Controlled interconversion of macrocyclic atropisomers via defined intermediates.

Macrocyclic conformations play a crucial role in regulating their properties. Our understanding of the determinants to control macrocyclic conformation interconversion is still in its infancy. Here we present a macrocycle, octamethyl cyclo[4](1,3-(4,6)-dimethylbenzene)[4]((4,6-benzene)(1,3-dicarboxylate) (OC-4), that can exist at 298 K as two stable atropisomers with C2v and C4v symmetry denoted as C2v-OC-4 and C4v-OC-4, respectively. Heating induces the efficient stepwise conversion of C2v- to C4v-OC-4 via a Cs-symmetric intermediate (Cs-OC-4). It differs from the typical transition state-mediated processes of simple C-C single bond rotations. Hydrolysis and further esterification with a countercation dependence promote the generation of C2v- and Cs-OC-4 from C4v-OC-4. In contrast to C2v-OC-4, C4v-OC-4 can bind linear guests to form pseudo-rotaxans, or bind C60 or C70 efficiently. The present study highlights the differences in recognition behavior that can result from conformational interconversion, as well as providing insights into the basic parameters that govern coupled molecular rotations.

Thermally-induced atropisomerism promotes metal-organic cage construction.

Molecular folding regulation with environmental stimuli is critical in living and artificial molecular machine systems. Herein, we described a macrocycle, cyclo[4] (1,3-(4,6-dimethyl)benzene)[4](1,3-(4,6-dimethyl)benzene)(4-pyridine). Under 298 K, it has three stable stiff atropisomers with names as 1 (Cs symmetry), 2 (Cs symmetry), and 3 (C4v symmetry). At 393 K, 1 can reversibly transform into 2, but at 473 K, it can irrevocably transform into 3. At 338 K, 3 and (PhCN)2PdCl2 complex to produce the metal-organic cage 4. Only at 338 K does the combination of 1 or 2 and (PhCN)2PdCl2 create a gel-like structure. Heating both gels to 473 K transforms them into 4. In addition to offering a thermally accelerated method for modifying self-assembled systems using macrocyclic building blocks, this study also has the potential to develop the nanoscale transformation material with a thermal response.

From Biomass to Functional Crystalline Diamond Nanothread: Pressure-Induced Polymerization of 2,5-Furandicarboxylic Acid.

2,5-Furandicarboxylic acid (FDCA) is one of the top-12 value-added chemicals from sugar. Besides the wide application in chemical industry, here we found that solid FDCA polymerized to form an atomic-scale ordered sp3-carbon nanothread (CNTh) upon compression. With the help of perfectly aligned π-π stacked molecules and strong intermolecular hydrogen bonds, crystalline poly-FDCA CNTh with uniform syn-configuration was obtained above 11 GPa, with the crystal structure determined by Rietveld refinement of the X-ray diffraction (XRD). The in situ XRD and theoretical simulation results show that the FDCA experienced continuous [4 + 2] Diels-Alder reactions along the stacking direction at the threshold C···C distance of ∼2.8 Å. Benefiting from the abundant carbonyl groups, the poly-FDCA shows a high specific capacity of 375 mAh g-1 as an anode material of a lithium battery with excellent Coulombic efficiency and rate performance. This is the first time a three-dimensional crystalline CNTh is obtained, and we demonstrated it is the hydrogen bonds that lead to the formation of the crystalline material with a unique configuration. It also provides a new method to move biomass compounds toward advanced functional carbon materials.

A hybrid aggregate FRET probe from the mixed assembly of cyanine dyes for highly specific monitoring of mitochondria autophagy.

Mitochondria autophagy, also known as mitophagy, is a process in which mitochondria are wrapped by autophagosomes and fused with lysosomes for degradation. This process is essential for mitochondrial quality control. Here, we developed a hybrid aggregate FRET probe through mixed assembly of two cyanine dyes FMOTY and AMTC. In live cells, FMOTY and AMTC exist independently in lysosomes and mitochondria and will not produce interfering FRET background signals. The FRET signal is only generated when mitochondria is transported to lysosomes during mitophagy. This allows the hybridized aggregate to be used as a highly specific probe for monitoring mitophagy.

A DNA small molecular probe with increasing K+ concentration promoted selectivity.

DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis. Most related reports were performed under specific salinity. Herein, 4-imino-3-(pyridin-2-yl)-4H-quinolizine-1-carbonitrile (IPQC) was generated via a facile procedure with high yield (85%). It is found that IPQC could act as a universal probe for most tested ssDNA, dsDNA and G4 DNA in low [K+] concentration (less than 20 mM). However, IPQC showed highly selective G4 DNA binding via UV-vis and fluorescence response in increasing [K+] (e.g., 150 mM) conditions. The ion atmosphere effects are instructive for DNA probe exploration. This provides guidance for the design, selection and optimization of the probes for target DNA sensing.

Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.

