Single-walled carbon nanotubes binding to human telomeric i-motif DNA: significant acceleration of S1 nuclease cleavage rate

The roles of DNA methylation on pH dependent i-motif (iM) formation in rice

I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences. The formation of iMs is sensitive to pH conditions and DNA methylation, although the extent of which is still unknown in both humans and plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation and sequencing (iM-IP-seq) along with bisulfite sequencing using CK (original genomic DNA without methylation-related treatments) and hypermethylated or demethylated DNA at both pH 5.5 and 7.0 in rice, establishing a link between pH, DNA methylation and iM formation on a genome-wide scale. We found that iMs folded at pH 7.0 displayed higher methylation levels than those formed at pH 5.5. DNA demethylation and hypermethylation differently influenced iM formation at pH 7.0 and 5.5. Importantly, CG hypo-DMRs (differentially methylated regions) and CHH (H = A, C and T) hyper-DMRs alone or coordinated with CG/CHG hyper-DMRs may play determinant roles in the regulation of pH dependent iM formation. Thus, our study shows that the nature of DNA sequences alone or combined with their methylation status plays critical roles in determining pH-dependent formation of iMs. It therefore deepens the understanding of the pH and methylation dependent modulation of iM formation, which has important biological implications and practical applications.

Protonation of Cytosine-Rich Telomeric DNA Fragments by Carboxylated Carbon Nanotubes: Insights from Computational Studies

In this work, we studied, using computational methods, the protonation reactions of telomeric DNA fragments being due to interaction with carboxylated carbon nanotubes. The applied computational methodology is divided into two stages. (i) Using classical molecular dynamics, we generated states in which carboxyl groups are brought to the vicinity of nitrogen atoms within the cytosine rings belonging to the DNA duplex. (ii) From these states, we selected two systems for systematic quantum chemical studies aimed at the analysis of proton-transfer reactions between the carboxyl groups and nitrogen atoms within the cytosine rings. Results of molecular dynamics calculations led to the conclusion that sidewall-functionalized carbon nanotubes deliver carboxyl groups slightly more effectively than the on-tip-functionalized ones. The latter can provide carboxyl groups in various arrangements and more diverse quality of approach of carboxyl groups to the cytosines; however, the differences between various arrangements of carboxyl groups are still not big. It was generally observed that narrow nanotubes can access the cytosine pocket easier than wider ones. Quantum chemical calculations led however to the conclusion that a direct proton transfer from the carboxyl group to the nitrogen atom within the cytosine ring is impossible under normal conditions. Precisely, we detected either very high activation barrier for the proton-transfer reaction or instability of the reaction product, i.e., its spontaneous decomposition toward reaction substrates.

β-Lactoglobulin amyloid fibril-templated gold nanoclusters for cellular multicolor fluorescence imaging and colorimetric blood glucose assay

β-Lactoglobulin amyloid fibril (BLGF)-capped gold nanoclusters (Au NCs) with red, green and blue emissions were fabricated via pH-dependent reduction strategy. The BLGF-Au NCs exhibited 3.2 times enhancement of fluorescence (λex = 500 nm, λem = 684 nm), a significant 42 nm red shift, a 11.57% quantum yield and a 1.4 μs decay time compared with native β-lactoglobulin (BLG)-stabilized Au NCs. Meanwhile, the multicolor Au NCs were employed for cell imaging via incubation with A549 cells for 14 h. According to the Michaelis-Menten equation, the kinetic parameters of the BLGF-Au NCs showed a lower Km value (66 μmol L-1) for 3,3,5,5-tetramethylbenzidine (TMB) and a higher vmax (3.74 × 10-8 M s-1) for H2O2, which are comparable with other artificial nanoenzymes and natural peroxidases. Based on the highly intrinsic peroxidase-like activity of the BLGF-Au NCs, a colorimetric method was developed for glucose determination with a detection limit of 1.5 μmol L-1 by determining the variation of the absorption at 652 nm, ranging from 5 to 100 μmol L-1. In addition, the glucose assay method also revealed a 101.02 to 104.16% recovery in a real human serum sample.

