Applications of guanine quartets in nanotechnology and chemical biology

Guanosine Monophosphate Induced Solubilization of Folic Acid Leading to Hydrogel Formation for Targeted Delivery of Hydrophilic and Hydrophobic Drugs

Hydrogels are emerging as one of the most sought-after drug carriers due to their biocompatibility, high water content mimicking tissue-like environment, injectability, and stimuli responsiveness. Sustained drug release accompanied by targeted delivery to cancer cells can abate numerous adverse side effects of conventional chemotherapy. Folate receptors are overexpressed in various cancer cells, and their high binding affinity to folic acid (FA) makes folic acid-anchored drug carriers a specific targeting entity. Reports of folic acid-based hydrogels are still scarce, owing to their low solubility in water. In this study, we present a simple approach to generate a self-assembled supramolecular hydrogel by employing an amphiphilic low molecular weight gelator (LMWG), guanosine monophosphate (GMP), which noncovalently interacts and coassembles with FA. The hydrogel shows biocompatibility, thermoreversibility, self-healing, injectability, thixotropy, and self-adhesive properties. The hydrogel could encapsulate and release both hydrophilic (doxorubicin) and hydrophobic (curcumin) drugs in a sustained manner. In vitro studies on cancer cells showed that encapsulating the drugs within the hydrogel matrix resulted in enhanced uptake by the cancer cells, thereby increasing their therapeutic efficacy through upregulating tumor suppressor, apoptotic gene expression, and inhibiting cell proliferation markers. Thus, a straightforward fabrication procedure, cost-effectiveness, and treatment potency make the FA-GMP hydrogel a promising drug carrier for practical use in biomedical applications.

Cu(I)-Induced G-Quartets: Robust Supramolecular Polymers Exhibiting Heating-Induced Aqueous Phase Transitions Into Gel or Precipitate

Certain proteins and synthetic covalent polymers experience aqueous phase transitions, driving functional self-assembly. Herein, we unveil the ability of supramolecular polymers (SPs) formed by G4.Cu+ to undergo heating-induced unexpected aqueous phase transitions. For the first time, guided by Cu+, guanosine (G) formed a highly stable G-quartet (G4.Cu+)/G-quadruplex as a non-canonical DNA secondary structure with temperature tolerance, distinct from the well-known G4.K+. The G4.Cu+ self-assembled in water through π-π stacking, metallophilic and hydrophobic interactions, forming thermally robust SPs. This enhanced stability is attributed to the stronger coordination of Cu+ to four carbonyl oxygens of G-quartet and the presence of Cu+- - -Cu+ attractive metallophilic interactions in Cu+-induced G-quadruplex, exhibiting a significantly higher interaction energy than K+ as determined computationally. Remarkably, the aqueous SP solution exhibited heating-induced phase transitions-forming a hydrogel through dehydration-driven crosslinking of SPs below cloud temperature (Tcp) and a hydrophobic collapse-induced solid precipitate above Tcp, showcasing a lower critical solution temperature (LCST) behavior. Notably, this LCST behavior of G4.Cu+ SP originates from biomolecular functionality rather than commonly exploited thermo-responsive oligoethylene glycols with supramolecular assemblies. Furthermore, exploiting the redox reversibility of Cu+/Cu2+, we demonstrated control over the assembly and disassembly of G-quartets/G-quadruplex and gelation reversibly.

Applications of catalytic systems containing DNA nucleobases (adenine, cytosine, guanine, and thymine) in organic reactions

In recent years, nucleobases have attracted special attention because of their abundant resources and multiple interaction sites, which enable them to interact with and functionalize other molecules. This review focuses on the catalytic activities of each of the four main nucleobases found in deoxyribonucleic acid (DNA) in various organic reactions. Based on the studies, most of the nucleobases act as heterogeneous catalytic systems. The authors hope their assessment will help chemists and biochemists to propose new procedures for utilizing nucleobases as catalysts in various organic synthetic transformations. The review covers the corresponding literature published till the end of August 2023.

