protocol

Atomistic simulation of biological molecules interacting with nanomaterials

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Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Abstract: The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

Cited by 5 publications

References 45 publications

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

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

A comparative simulation study of piezoelectric properties in zigzag and armchair boron nitride nanotubes: by discovering a pioneering protocol

Atomistic simulation of biological molecules interacting with nanomaterials

Contact Info

Product

Resources

About

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

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