Syntheses and Evaluation of New Bisacridine Derivatives for Dual Binding of G-Quadruplex and i-Motif in Regulating Oncogene c-myc Expression

The c-myc oncogene is an important regulator for cell growth and differentiation, and its aberrant overexpression is closely related to the occurrence and development of various cancers. Thus, the suppression of c-myc transcription and expression has been investigated for cancer treatment. In this study, various new bisacridine derivatives were synthesized and evaluated for their binding with c-myc promoter G-quadruplex and i-motif. We found that a9 could bind to and stabilize both G-quadruplex and i-motif, resulting in the downregulation of c-myc gene transcription. a9 could inhibit cancer cell proliferation and induce SiHa cell apoptosis and cycle arrest. a9 exhibited tumor growth inhibition activity in a SiHa xenograft tumor model, which might be related to its binding with c-myc promoter G-quadruplex and i-motif. Our results suggested that a9 as a dual G-quadruplex/i-motif binder could be effective in both oncogene replication and transcription and become a promising lead compound for further development with improved potency and selectivity.

Carbon Nanotubes and Short Cytosine-Rich Telomeric DNA Oligomeres as Platforms for Controlled Release of Doxorubicin-A Molecular Dynamics Study

This work deals with molecular dynamics analysis of properties of systems composed of carbon nanotubes and short telomeric DNA strands able to fold into i-motif structures at slightly acidic pH conditions. The studies are focused on possible application of such constructs as pH-controlled drug delivery and release systems. We study two different approaches. The first assumes that folding/unfolding property of these DNA strands might realize a gate closing/opening mechanism with carbon nanotube as a container for drug molecules. The second approach assumes that these DNA strands can modulate the drug intercalating property as a function of pH. As a model drug molecule we used doxorubicin. We found that the first approach is impossible to realize because doxorubicin is not effectively locked in the nanotube interior by DNA oligonuceotides. The second approach is more promising though direct drug release was not observed in unbiased molecular dynamics simulations. However, by applying detailed analysis of pair interaction energies, mobilities and potential of mean force we can show that doxorubicin can be released when the DNA strands fold into i-motifs. Carbon nanotube in that latter case acts mainly as a carrier for active phase which is composed of DNA fragments able to fold into noncanonical tetraplexes (i-motif).

A label-free protamine-assisted colorimetric sensor for highly sensitive detection of S1 nuclease activity

A label-free, simple and rapid colorimetric method for the sensitive detection of S1 nuclease activity based on protamine-assisted aggregation of gold nanoparticles.

Interaction of Human Telomeric i-Motif DNA with Single-Walled Carbon Nanotubes: Insights from Molecular Dynamics Simulations

This work deals with molecular dynamics simulations of human telomeric i-motif DNA interacting with functionalized single-walled carbon nanotubes. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e., unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. These i-motifs interact with two kinds of carbon nanotubes differing mainly in chirality (diameter), i.e., (10, 0) and (20, 0). Additionally, these nanotubes were on-tip functionalized by amino groups or by guanine- containing residues. We found that protonated i-motif adsorbs strongly, although not specifically, on the nanotube surfaces with its 3' and 5' ends directed toward the surface and that adsorption does not affect the i-motif shape and hydrogen bonds existing between C:C⁺ pairs. The functional groups on the nanotube tips have minimal effect either on position of i-motif or on its binding strength. Unprotonated i-motif, in turn, deteriorates significantly during interaction with the nanotubes and its binding strength is rather high as well. We found that (10, 0) nanotubes destroy the i-motif shape faster than (20, 0). Moreover the i-motif either tries to wrap the nanotube or migrates to its tip and becomes immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3' end into the nanotube interior. No hydrogen bonds exist within the unprotonated i-motif prior to and after adsorption on the nanotube. Thus, carbon nanotubes do not improve the stability of unprotonated i-motif due to simple adsorption or just physical interactions. We hypothesize that the stabilizing effect of carbon nanotubes reported in the literature is due to proton transfer from the functional group in the nanotube to cytosines and subsequent formation of C:C⁺ pairs.