Role of Secondary Structure and Time-Dependent Binding on Disruption of Phthalocyanine Aggregates by Guanine-Rich Nucleic Acids

Phthalocyanines are versatile photodynamic therapy agents whose biological activity depends on their aggregation state, which is expected to be influenced by binding to biomolecules. Here, guanine-rich nucleic acid binding of a water-soluble cationic, regiopure C4h zinc phthalocyanine bearing four triethylene glycol methyl ether and four N-methyl-4-pyridinium substituents (1) is reported. In contrast to double-stranded DNA, guanine systems GpG, (GG)10, poly(G) and quadruplex DNA are shown to effectively disrupt phthalocyanine aggregates in buffered solution. This process is accompanied by evolution of the Q-band absorbance and enhanced emission. Increasing the sequence length from GpG to (GG)10 increases the binding and confirms the importance of multiple binding interactions. Enhanced binding in the presence of KCl suggests the importance of nucleobase hydrogen-bonded mosaics in phthalocyanine binding. Notably, the (GT)10 sequence is even more effective than quadruplex and pure guanine systems at disrupting the aggregates of 1. Significant time-dependent binding of 1 with poly(G) reveals biexponential binding over minutes and hours, which is linked to local conformations of poly(G) that accommodate monomers of 1 over time. The study highlights the ability of biomacromolecules to disrupt phthalocyanines aggregates over time, which is an important consideration when rationalizing photoactivity of photosensitizers in-vivo.

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space

Guanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies, as GQs are potential targets for anticancer drugs and other therapeutics. Although experimental and theoretical techniques have provided valuable insights into different stages of the GQ folding, the structural complexity of GQs poses significant challenges, and our understanding remains incomplete. This study introduces a novel computational protocol for folding an entire GQ from single-strand conformation to its native state. By combining two complementary enhanced sampling techniques, we were able to model folding pathways, encompassing a diverse range of intermediates. Although our investigation of the GQ free energy surface (FES) is focused solely on the folding of the all-anti parallel GQ topology, this protocol has the potential to be adapted for the folding of systems with more complex folding landscapes.

Small molecule-based regulation of gene expression in human astrocytes switching on and off the G-quadruplex control systems

A great deal of attention is being paid to strategies seeking to uncover the biology of the four-stranded nucleic acid structure G-quadruplex (G4) via their stabilization in cells with G4-specific ligands. The conventional definition of chemical biology implies that a complete assessment of G4 biology can only be achieved by implementing a complementary approach involving the destabilization of cellular G4s by ad hoc molecular effectors. We report here on an unprecedented comparison of the cellular consequences of G4 chemical stabilization by pyridostatin (PDS) and destabilization by phenylpyrrolocytosine (PhpC) at both transcriptome- and proteome-wide scales in patient-derived primary human astrocytes. Our results show that the stabilization of G4s by PDS triggers the dysregulation of many cellular circuitries, the most drastic effects originating in the downregulation of 354 transcripts and 158 proteins primarily involved in RNA transactions. In contrast, destabilization of G4s by PhpC modulates the G4 landscapes in a far more focused manner with upregulation of 295 proteins, mostly involved in RNA transactions as well, thus mirroring the effects of PDS. Our study is the first of its kind to report the extent of G4-associated cellular circuitries in human cells by systematically pitting the effect of G4 stabilization against destabilization in a direct and unbiased manner.

Protocol for cellular RNA G-quadruplex profiling using G4RP.v2

The isolation of G-quadruplexes (G4s) from human cells using specific molecular tools constitutes an invaluable step forward in uncovering the biology of these higher-order DNA and RNA structures. Here, we present an improved version of the G4-RNA precipitation (G4RP) protocol developed to identify RNA G4s from human cancer cells. We describe steps for cell treatment and lysis, chemoprecipitation of G4s using TASQ tools, go/no-go steps, and quantitative reverse-transcription PCR (RT-qPCR) quantification and analysis. For complete details on the use and execution of this protocol, please refer to Mitteaux et al.1.

