Self-assembly of single-stranded RNA on carbon nanotube: polyadenylic acid to form a duplex structure

Single-walled carbon nanotubes-based RNA protection and extraction improves RT-qPCR sensitivity for SARS-CoV-2 detection

The false-negative result of nucleic acid testing is an important cause of continued spread of COVID-19, while SARS-CoV-2 RNA degradation during transportation and nucleic acid extraction can lead to false-negative results. Here, we investigated that single-walled carbon nanotubes (SCNTs) could protect RNA from degradation for at least 4 days at room temperature. By constructing magnetism-functionalized SCNTs (MSCNTs), we developed a method that enabled protection and simple extraction of SARS-CoV-2 RNA, and the RNA-bound MSCNTs can be directly used for reverse transcription polymerase chain reaction (RT-qPCR) detection. The experimental results showed that 1 μg of MSCNTs adsorbed up to 24 ng of RNA. Notably, the MSCNTs-based method for extracting SARS-CoV-2 RNA from simulated nasopharyngeal swabs and saliva samples with mean recovery rates of 103% and 106% improved the sensitivity of RT-qPCR detection by 8-32 fold in comparison to current common methods. This improvement was largely attributable to the protection of RNA, enabling increased RNA load for downstream assays.

Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)₁₀ oligonucleotide on graphene is compared with the graphene adsorption of (rC)₁₀. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.

Inorganic Nanoparticles as Drug Delivery Systems and Their Potential Role in the Treatment of Chronic Myelogenous Leukaemia

Chronic myeloid leukemia is a myeloproliferative disease where cells of myeloid linage display a t(9;22) chromosomal translocation leading to the formation of the BCR/ABL fusion gene and the continuous activation of tyrosine kinases. This malignancy has a peak incidence at 45 to 85 years, accounting for 15% of all leukemias in adults. Controlling the activity of tyrosine kinase became the main strategy in chronic myeloid leukemia treatment, with imatinib being placed at the forefront of current treatment protocols. New approaches in future anticancer therapy are emerging with nanomedicine being gradually implemented. Setting through a thorough survey of published literature, this review discusses the use of inorganic nanoparticles in chronic myeloid leukemia therapy. After an introduction on the basics of chronic myeloid leukemia, a description of the current treatment modalities of chronic myeloid leukemia and drug-resistance mechanisms is presented. This is followed by a general view on the applications of nanostrategies in medicine and then a detailed breakdown of inorganic nanocarriers and their uses in chronic myeloid leukemia treatment.

Heightened Integration of POM-based Metal-Organic Frameworks with Functionalized Single-Walled Carbon Nanotubes for Superior Energy Storage

To increase the conductivity of polyoxometalate-based metal-organic frameworks (POMOFs) and promote their applications in the field of energy storage, herein, a simple approach was employed to improve their overall electrochemical performances by introducing a functionalized single-walled carbon nanotubes (SWNT-COOH). A new POMOF compound, [Cu₁₈ (trz)₁₂ Cl₃ (H₂ O)₂ ][PW₁₂ O₄₀ ] (CuPW), was successfully synthesized, then the size-matched functionalized SWNT-COOH was introduced to fabricate CuPW/SWNT-COOH composite (PMNT-COOH) by employing a simple sonication-driven periodic functionalization strategy. When the PMNT-COOH nanocomposite was used as the anode material for Lithium-ion batteries (LIBs), PMNT-COOH(3) (CuPWNC:SWNT-COOH=3:1) showed superior behavior of energy storage, a high reversible capacity of 885 mA h g^-1 up to a cycle life of 170 cycles. The electrochemical results indicate that the uniform packing of SWNT-COOH provided a favored contact between the electrolyte and the electrode, resulting in enhanced specific capacity during lithium insertion/extraction process. This fabrication of PMNT-COOH nanocomposite opens new avenues for the design and synthesis of new generation electrode materials for LIBs.

Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.