Monitoring autophagy can provide valuable insights into understanding human pathological mechanisms, developing novel drugs, and exploring autophagy control approaches. Here, we proposed a new strategy to specifically monitor autophagy by lighting up the G-quadruplex structures entering autolysosomes. Based on this strategy, we designed a small-molecule fluorescent probe for autophagy imaging. This work not only opens up a new way for developing autophagy probes, but also provides an effective tool for autophagy research.

Evaluation of the selectivity of G-quadruplex ligands in living cells with a small molecule fluorescent probe.

G-quadruplex has been an emerging target for drug design due to its physiologically important roles in oncology. A number of quadruplex-interactive ligands have been developed by synthetic and medicinal chemists over the past decades. However, the great challenge still remains that the method for detecting the specific targeting of these ligands to the G-quadruplex structures in cells is still lacking. Herein, a detection system for directly identifying the specific targeting of a ligand to DNA G-quadruplexes in cells was constructed by using a small-molecular fluorescent probe (IMT) as a fluorescent indicator. Four typical ligands have been successfully evaluated, demonstrating the promising application of this detection system in the screening and evaluation of quadruplex-specific therapeutic agents.

Spontaneous formation and reversible transformation between achiral J- and chiral H-aggregates of cyanine dye MTC.

Chirality at a supramolecular level is currently attracting great attention attributed to rapid developments in supramolecular chemistry. Herein, we report a new type of chiral self-assembly based on the cyanine dye MTC. The chiral H-aggregates of MTC could form spontaneously from achiral J-aggregates, and could return back to achiral J-aggregates in high concentration on increasing the solution temperature.

Insulin-like growth factor type I selectively binds to G-quadruplex structures.

BACKGROUND: G-quadruplex has been viewed as a promising therapeutic target in oncology due to its potentially important roles in physiological and pathological processes. Emerging evidence suggests that the biological functions of G-quadruplexes are closely related to the binding of some proteins. Insulin-like growth factor type I (IGF-1), as a significant modulator of cell growth and development, may serve as a quadruplex-binding protein. METHODS: The binding affinity and selectivity of IGF-1 to different DNA motifs in solution were measured by using fluorescence spectroscopy, Surface Plasmon Resonance (SPR), and force-induced remnant magnetization (FIRM). The effects of IGF-1 on the formation and stability of G-quadruplex structures were evaluated by circular dichroism (CD) and melting fluorescence resonance energy transfer (FRET) spectroscopy. The influence of quadruplex-specific ligands on the binding of G-quadruplexes with IGF-1 was determined by FIRM. RESULTS: IGF-1 shows a binding specificity for G-quadruplex structures, especially the G-quadruplex structure with a parallel topology. The quadruplex-specific ligands TMPyP4 and PDS (Pyridostatin) can inhibit the interaction between G-quadruplexes and proteins. CONCLUSIONS: IGF-1 is demonstrated to selectively bind with G-quadruplex structures. The use of quadruplex-interactive ligands could modulate the binding of IGF-1 to G-quadruplexes. GENERAL SIGNIFICANCE: This study provides us with a new perspective to understand the possible physiological relationship between IGF-1 and G-quadruplexes and also conveys a strategy to regulate the interaction between G-quadruplex DNA and proteins.

Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe.

G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.

Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure.

G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.

Direct visualization of nucleolar G-quadruplexes in live cells by using a fluorescent light-up probe.

BACKGROUND: Direct detection of G-quadruplexes in human cells has become an important issue due to the vital role of G-quadruplex related to biological functions. Despite several probes have been developed for detection of the G-quadruplexes in cytoplasm or whole cells, the probe being used to monitor the nucleolar G-quadruplexes is still lacking. METHODS: Formation of the nucleolar G-quadruplex structures was confirmed by using circular dichroism (CD) spectroscopy. The binding affinity and selectivity of Thioflavin T (ThT) towards various DNA/RNA motifs in solution and gel system were measured by using fluorescence spectroscopy and polyacrylamide gel electrophoresis (PAGE), respectively. G-quadruplex imaging in live cells was directly captured by using confocal laser scanning microscopy (CLSM). RESULTS: Formation of the rDNA and rRNA G-quadruplex structures is demonstrated in vitro. ThT is found to show much higher affinity and selectivity towards these G-quadruplex structures versus other nucleic acid motifs either in solution or in gel system. The nucleolar G-quadruplexes in living cells are visualized by using ThT as a fluorescent probe. G-quadruplex-ligand treatments in live cells lead to sharp decrease of ThT signal. CONCLUSIONS: The natural existence of the G-quadruplexes structure in the nucleoli of living cells is directly visualized by using ThT as an indicator. GENERAL SIGNIFICANCE: The research provides substantive evidence for formation of the rRNA G-quadruplex structures, and also offers an effective probe for direct visualization of the nucleolar G-quadruplexes in living cells.

Serum Metabolomics of Burkitt Lymphoma Mouse Models.

