Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide

Xu, Zhen; Lei, Xiaoling; Tu, Yusong; Tan, Zhi-Jie; Song, Bo; Fang, Haiping

doi:10.1002/chem.201701733

Cited by 63 publications

(41 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For both the double-stranded and single-stranded DNA molecules we used the Dickerson-Drew dodecamer [14] with the following sequence, 5'-CGCGAATTCGCG-3', which has been extensively used in similar MD studies [9][10][11]15]. The choice was motivated from an aim to advance the results of previous studies [9][10][11] with direct comparison to their findings. The double-stranded B-DNA structure was generated using the Nucleic Acid Builder (NAB), part of the AmberTools18 package [16], and converted into GROMACS [17] topology using the tools Leap and Parmed, components of AmberTools18.…”

Section: Generation Of the Dna Moleculesmentioning

confidence: 99%

“…tween DNA molecules and graphene only in the presence of Na + ions and indicated it verned by π-π stacking between the aromatic rings of the graphene layer and the exposed bas the oligonucleotides, hydrogen bonds and electrostatic interactions [9][10][11].…”

Section: Generation Of the Dna Moleculesmentioning

confidence: 99%

“…The resulting charge repulsion lowers the binding affinity of the dsDNA to the negatively charged oxygen atoms on the GO surface. Both experimental and computational studies have investigated the different aspects regarding the effect of using nucleic acids and different graphenic molecules [9][10][11][12][13]. Experimental studies showed that both Mg 2+ ions and functionalized derivatives of graphene, in particular an aminated polyethylene glycol-functionalized reduced graphene oxide (rGO-PEG-NH 2 ), markedly influenced detection of DNA hybridization [12,13].…”

Section: Introductionmentioning

confidence: 99%

“…Experimental studies showed that both Mg 2+ ions and functionalized derivatives of graphene, in particular an aminated polyethylene glycol-functionalized reduced graphene oxide (rGO-PEG-NH 2 ), markedly influenced detection of DNA hybridization [12,13]. Previous computational studies investigated the mechanism of adsorption between DNA molecules and graphene only in the presence of Na + ions and indicated it is governed by π-π stacking between the aromatic rings of the graphene layer and the exposed bases of the oligonucleotides, hydrogen bonds and electrostatic interactions [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

“…Molecular Dynamics (MD) simulations can provide sophisticated information regarding molecular interactions at a nano-perspective, currently unachievable by other means. Here, we aimed to advance the existing MD studies regarding the dynamic process of oligonucleotide adsorption on GO [9][10][11], for both the ssDNA and dsDNA molecules, that have yet to assess the influence of ions and further graphene derivatives in a more complex milieu due to the addition of ions. Thus, we provide a computational nano-perspective with the purpose of generating new insights to help explain and complement experimental observation.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

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

et al. 2020

View full text Add to dashboard Cite

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.

show abstract

Section: Generation Of the Dna Moleculesmentioning

confidence: 99%

Section: Generation Of the Dna Moleculesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

et al. 2020

View full text Add to dashboard Cite

show abstract

Surface Functionalization of Graphene‐Based Materials: Biological Behavior, Toxicology, and Safe‐By‐Design Aspects

et al. 2021

View full text Add to dashboard Cite

drug delivery, bioimaging probes, antibacterial agents, and tissue engineering. [2] The advantage of GBMs over other nanomaterials (NMs) in biomedical application is their high specific surface area which allows high density functionalization and drug loading on both sides of the planar structure. [3] The π-conjugated system offers high capacity for GBMs to interact with various organic compounds with aromatic structures through π-π stacking during fabrication of graphene composites or for immobilization of biomolecules such as nucleic acids, peptides, antibodies, or other therapeutic substances. [4] The same properties may also raise concerns regarding the potential risk that GBMs may cause to human health through binding of key signaling molecules for example. GBMs may interact with biomolecules, changing the structure of protein or DNA or induce oxidative damage, and so on. [5] Therefore, prior to the widespread use of GBMs, it is imperative to evaluate their potential risk to environmental and human health and to establish a proactive approach for the safe design of these materials.In a recent review article, Fadeel et al. comprehensively examined the literature on the effects of GBMs on human health and the environment and gave an overview of the state-of-the-art of safety assessment of GBMs, highlighting the importance of The increasing exploitation of graphene-based materials (GBMs) is driven by their unique properties and structures, which ignite the imagination of scientists and engineers. At the same time, the very properties that make them so useful for applications lead to growing concerns regarding their potential impacts on human health and the environment. Since GBMs are inert to reaction, various attempts of surface functionalization are made to make them reactive. Herein, surface functionalization of GBMs, including those intentionally designed for specific applications, as well as those unintentionally acquired (e.g., protein corona formation) from the environment and biota, are reviewed through the lenses of nanotoxicity and design of safe materials (safe-by-design). Uptake and toxicity of functionalized GBMs and the underlying mechanisms are discussed and linked with the surface functionalization. Computational tools that can predict the interaction of GBMs behavior with their toxicity are discussed. A concise framing of current knowledge and key features of GBMs to be controlled for safe and sustainable applications are provided for the community.

show abstract

Poly‐Cytosine Deoxyribonucleic Acid Strongly Anchoring on Graphene Oxide Due to Flexible Backbone Phosphate Interactions

Lopez

Zhao

Huang

et al. 2020

Adv Materials Inter

View full text Add to dashboard Cite

Finding DNA sequences that can strongly adsorb on various nanomaterials is critically important for preparing bioconjugates, biosensors, and drug delivery. Poly‐cytosine (poly‐C) DNA is found to have stronger affinity compared to other DNA sequences of the same length on various nanomaterials ranging from graphene oxide (GO), MoS2, to many metal oxides and phosphates. In this work, the authors aim to understand the reason for such high affinity by varying pH and DNA sequence along with conducting molecular dynamics (MD) simulations using GO as a model surface. Poly‐C DNA adsorbs stronger only at neutral or basic pH, while its adsorption at acidic pH is weaker than other DNA homopolymers. The DNA sequence is further varied by inserting thymine into poly‐C DNA and by varying thymine/cytosine ratios, all confirming that a folded i‐motif structure is detrimental for adsorption. Using MD simulations, the authors reveal that the stronger adsorption of poly‐C DNA at neutral pH is due to more contributions from the phosphate backbone hydrogen bonding with GO surface relating to the flexibility of the DNA. Poly‐C DNA also uses its phosphate backbone to interact with metal oxide and phosphate nanoparticles, and this phosphate backbone interaction can unify all these observations.

show abstract

Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide

Cited by 63 publications

References 54 publications

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

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

Surface Functionalization of Graphene‐Based Materials: Biological Behavior, Toxicology, and Safe‐By‐Design Aspects

Poly‐Cytosine Deoxyribonucleic Acid Strongly Anchoring on Graphene Oxide Due to Flexible Backbone Phosphate Interactions

Contact Info

Product

Resources

About