DNA-Free Guanosine-Based Polymer Nanoreactors with Multienzyme Activities for Ferroptosis-Apoptosis Combined Antitumor Therapy

Concurrent induction of ferroptosis and apoptosis by enzyme catalysis represents a promising modality for cancer therapy. Inspired by the structures of DNA and G-quadruplex/hemin DNAzyme, a DNA-free guanosine-based polymer nanoreactor (HPG@hemin-GOx) is prepared as a ferroptosis-apoptosis inducer by a one-step assembly of phenylboronic acid-modified hyaluronic acid (HA-PBA), guanosine (G), hemin, and glucose oxidase (GOx). HPG@hemin-GOx shows GOx, peroxidase (POD)-like, catalase (CAT)-like, and glutathione peroxidase (GPX)-like activities. The GOx activity of the nanoreactor can increase intracellular hydrogen peroxide (H2O2) levels by oxidizing glucose in the presence of oxygen. The POD-like activity of HPG@hemin-GOx can then induce the generation of hydroxyl radicals utilizing generated H2O2. Meanwhile, the production of oxygen by the CAT-like activity can facilitate the oxygen-consuming glucose oxidation process of GOx, thus promoting the generation of intracellular reactive oxygen species (ROS). Moreover, the GPX-like activity of HPG@hemin-GOx can deplete intracellular glutathione and thus downregulate GPX4 expression. Consequently, HPG@hemin-GOx induces apoptosis and ferroptosis by ROS-mediated damages of nuclear DNA and mitochondria, and GPX4 depletion-induced lipid peroxidation accumulation, resulting in a strong anticancer effect as demonstrated both in vitro and in vivo. This work provides a method for the construction of polymeric nanoreactors with multienzyme activities for ferroptosis-apoptosis synergistic anticancer therapy.

Functionalized DNA secondary structures and nanostructures for specific protein modifications

The development of non-biological applications of DNA has not only resulted in delicately shaped DNA-based nano-objects with complex functions but also spawned their use for novel catalytic applications. From the multitude of applications of DNAzymes that operate on a relatively simple substrate, we have witnessed the emergence of multifunctional catalytically active DNA-based nanostructures for one of the most challenging tasks known to a chemist: the controlled and precise modification of a wild-type protein in its natural environment. By incorporating various elements associated with post-translational modification (PTM) writer enzymes into complex nanostructures, it is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger, clearly illustrating the promising future for this approach.

Exploring the Electronic Interactions of Adenine, Cytosine, and Guanine with Graphene: A DFT Study

This study has provided new insights into the interaction between graphene and DNA nucleobases (adenine, cytosine, and guanine). It compares how each nucleobase interacts with graphene, examining their selectivity and binding energy. The research also explores how these interactions impact the electronic properties of graphene, showing potential applications in graphene-based biosensors and DNA sequencing technologies. Additionally, the findings suggest potential uses in DNA sensing and the functionalization of graphene for various biomedical applications. This study employs density functional theory (DFT) methods, utilizing the B3LYP functional with the 6-311G basis set, to explore the electronic interactions between DNA nucleobases (adenine, cytosine, and guanine) with pure graphene (Gr). We investigate various properties, including adsorption energy, HOMO-LUMO energy levels, charge transfer mechanisms, dipole moments, energy gaps, and density of states (DOS). Our findings indicate that cytosine interacts most favorably with graphene through its oxygen site (Gr-Cyt-O), exhibiting the strongest adsorption. Additionally, adenine's interaction significantly enhances its electronegativity and chemical potential, particularly at the nitrogen position, while decreasing its electrophilicity. Guanine, characterized by the smallest energy gap, demonstrates the highest conductivity among the nucleobases. These results suggest that graphene possesses advantageous properties as an adsorbent for guanine, highlighting its potential applications in biosensor technology.