POMOF/SWNT Nanocomposites with Prominent Peroxidase-Mimicking Activity for l-Cysteine "On-Off Switch" Colorimetric Biosensing

In order to explore novel colorimetric biosensors with high sensibility and selectivity, two new Keggin polyoxometalates (POMs)-based Cu-trz (1,2,4-triazole) metal-organic frameworks (MOFs) with suitable specific surface areas and multiple active sites were favorably fabricated; then single-walled carbon nanotubes (SWNTs) were merged with new POMOFs to construct POMOF/SWNT nanocomposites. Herein, POMOF/SWNT nanocomposites as peroxidase mimics were explored for the first time, and the peroxidase-mimicking activity of the prepared POMOF/SWNT nanocomposites is heavily dependent on the mass ratio of POMOFs and SWNTs, in which the maximum activity is achieved at the mass ratio of 2.5:1 (named PMNT-2). More importantly, PMNT-2 exhibits the lowest limit of detection (0.103 μM) among all reported materials to date and the assumable selectivity toward l-cysteine (l-Cys) detection. With these findings, a convenient, sensitive, and effective "on-off switch" colorimetric platform for l-Cys detection has been successfully developed, providing a promising prospect in the biosensors and clinical diagnosis fields.

Metal–oxygen clusters as peroxidase mimics for their multifarious applications in colorimetric sensors

Metal–oxygen cluster (Fe₂₈) was certified to own inherent peroxidase-like performance, which displayed multi-functional applications in H₂O₂, glucose and dopamine detection.

Visual detection of H2O2 and melamine based on PW11MO39n− (M = Cu2+, Co2+, Mn2+, Fe3+) and PW9M3O34n− (M = Cu2+, Co2+, Mn2+, Fe3+)

The peroxidase-like activity of transition metal-substituted polyoxometalates (PW₁₁MO₃₉ⁿ⁻, PW₉M₃O₃₄ⁿ⁻, abbreviated as PW₁₁M and PW₉M₃, where M = Cu²⁺, Co²⁺, Mn²⁺, Fe³⁺) in the oxidation of 3,3′,5,5′-tetramethylbenzidine by H₂O₂ was valuated.

Carbon Nanomaterials and DNA: from Molecular Recognition to Applications

DNA is polymorphic. Increasing evidence has indicated that many biologically important processes are related to DNA's conformational transition and assembly states. In particular, noncanonical DNA structures, such as the right-handed A-form, the left-handed Z-form, the triplex, the G-quadruplex, the i-motif, and so forth, have been specific targets for the diagnosis and therapy of human diseases. Meanwhile, they have been widely used in the construction of smart DNA nanomaterials and nanoarchitectures. As rising stars in materials science, the family of carbon nanomaterials (CNMs), including two-dimensional graphene, one-dimensional carbon nanotubes (CNTs), and zero-dimensional graphene or carbon quantum dots (GQDs or CQDs), interact with DNA and are able to regulate the conformational transitions of DNA. The interaction of DNA with CNMs not only opens new opportunities for specific molecular recognition, but it also expands the promising applications of CNMs from materials science to biotechnology and biomedicine. In this Account, we focus on our contributions to the field of interactions between CNMs and DNA in which we have explored their promising applications in nanodevices, sensing, materials synthesis, and biomedicine. For one-dimensional CNTs, two-dimensional graphene, and zero-dimensional GQDs and CQDs, the basic principles, binding modes, and applications of the interactions between CNMs and DNA are reviewed. We aim to give prominence to the important status of CNMs in the field of molecular recognition for DNA. First, we summarized our discovery of the interactions between single-walled carbon nanotubes (SWNTs) with duplex, triplex, and human telomeric i-motif DNA and their interesting applications. For example, SWNTs are the first chemical agents that can selectively stabilize human telomeric i-motif DNA and induce its formation under physiological conditions. On the basis of this principle, two types of nanodevices were designed. One was used for highly sensitive detection of ppm levels of SWNTs in cells, and the other monitored i-motif DNA formation. Further studies indicated that SWNTs could inhibit telomerase activity in living cells and cause telomere dysfunction, providing new insight into the biological effects of SWNTs. Then, some applications that are based on the interactions between graphene and DNA are also summarized. Combined with other nanomaterials, such as metal and upconversion nanoparticles, several hybrid nanomaterials were successfully constructed, and a series of DNA logic gates were successfully developed. Afterwards, the newcomer of the carbon nanomaterials family, carbon quantum dots (CQDs), were found to be capable of modulating right-handed B-form DNA to left-handed Z-form DNA. These were further used to design FRET logic gates that were based on the CQD-derived DNA conformational transition. Taking into account the remaining challenges and promising aspects, CNM-based DNA nanotechnology and its biomedical applications will attract more attention and produce new breakthroughs in the near future.