Burkitt lymphoma (BL) is a rare and highly aggressive type of non-Hodgkin lymphoma. The mortality rate of BL patients is very high due to the rapid growth rate and frequent systemic spread of the disease. A better understanding of the pathogenesis, more sensitive diagnostic tools and effective treatment methods for BL are essential. Metabolomics, an important aspect of systems biology, allows the comprehensive analysis of global, dynamic and endogenous biological metabolites based on their nuclear magnetic resonance (NMR) and mass spectrometry (MS). It has already been used to investigate the pathogenesis and discover new biomarkers for disease diagnosis and prognosis. In this study, we analyzed differences of serum metabolites in BL mice and normal mice by NMR-based metabolomics. We found that metabolites associated with energy metabolism, amino acid metabolism, fatty acid metabolism and choline phospholipid metabolism were altered in BL mice. The diagnostic potential of the metabolite differences was investigated in this study. Glutamate, glycerol and choline had a high diagnostic accuracy; in contrast, isoleucine, leucine, pyruvate, lysine, α-ketoglutarate, betaine, glycine, creatine, serine, lactate, tyrosine, phenylalanine, histidine and formate enabled the accurate differentiation of BL mice from normal mice. The discovery of abnormal metabolism and relevant differential metabolites may provide useful clues for developing novel, noninvasive approaches for the diagnosis and prognosis of BL based on these potential biomarkers.

Reversible regulation of the supramolecular chirality of a cyanine dye by using the G-quadruplex structure as a template.

Multiple cycle regulation of the supramolecular chirality of a cyanine dye has been successfully achieved by using DNA G-quadruplexes as templates, which is easily controllable by repeated addition of Ag(+) and cysteine (Cys). This work provides an easy and controllable strategy for the chiral regulation of supramolecules.

Thioflavin T as an efficient fluorescence sensor for selective recognition of RNA G-quadruplexes.

RNA G-quadruplexes (G4s) play important roles in translational regulation, mRNA processing events and gene expression. Therefore, a fluorescent probe that is capable of efficiently recognizing RNA G-quadruplex structures among other RNA forms is highly desirable. In this study, a water-soluble fluorogenic dye (i.e., Thioflavin T (ThT)) was employed to recognize RNA G-quadruplex structures using UV-Vis absorption spectra, fluorescence spectra and emission lifetime experiments. By stacking on the G-tetrad, the ThT probe exhibited highly specific recognition of RNA G-quadruplex structures with striking fluorescence enhancement compared with other RNA forms. The specific binding demonstrates that ThT is an efficient fluorescence sensor that can distinguish G4 and non-G4 RNA structures.

Colorimetric detection of sodium ion in serum based on the G-quadruplex conformation related DNAzyme activity.

There has been a big challenge in developing the Na(+) sensor that can be practically used in the physiological system with the interference of large amounts of K(+). In this research, a novel Na(+) sensor has been designed based on the G-quadruplex-conformation related DNAzyme activity. The sensor exhibits high selectivity and sensitivity with the detection limit of 0.6 µM, which enables the sensor to be practically used in determination of the Na(+) level in serum. The research not only provides a simple Na(+) sensor but also opens a new way for developing the detection technology of Na(+).

Stabilizing G-quadruplex DNA by methylazacalix[n]pyridine through shape-complementary interaction.

It is found that G-quadruplexes have important functions in biological systems, such as gene expression. Molecules which can stabilize the G-quadruplex structure may have potential application in regulating the expression of gene. A series of methylazacalix[n]pyridine (n=4, 6, 7, 8, 9) has been tested to stabilize the intermolecular human telomeric G-quadruplex (T12 and H12), intramolecular TBA, c-kit and bcl-2 G-quadruplex by CD denaturation experiments. The results showed that only methylazacalix[6]pyridine (MACP6) can stabilize the intermolecular G-quadruplex formed from the 12bp human telomere. Further studies evidenced that the shape-complementary binding mode was what contributed to the interaction between MACP6 and T12 G-quadruplex.

Directly lighting up RNA G-quadruplexes from test tubes to living human cells.

RNA G-quadruplexes (G4s) are one of the key components of the transcriptome that act as efficient post-transcriptional regulatory elements in living cells. To conduct further studies of the unique biological functions of RNA G4s, techniques need to be developed that can efficiently recognize RNA G4 structures under various conditions, in fixed cells and living cells, as well as in vitro. This paper presents the development of such a method, a new technique using a cyanine dye called CyT, which can detect both canonical and non-canonical RNA G4 structures from test tubes to living human cells. The ability of CyT to distinguish between G4 and nonG4 RNA offers a promising tool for future RNA G4-based biomarker discovery and potential diagnostic applications.

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch.

Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and (1)H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.

A colorimetric lead (II) ions sensor based on selective recognition of G-quadruplexes by a clip-like cyanine dye.

A probe for colorimetric detecting lead ion (Pb(2+)) has been designed by using a newly synthesized clip-like cyanine dye and G-quadruplex. The unique structure of the clip-like cyanine dye endowed the probe with a high selectivity towards Pb(2+). Significant changes in absorption spectra of the cyanine dye recognizing the Pb(2+)-induced conformational transition of G-quadruplexes made the probe show a high sensitivity towards Pb(2+) with a detection limit of 1nM. The excellent performance enabled the probe to be practically applied in measuring the Pb(2+) pollution in freshwater system.