ROS/pH dual-responsive quercetin-loaded guanosine borate supramolecular hydrogel enema in dextran sulfate sodium-induced colitis in mice

Ulcerative colitis (UC) is an inflammatory bowel disease that predominantly impacts the colon, typically starting in the rectum. A significant characteristic of UC is its propensity to affect the distal colon, which is particularly beneficial for targeted treatments such as enemas. This localized approach ensures that the medication is delivered directly to the affected areas, resulting in minimal systemic absorption. In this research, we have formulated a novel stimuli-responsive quercetin-loaded guanosine borate supramolecular hydrogel (named GBQ hydrogel), designed to prolong the residence time of the drug and protect the ulcerated intestinal tissues. The GBQ hydrogel has exhibited excellent injectability, self-healing capabilities, and biocompatibility, rendering it an ideal candidate for enema administration. In vitro studies have highlighted its ROS/pH dual-responsive release profile, which mimics the microenvironment of intestinal inflammation. Furthermore, we assessed the efficacy of the GBQ hydrogel on dextran sulfate sodium (DSS)-induced colitis, a common animal model for UC. Our findings indicate that the GBQ hydrogel significantly reduces disease activity, mitigates oxidative stress, restores the intestinal mucosal barrier, and prevents colonic cell apoptosis. Collectively, this study underscores the therapeutic potential of the GBQ hydrogel in managing inflammatory bowel conditions and paves the way for a novel hydrogel enema-based treatment strategy for UC.

Hydration effect and molecular geometry conformation as critical factors affecting the longevity stability of G4-structure-based supramolecular hydrogels

Nucleoside-derived supramolecular hydrogels based on G4-structures have been extensively developed in the biomedical sector and recognized for superior excellent biocompatibility and biodegradability. However, limited longevity and stability present a significant challenge. Chemical modifications in the molecular structure have been shown to enhance the longevity stability of G4-structure-based supramolecular hydrogels, but the precise way in which the molecular structure impacts the stability of the G4-structures and consequently affects the properties of the hydrogel remains to be elucidated. This issue represents a notable challenge in the field, which restricts their further applications to some extent. In this study, single crystals of Gd, αGd and αGd* were cultivated and compared with G. Notably, before this study, the single crystal structures of all natural nucleosides, with the exception of Gd, had been determined. The investigation into the molecular structure and supramolecular self-assembly properties of four guanosine analogs at the atomic scale revealed that the formation of G-quartets is critical for their ability to form hydrogels. The stability of the sugar ring geometry conformation (an intrinsic factor) and the disorder and strength of the hydration effect (extrinsic factors) are vital for maintaining the stability of the G4-structures. The rapid cooling changes the molecular geometry conformation, and the organic solvent changes the hydration effect, which can improve the longevity stability of G4-structure-based supramolecular hydrogels instead of chemical modifications. Consequently, the lifespan of the hydrogels was extended from 2 h to over one week. This advancement is expected to offer significant insights for future research in designing and developing G4-structure-based supramolecular hydrogels.

Hindered intermolecular stacking of anti-parallel telomeric G-quadruplexes

Telomeric G-quadruplexes (G4s) are non-canonical DNA structures composed of TTAGGG repeats. They are extensively studied both as biomolecules key for genome stability and as promising building blocks and functional elements in synthetic biology and nanotechnology. This is why it is extremely important to understand how the interaction between G4s is affected by their topology. We used small-angle x-ray scattering to investigate the end-to-end stacking of antiparallel telomeric G-quadruplexes formed by the sequence AG3(T2AG3)3. To represent the experimental data, we developed a highly efficient coarse-grained fitting tool, which successfully described the samples as an equilibrium mixture of monomeric and dimeric G4 species. Our findings indicate that the antiparallel topology prevents the formation of long multimeric structures under self-crowding conditions, unlike the hybrid/parallel structures formed by the same DNA sequence. This result supports the idea that the stacking of monomeric G-quadruplexes is strongly affected by the presence of diagonal loops.