Liquid interfaces with pH-switchable nanoparticle arrays

Stimuli-responsive 2D nanoscale systems offer intriguing opportunities for creating switchable interfaces. At liquid interfaces, such systems can provide control over interfacial energies, surface structure, and rheological and transport characteristics, which is relevant, for example, to bio- and chemical reactors, microfluidic devices, and soft robotics. Here, we explore the formation of a pH-responsive membrane formed from gold nanoparticles grafted with DNA (DNA-NPs) at a liquid-vapor interface. A DNA-NP 2D hexagonal lattice can be reversibly switched by pH modulation between an expanded state of non-connected nanoparticles at neutral pH and a contracted state of linked nanoparticles at acidic pH due to the AH+-H+A base pairing between A-motifs. Our in situ surface X-ray scattering studies reveal that the reversible lattice contraction can be tuned by the length of pH-activated linkers, with up to ∼71% change in surface area.

Small molecule induced poly(A) single strand to self-structure conformational switching: evidence for the prominent role of H-bonding interactions

All messenger RNAs (mRNAs) have a polyadenylic acid tail that is added during post transcriptional RNA processing. Investigation of the structure-function and interactions of polyadenylic acid is an important area to target for cancer and related diseases. Jatrorrhizine and coptisine are two important isoquinoline alkaloids that are structurally very similar, differing only in the substituents on the isoquinoline chromophore. Here we demonstrate that these alkaloids differentially induce a self-structure in single stranded poly(A) using absorbance, thermal melting and differential scanning calorimetry experiments. Jatrorrhizine was found to be more effective than coptisine in binding to poly(A) from spectroscopy and calorimetry data. Molecular modeling results suggested the involvement of more H-bonds in the complexation of the former with poly(A). It appears that the presence of substituents on the alkaloid that can form H-bonding interactions with the adenine nucleotides may play a critical role in the binding and structural rearrangement of poly(A) into the self-structure. The atomic force microscopy data directly visualized the poly(A) self-structured network. We propose a plausible mechanism of the small molecule induced self-structure formation in poly(A). The results presented here may help in the design of effective poly(A) targeted molecules for therapeutic use.

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA₇, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA₇ forms well-ordered crystals, whereas rA₆ forms fragile crystalline-like structures, and rA₅, rA₈ and rA₁₁ fail to crystallize. Our findings support studies from ∼50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA₇ and begins to plateau with rA₈; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP−rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.

Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure

The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.

Application of Carbon Nanotubes in Nanomedicine

Carbon Nanotubes (CNTs) have become a technological field with great potential since they can be applied in almost every aspect of modern life. One of the sectors where CNTs are expected to play a vital role is the field of medical science. This chapter focuses on the latest developments in applications of CNTs for nanomedicine. A brief history of CNTs and a general introduction to the field are presented. Then, the preparation of CNTs that makes them ideal for use in medical applications is highlighted. Examples of common applications, including cell penetration, drug delivery, and gene delivery and imaging are given. Finally, the toxicity of carbon nanotubes is discussed.

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

Self-assembly of polydeoxyadenylic acid studied at the single-molecule level

The investigation on the self-assembly of polydeoxyadenylic acid (poly(dA)) is highly important to fully understand its biological function and for its application in the field of nanotechnology. Using the fluorescence resonance energy transfer (FRET) technique, we report investigations for the self-assembly of adenine oligomers induced by pH and coralyne binding at the single-molecule level and in the bulk phase. Results presented here show that A-motif 1 (Alexa488-5'-(dA)(20)-3'-Cy5-5'-(dA)(20)-3'-Alexa488) forms the wire-type duplex at acidic pH, whereas the same conformation of A-motif 2 (Alexa488-5'-(dA)(20)-3'-Cy5-3'-(dA)(20)-5'-Alexa488) is induced by coralyne binding at neutral pH. These results indicate that poly(dA) at acidic pH forms a right-handed helical duplex with parallel-mannered chains, whereas the coralyne-poly(dA) binding induces a stable antiparallel duplex. Furthermore, we found that the antiparallel duplex of poly(dA) formed by coralyne binding has a rather extended and less twisted structure as compared to the parallel duplex of poly(dA) formed at acidic pH. On the other hand, from dilution experiments, we found that the parallel duplex formed at acidic pH is converted to "S-form", which has the single-stranded structure with short intramolecular double-stranded regions formed by intramolecular A:A base pairing, while the A-motif-coralyne assembly is dissociated into single strands below a certain concentration. The formation of S-form with a short intramolecular double-stranded region formed at acidic pH and very low concentration is confirmed by the quantitative analysis of FCS curve to measure the hydrodynamic radius of a molecule.

