Defect-Induced Double-Stranded DNA Unwinding on Graphene

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene

The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.

Recent advances in biological applications of nanomaterials through defect engineering

In recent years, defect engineering sprung up in the artificial nanomaterials (NMs) has attracted significant attention, since the physical and chemical properties of NMs could be largely optimized based on the rational control of different defect types and densities. Defective NMs equipped with the improved electric and catalytic ability, would be widely utilized as the photoelectric device and catalysts to alleviate the growing demands of industrial production and environmental treatments. In particular, considering that the features of targeting, adsorptive, loading and optical could be adjusted by the introduction of defects, numerous defective NMs are encouraged to be applied in the biological fields including bacterial inactivation, cancer therapy and so on. And this review is devoted to summarize the recent biological applications of NMs with abundant defects. Moreover, the opportunity of these defective NMs released into the surrounding environment continue to increase, the direct and indirect contact with biological molecules and organisms would be inevitable. Due to its high reactivity and adsorption triggered by defects, NMs tend to exhibit overestimate biological behaviors and effects on organisms. Thus, the sections regarding toxicological effects of NMs with abundant defects are also carried out to supplement the safety assessments of NMs and guide further applications in the industrial production and living.