Ag+-Induced Supramolecular Polymers of Folic Acid: Reinforced by External Kosmotropic Anions Exhibiting Salting Out

Introducing kosmotropic salts enhances protein stability and reduces solubility by withdrawing water from the protein surface, leading to 'salting out', a phenomenon we have mimicked in supramolecular polymers (SPs). Under the guidance of Ag+, folic acid (FA) self-assembled in water through slipped-stacking and hydrophobic interactions into elongated, robust one-dimensional SPs, resulting in thermo-stable supergels. The SPs exhibited temperature and dilution tolerance, attributed to the stability of the FA-Ag+ complex and its hydrophobic stacking. Importantly, FA-Ag+ SP's stability has been augmented by the kosmotropic anions, such as SO42-, strengthening hydrophobic interactions in the SP, evident from the enhanced J-band, causing improvement of gel's mechanical property. Interestingly, higher kosmotrope concentrations caused a significant decrease in SP's solubility, leading to precipitation of the reinforced SPs─a 'salting out' effect. Conversely, chaotropes like ClO4- slightly destabilized hydrophobic stacking and promoted an extended conformation of individual SP chain with enhanced solubility, resembling a 'salting in' effect.

Discovery and development of tyrosine-click (Y-click) reaction for the site-selective labelling of proteins

With the versatile utility of bio-conjugated peptides and proteins in the fields of agriculture, food, cosmetics and pharmaceutical industry, the design of smart protocols to conjugate and modulate biomolecules becomes highly desirable. During this process, the most important consideration for biochemists is the retention of configurational integrity of the biomolecules. Moreover, this type of bioconjugation of peptide and protein becomes frivolous if the reaction is not performed with precise amino acid residues. Hence, chemo-selective, as well as site-selective reactions, that are biocompatible and possess an appropriate level of reactivity are necessary. Based on click chemistry, there are so many tyrosine (Y) conjugation strategies, such as sulfur-fluoride exchange (SuFEx), sulfur-triazole exchange (SuTEx), coupling with π-allyl palladium complexes, diazonium salts, diazodicarboxyamide-based reagents etc. Among these techniques, diazodicarboxyamide-based Y-conjugation, which is commonly known as the "tyrosine-click (Y-click) reaction", has met the expectations of synthetic and biochemists for the tyrosine-specific functionalization of biomolecules. Over the past one and a half decades, significant progress has been made in the classical organic synthesis approach, as well as its biochemical, photochemical, and electrochemical variants. Despite such progress and increasing importance, the Y-click reaction has not been reviewed to document variations in its methodology, applications, and broad utility. The present article aims to provide a summary of the approaches for the modulation of biomolecules at the hotspot of tyrosine residue by employing the Y-click reaction. The article also highlights its application for the mapping of proteins, imaging of living cells, and in the fields of analytical and medicinal chemistry.

Green synthesis of chitosan gum acacia based biodegradable polymeric nanoparticles to enhance curcumin's antioxidant property: an in vivo zebrafish (Danio rerio) study

Green-synthesis of biodegradable polymeric curcumin-nanoparticles using affordable biodegradable polymers to enhance curcumin's solubility and anti-oxidative potential. The curcumin-nanoparticle was prepared based on the ionic-interaction method without using any chemical surfactants, and the particle-size, zeta-potential, surface-morphology, entrapmentefficiency, and in-vitro drug release study were used to optimise the formulation. The antioxidant activity was investigated using H2DCFDA staining in the zebrafish (Danio rerio) model. The mean-diameter of blank nanoparticles was 178.2 nm (±4.69), and that of curcuminnanoparticles was about 227.7 nm (±10.4), with a PDI value of 0.312 (±0.023) and 0.360 (±0.02). The encapsulation-efficacy was found to be 34% (±1.8), with significantly reduced oxidative-stress and toxicity (∼5 times) in the zebrafish model compared to standard curcumin. The results suggested that the current way of encapsulating curcumin using affordable, biodegradable, natural polymers could be a better approach to enhancing curcumin's water solubility and bioactivity, which could further be translated into potential therapeutics.