i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid

Thermodynamic analyses and molecular dynamics calculations demonstrated that i-motifs in a hydrated ionic liquid of choline dihydrogen phosphate (choline dhp) were more stable than G-quadruplexes due to choline ion binding to loop regions in the i-motifs. Interestingly, the i-motifs formed even at physiological pH in the choline dhp-containing solution.

G-quadruplex DNA/protoporphyrin IX-based synergistic platform for targeted photodynamic cancer therapy

Photodynamic therapy (PDT) is an emerging technique to induce cancer cell death. However, the tumor specificity, cellular uptake and biodistribution of many photosensitizers urgently need to be improved. In this regard, we show here that the integrated nanoassemblies based on G-quadruplex DNAs (GQDs)/protoporphyrin IX (PPIX) can serve as a synergistic platform for targeted high-performance PDT. In the nanoassemblies, GQDs function as carriers of sensitiser PPIX and confers the system cancer cell targeting ability. After nucleolin-mediated efficient binding and cellular uptake of GQDs/PPIX assemblies, the strong red fluorescence of GQDs/PPIX complex provides a powerful tool for biological imaging. Moreover, the reactive oxygen species (ROS) generated by GQDs/PPIX under light illumination can effectively kill cancer cells. The present approach is simply composed by DNA and photosensitizers, thereby avoiding any complicated and time-consuming covalent modification or chemical labeling procedure.

A dual-amplification fluorescent sensing platform for ultrasensitive assay of nuclease and ATP based on rolling circle replication and exonuclease III-aided recycling

A ultrasensitive, easy operated and robust assay of S1 nuclease in real samples and ATP has been successfully achieved with the dual-amplification strategy based on rolling circle replication and Exo III-aided recycling.

Structure, stability and behaviour of nucleic acids in ionic liquids

Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are 'green' solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A-T base pairs are more stable than G-C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson-Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices.

i-Motif DNA: structure, stability and targeting with ligands

i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure.

Artificial evolution of graphene oxide chemzyme with enantioselectivity and near-infrared photothermal effect for cascade biocatalysis reactions

It is highly desirable and challenging when the chemzyme can be not only simply duplicating and imitating the properties of natural enzymes, but also introducing additional new features for practical applications. Herein, we report a zinc-finger-protein like α-helical chiral metallo-supramolecular complex ([Fe2L3](4+)) functionalized graphene oxide (GO-COOH) as a peroxidase mimic. This artificial enzyme integrates the characteristics of both chiral metallo-supramolecular complex and GO-COOH, and shows excellent catalytic activity. More intriguingly, the novel chemzyme turn out to have enantioselectivity and near-infrared photothermal effect. To the best of our knowledge, this is the first example that the chemzyme has such new features. Based on these properties, we have demonstrated three examples for the applications of our designed enzyme: 1) Intracellular H2O2 detection in PC12 cells against Alzheimer's disease; 2) Discrimination between the chiral drug, Levodopa (L-dopa), the gold standard for treating Parkinson's disease and its enantiomer, D-dopa. This is important because L-dopa is the most effective drug at present used to combat Parkinson's disease while D-dopa is inactive and can even cause side effects, thus for drug efficacy it must be free of D-dopa in the formulation; 3) Remote control of enzyme cascade biocatalysis reactions using high transparent, bio-friendly near-infrared (NIR) light. NIR allows remote activation with relatively high spatial and temporal precision. Our work will provide new insights into design and construction of novel chemzyme with more advanced features beyond intrinsic enzyme property.

Studying the influence of the pyrene intercalator TINA on the stability of DNA i-motifs

Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-motif structures was studied by using UV melting temperature measurements and circular dichroism spectra at different pH values under noncrowding and crowding conditions (20% poly(ethylene glycol)). When TINA ((R)-3-((4-(1-pyrenylethynyl)benzyl)oxy) propane-1,2-diol) is inserted, the oligonucleotides could form an i-motif at a higher pH than observed for the corresponding wildtype oligonucleotide.

