Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane

DNA fragment translocation through the lipid membrane assisted by carbon nanotube

DNA delivery through cell membrane is a fundamental step for efficiency gene therapy. As a potential DNA carrier, carbon nanotubes (CNTs) have been extensively studied due to its unique properties. However, the mechanism of DNA translocation with CNTs through cell membrane is still not well understood. In this study, the DNA translocation process through POPC (1-palmitoyl-2-oleoylphosphatidylcholine) membrane with the assistance of CNTs was explored by molecular dynamics (MD) simulation. Our simulation results demonstrated that the CNTs could insert steadily into the POPC membrane, and DNA molecules tends to insert into the inner space of CNTs. With the assistance of CNTs, the free energy of nucleotides passing through the POPC membrane decreases. Moreover, the free energy of nucleotides (DA (deoxyadenosine), DT (deoxythymidine), DC (deoxycytidine), and DG (deoxyguanosine)) passing through POPC membrane follows the order: DA (deoxyadenosine) > DG (deoxyguanosine) > DC (deoxycytidine) > DT (deoxythymidine). These results may promote the design and application of CNT-based gene delivery system.

Chiral Brønsted Acid-Catalyzed Enantioselective α-Amidoalkylation Reactions: A Joint Experimental and Predictive Study

Enamides with a free NH group have been evaluated as nucleophiles in chiral Brønsted acid-catalyzed enantioselective α-amidoalkylation reactions of bicyclic hydroxylactams for the generation of quaternary stereocenters. A quantitative structure-reactivity relationship (QSRR) method has been developed to find a useful tool to rationalize the enantioselectivity in this and related processes and to orient the catalyst choice. This correlative perturbation theory (PT)-QSRR approach has been used to predict the effect of the structure of the substrate, nucleophile, and catalyst, as well as the experimental conditions, on the enantioselectivity. In this way, trends to improve the experimental results could be found without engaging in a long-term empirical investigation.

Biomimetic Solid-State Nanochannels: From Fundamental Research to Practical Applications

In recent years, solid-state smart nanopores/nanochannels for intelligent control of the transportation of ions and molecules as organisms have been extensively studied, because they hold great potential applications in molecular sieves, nanofluidics, energy conversion, and biosensors. To keep up with the fast development of this field, it is necessary to summarize the construction, characterization, and application of biomimetic smart nanopores/nanochannels. These can be classified into four sections: the fabrication of solid-state nanopores/nanochannels, the functionalization methods and materials, the mechanism explanation about the ion rectification, and the practical applications. A brief conclusion and outlook for the biomimetic nanochannels is provided, highlighting those that could be developed and integrated into devices for use in tackling current and the future problems including resources, energy, environment, and health.

Nanomechanics of Protein Unfolding Outside a Generic Nanopore

Protein folding and unfolding have been the subject of active research for decades. Most of previous studies in protein unfolding were focused on temperature, chemical, and/or force (such as in atomic force microscopy (AFM)) induced denaturations. Recent studies on the functional roles of proteasomes (such as ClpXP) revealed a different unfolding process in cell, during which a target protein is mechanically unfolded and pulled into a confined, pore-like geometry for degradation. While the proteasome nanomachine has been extensively studied, the mechanism for unfolding proteins with the proteasome pore is still poorly understood. Here, we investigate the mechanical unfolding process of ubiquitin with (or really outside) a generic nanopore, and compare such process with that in the AFM pulling experiment. Unexpectedly, the required force for protein unfolding through a pore can be much smaller than that by the AFM. Simulation results also unveiled different nanomechanics, tearing fracture vs shearing friction, in these two distinct types of mechanical unfoldings.

Silver(I) ions modulate the stability of DNA duplexes containing cytosine, methylcytosine and hydroxymethylcytosine at different salt concentrations

Silver(I) ions can stabilize cytosine-cytosine, cytosine (C)-methylcytosine (5mC) and cytosine-hydroxymethylcytosine (5hmC) mismatched-base pairs. While cytosine modifications regulate DNA stability to regulate cellular functions, silver ions can modulate the stability of C-C, C-5mC and C-5hmC containing DNA duplexes in a salt concentration dependent manner.