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.

Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble

G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. Here, we achieved complete folding of a three-quartet parallel DNA G4 with (GGGA)3GGG sequence using all-atom explicit-solvent enhanced-sampling molecular dynamics (MD) simulations. The simulations suggested early formation of guanine stacks in the G-tracts, which behave as semi-rigid blocks in the folding process. The folding continues via the formation of a collapsed compact coil-like ensemble. Structuring of the G4 from the coil then proceeds via various cross-like, hairpin, slip-stranded and two-quartet ensembles and can bypass the G-triplex structure. Folding of the parallel G4 does not appear to involve any salient intermediates and is a multi-pathway process. We also carried out an extended set of simulations of parallel G-hairpins. While parallel G-hairpins are extremely unstable when isolated, they are more stable inside the coil structure. On the methodology side, we show that the AMBER DNA force field predicts the folded G4 to be less stable than the unfolded ensemble, uncovering substantial force-field issues. Overall, we provide unique atomistic insights into the folding landscape of parallel-stranded G4 but also reveal limitations of current state-of-the-art MD techniques.

Polyoxometalate-Guanosine Monophosphate Hydrogels with Haloperoxidase-like Activity for Antibacterial Performance

Haloperoxidases represent an important class of enzymes that nature adopts as a defense mechanism to combat the colonial buildup of microorganisms on surfaces, commonly known as biofouling. Subsequently, there has been tremendous focus on the development of artificial haloperoxidase mimics that can catalyze the oxidation of X- (halide ion) in the presence of H2O2 to form HOX. The natural intermediate HOX disrupts the bacterial quorum sensing, thus preventing biofilm formation. Herein, we report a simple method for the formation of supramolecular hydrogels through the self-assembly of Keggin-structured polyoxometalates, phosphotungstic acid, and silicotungstic acid with the small biomolecule guanosine monophosphate (GMP) in an aqueous medium. The polyoxometalate-GMP hydrogels that contained highly entangled nanofibers were mechanically robust and showed thixotropic properties. The gelation of the polyoxometalates with GMP not only rendered manifold enhancement in biocompatibility but also the fibril network in the hydrogel provided high water wettability and the polyoxometalates acted as an efficient haloperoxidase mimic to trigger oxidative iodination, as demonstrated by a haloperoxidase assay. The antifouling activity of the phosphotungstic acid-GMP hydrogel was demonstrated against both Gram-positive and Gram-negative bacteria, which showed enhanced antibacterial performance of the hydrogel as compared to the polyoxometalate alone. We envision that the polyoxometalate-GMP hydrogels may facilitate mechanically robust coatings in a simple pathway that can be useful for antifouling applications.

Self-oriented anisotropic structure of G-hydrogels as a delicate balance between attractive and repulsive forces

Guanine (G) hydrogels are very attractive materials made by the supramolecular organization of G-derivatives in water. In this paper, hydrogels composed of guanosine 5'-monophosphate (GMP) and guanosine (Gua), that make long, flexible and knotted G-quadruplexes, were investigated by small- and wide-angle X-ray scattering (SAXS and WAXS) to comprehend the origin of their unique orientational properties. The SAXS intensity, analysed at a fixed scattering vector modulus Q as a function of polar angle, allowed us to derive the Maier-Saupe orientation parameter m. The strong dependence of m on hydrogel composition and temperature demonstrated that the preferred orientation is controlled by the quadruplex surface charge and flexibility. Indeed, a possible correlation between the orientation parameter m and the quadruplex-to-quadruplex lateral interactions was explored. Results confirmed that the balance between attractive and repulsive interactions plays a main role in the orientational anisotropy: quadruplex clusters lose their orientational properties when attractive interactions decrease. The key role of the number of negative charges per unit length of the G-quadruplex filaments was confirmed by Atomic Force Microscopy (AFM) observations. Indeed, directionality histograms showed that in the presence of a large amount of Gua, G-quadruplexes follow preferential orientations other than those related to the strong interactions with the K+ pattern on the mica surface. The fact that lateral quadruplex-to-quadruplex interactions, even in the presence of external (opposing) forces, can tune the hydrogel alignment in a given preferred direction provides novel possibilities for scaffold/3D printing applications.