Fundamental aspects of the nucleic acid i-motif structures

The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.

Peroxidase-like activity of Fe3O4@carbon nanoparticles enhances ascorbic acid-induced oxidative stress and selective damage to PC-3 prostate cancer cells

Ascorbic acid (AA) is capable of inhibiting cancer cell growth by perturbing the normal redox state of cells and causing toxic effects through the generation of abundant reactive-oxygen species (ROS). However, the clinical utility of AA at a tolerable dosage is plagued by a relatively low in vivo efficacy. This study describes the development of a peroxidase-like composite nanoparticle for use in an AA-mediated therapeutic strategy. On the basis of a high-throughput, one-pot solvothermal approach, Fe3O4@C nanoparticles (NPs) were synthesized and then modified with folic acid (FA) on the surface. Particular focus is concentrated on the assessment of peroxidase-like catalytic activity by a chromogenic reaction in the presence of H2O2. The carbon shell of Fe3O4@C NPs contains partially graphitized carbon and thus facilitates electron transfer in the catalytic decomposition of H2O2, leading to the production of highly reactive hydroxyl radicals. Along with magnetic responsiveness and receptor-binding specificity, the intrinsic peroxidase-like catalytic activity of Fe3O4@C-FA NPs pronouncedly promotes AA-induced oxidative stress in cancer cells and optimizes the ROS-mediated antineoplastic efficacy of exogenous AA. In vitro experiments using human prostate cancer PC-3 cells demonstrate that Fe3O4@C-FA NPs serve as a peroxidase mimic to create hydroxyl radicals from endogenous H2O2 that is yielded in response to exogenous AA via an oxidative stress process. The usage of a dual agent leads to the enhanced cytotoxicity of PC-3 cells, and, because of the synergistic effect of NPs, the administrated dosage of AA is reduced markedly. However, because normal cells (HEK 293T cells) appear to have a higher capacity to cope with additionally generated ROS than cancer cells, the NP-AA combination shows little damage in this case, proving that selective killing of cancer cells could be achieved owing to preferential accumulation of ROS in cancer cells. A possible ROS-mediated mechanism is discussed to elucidate the pharmaceutical profile of the NP-AA agent. In general, this foundational study reveals that the peroxidase-like nanomaterials are applicable for modulating oxidative stress for the selective treatment of cancer cells by generating a high level of endogenous ROS.

Nuclease cleavage-assisted target recycling for signal amplification of free-label impedimetric aptasensors

A simple, novel, label-free impedimetric aptasensor with signal amplification is developed for ultrasensitive detection of small molecules on a carbon nanotubes-based sensing platform by combining target-induced release of the aptamers and nuclease cleavage-assisted target recycling.

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.

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.

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.

Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: more water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration. However, crowding can not induce i-motif formation at physiological pH. Intriguingly, single-walled carbon nanotubes (SWNTs) can drive i-motif formation under cell-mimic crowding conditions and cause more water to be released. To our knowledge, there is no report to show how SWNTs can influence DNA under cell-mimic crowding conditions. Our results indicate that SWNTs may have the potential to modulate the structure of human telomeric DNA in vivo, like DNA B-A transitions and B-Z changes on SWNTs in live cells, which demonstrates potential for drug design and cancer therapy.

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

All messenger-RNA (mRNA) molecules in eukaryotic cells have a polyadenylic acid [poly(rA)] tail at the 3'-end and human poly(rA) polymerase (PAP) has been considered as a tumor-specific target. A ligand that is capable of recognizing and binding to the poly(rA) tail of mRNA might interfere with the full processing of mRNA by PAP and can be a potential therapeutic agent. We report here for the first time that single-walled carbon nanotubes (SWNTs) can cause single-stranded poly(rA) to self-structure and form a duplex structure, which is studied by UV melting, atomic force microscopy, circular dichroism spectroscopy, and NMR spectrometry. SWNTs have shown potential applications that range from nanodevices, gene therapy, and drug delivery to membrane separations. Our studies may provide new insights into the application of SWNTs under physiological conditions, possibly being used as probes that target specific gene sequences.