Stabilization of unstable CGC+ triplex DNA by single-walled carbon nanotubes under physiological conditions

Triplex formation is a promising strategy for realizing artificially controlling of gene expression, reversible assembly of nanomaterials and DNA nanomachine and single-walled nanotubes (SWNTs) have been widely used as gene and drug delivery vector or as 'building blocks' in nano-/microelectronic devices. CGC(+) triplex is not as stable as TAT triplex. The poor stability of CGC(+) triplex limits its use in vitro and in vivo. There is no ligand that has been reported to selectively stabilize CGC(+) triplets rather than TAT. Here, we report that SWNTs can cause d(CT) • d(AG) duplex disproportionation into triplex d(C(+)T) • d(AG) • d(CT) and single-strand d(AG) under physiological conditions. SWNTs can reduce the stringency of conditions for CGC(+) triplex formation studied by UV-vis, CD, DNA melting, light scattering and atomic force microscopy. Further studies indicate that electrostatic interaction is crucial for d(CT) • d(AG) repartition into triplex d(C(+)T) • d(AG) • d(CT). Our findings may facilitate utilization of SWNTs-DNA complex in artificially controlling of gene expression, nanomaterials assembly and biosensing.

Triplex inducer-directed self-assembly of single-walled carbon nanotubes: a triplex DNA-based approach for controlled manipulation of nanostructures

As a promising strategy for artificially control of gene expression, reversible assembly of nanomaterials and DNA nanomachine, DNA triplex formation has received much attention. Carbon nanotubes as gene and drug delivery vector or as ‘building blocks’ in nano/microelectronic devices have been successfully explored. Therefore, studies on triplex DNA-based carbon nanotube hybrid materials are important for development of smart nanomaterials and for gene therapy. In this report, a small molecule directed single-walled carbon nanotubes (SWNTs) self-assembly assay has been developed by disproportionation of SWNTs–dT₂₂·dA₂₂ duplex into triplex dT₂₂·dA₂₂·dT₂₂ and dA₂₂ by a triplex formation inducer, coralyne. This has been studied by circular dichroism, light scattering (LS) spectroscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), electrophoretic mobility shift assay and supported by using DNA random sequence. In contrast, SWNTs do not aggregate under the same experimental conditions when the small molecules used can not induce dT₂₂·dA₂₂·dT₂₂ triplex formation. Therefore, this novel small molecule-directed SWNTs self-assembly assay has also been used for screening of triplex inducers in our studies.

DNA and carbon nanotubes as medicine

The identification of disease-related genes and their complete nucleotide sequence through the human genome project provides us with a remarkable opportunity to combat a large number of diseases with designed genes as medicine. However, gene therapy relies on the efficient and nontoxic transport of therapeutic genetic medicine through the cell membranes, and this process is very inefficient. Carbon nanotubes, due to their large surface areas, unique surface properties, and needle-like shape, can deliver a large amount of therapeutic agents, including DNA and siRNAs, to the target disease sites. In addition, due to their unparalleled optical and electrical properties, carbon nanotubes can deliver DNA/siRNA not only into cells, which include difficult transfecting primary-immune cells and bacteria, they can also lead to controlled release of DNA/siRNA for targeted gene therapy. Furthermore, due to their wire shaped structure with a diameter matching with that of DNA/siRNA and their remarkable flexibility, carbon nanotubes can impact on the conformational structure and the transient conformational change of DNA/RNA, which can further enhance the therapeutic effects of DNA/siRNA. Synergistic combination of the multiple capabilities of carbon nanotubes to deliver DNA/siRNAs will lead to the development of powerful multifunctional nanomedicine to treat cancer or other difficult diseases. In this review, we summarized the current studies in using CNT as unique vehicles in the field of gene therapy.

P-glycoprotein antibody functionalized carbon nanotube overcomes the multidrug resistance of human leukemia cells

Multidrug resistance (MDR), which is related to cancer chemotherapy, tumor stem cells, and tumor metastasis, is a huge obstacle for the effective cancer therapy. One of the underlying mechanisms of MDR is the increased efflux of anticancer drugs by overexpressed P-glycoprotein (P-gp) of multidrug resistant cells. In this work, the antibody of P-gp (anti-P-gp) functionalized water-soluble single-walled carbon nanotubes (Ap-SWNTs) loaded with doxorubicin (Dox), Dox/Ap-SWNTs, were synthesized for challenging the MDR of K562 human leukemia cells. The resulting Ap-SWNTs could not only specifically recognize the multidrug resistant human leukemia cells (K562R), but also demonstrate the effective loading and controllable release performance for Dox toward the target K562R cells by exposing to near-infrared radiation (NIR). The recognition capability of Ap-SWNTs toward the K562R cells was confirmed by flow cytometry (FCM) and confocal laser scanning microscopy (CLSM). The binding affinity of Ap-SWNTs toward drug-resistant K562R cells was ca. 23-fold higher than that toward drug-sensitive K562S cells. Additionally, CLSM indicated that Ap-SWNTs could specifically localize on the cell membrane of K562R cells and the fluorescence of Dox in K562R cells could be significantly enhanced after the employment of Ap-SWNTs as carrier. Moreover, the composite of Dox and Ap-SWNTs (Dox/Ap-SWNTs) expressed 2.4-fold higher cytotoxicity and showed the significant cell proliferation suppression toward K562R leukemia cells (p < 0.05) as compared with free Dox which is popularly employed in clinic trials. These results suggest that the Ap-SWNTs are the promising drug delivery vehicle for overcoming the MDR induced by the overexpression of P-gp on cell membrane. Ap-SWNTs loaded with drug molecules could be used to suppress the proliferation of multidrug resistant cells, destroy the tumor stem cells, and inhibit the metastasis of tumor.

Knocking-down cyclin A(2) by siRNA suppresses apoptosis and switches differentiation pathways in K562 cells upon administration with doxorubicin

Cyclin A₂ is critical for the initiation of DNA replication, transcription and cell cycle regulation. Cumulative evidences indicate that the deregulation of cyclin A₂ is tightly linked to the chromosomal instability, neoplastic transformation and tumor proliferation. Here we report that treatment of chronic myelogenous leukaemia K562 cells with doxorubicin results in an accumulation of cyclin A₂ and follows by induction of apoptotic cell death. To investigate the potential preclinical relevance, K562 cells were transiently transfected with the siRNA targeting cyclin A₂ by functionalized single wall carbon nanotubes. Knocking down the expression of cyclin A₂ in K562 cells suppressed doxorubicin-induced growth arrest and cell apoptosis. Upon administration with doxorubicin, K562 cells with reduced cyclin A₂ showed a significant decrease in erythroid differentiation, and a small fraction of cells were differentiated along megakaryocytic and monocyte-macrophage pathways. The results demonstrate the pro-apoptotic role of cyclin A₂ and suggest that cyclin A₂ is a key regulator of cell differentiation. To the best of our knowledge, this is the first report that knocking down expression of one gene switches differentiation pathways of human myeloid leukemia K562 cells.