Programmable supramolecular chirality in non-equilibrium systems affording a multistate chiroptical switch

The dynamic regulation of supramolecular chirality in non-equilibrium systems can provide valuable insights into molecular self-assembly in living systems. Herein, we demonstrate the use of chemical fuels for regulating self-assembly pathway, which thereby controls the supramolecular chirality of assembly in non-equilibrium systems. Depending on the nature of different fuel acids, the system shows pathway-dependent non-equilibrium self-assembly, resulting in either dynamic self-assembly with transient supramolecular chirality or kinetically trapped self-assembly with inverse supramolecular chirality. More importantly, successive conducting of chemical-fueled process and thermal annealing process allows for the sequential programmability of the supramolecular chirality between four different chiral hydrogels, affording a new example of a multistate supramolecular chiroptical switch that can be recycled multiple times. The current finding sheds new light on the design of future supramolecular chiral materials, offering access to alternative self-assembly pathways and kinetically controlled non-equilibrium states.

Stacked or Folded? Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers

Self-assembled nanotubes exhibit impressive biological functions that have always inspired supramolecular scientists in their efforts to develop strategies to build such structures from small molecules through a bottom-up approach. One of these strategies employs molecules endowed with self-recognizing motifs at the edges, which can undergo either cyclization-stacking or folding-polymerization processes that lead to tubular architectures. Which of these self-assembly pathways is ultimately selected by these molecules is, however, often difficult to predict and even to evaluate experimentally. We show here a unique example of two structurally related molecules substituted with complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway taken is determined by chelate cooperativity, that is, by their propensity to assemble in specific cyclic structures through Watson-Crick pairing. Because of chelate cooperativities that differ in several orders of magnitude, these molecules exhibit distinct supramolecular scenarios prior to their polymerization that generate self-assembled nanotubes with different internal monomer arrangements, either stacked or coiled, which lead at the same time to opposite helicities and chiroptical properties.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including a very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism, i.e.,: (i) the more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened, (ii) the more parallel the direction of force was, GQ opening and cross-like GQs were more likely to occur, (iii) strand slippage mechanism was possible for GQs with an all-anti pattern in a strand, and (iv) slower pulling velocity led to richer structural dynamics with sampling of more intermediates and partial refolding events. We also identified that a GQ may eventually unfold after a force drop under forces smaller than those that the GQ withstood before the drop. Finally, we found out that different unfolding intermediates could have very similar chain end-to-end distances, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.

The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations

Chemical biology hinges on multivalent molecular tools that can specifically interrogate and/or manipulate cellular circuitries from the inside. The success of many of these approaches relies on molecular tools that make it possible to visualize biological targets in cells and then isolate them for identification purposes. To this end, click chemistry has become in just a few years a vital tool in offering practically convenient solutions to address highly complicated biological questions. We report here on two clickable molecular tools, the biomimetic G-quadruplex (G4) ligands MultiTASQ and ^azMultiTASQ, which benefit from the versatility of two types of bioorthogonal chemistry, CuAAC and SPAAC (the discovery of which was very recently awarded the Nobel Prize of chemistry). These two MultiTASQs are used here to both visualize G4s in and identify G4s from human cells. To this end, we developed click chemo-precipitation of G-quadruplexes (G4-click-CP) and in situ G4 click imaging protocols, which provide unique insights into G4 biology in a straightforward and reliable manner.

Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs

The search for G-quadruplex (G4)-forming sequences across the genome is motivated by their involvement in key cellular processes and their putative roles in dysregulations underlying human genetic diseases. Sequencing-based methods have been developed to assess the prevalence of DNA G4s genome wide, including G4-seq to detect G4s in purified DNA (in vitro) using the G4 stabilizer PDS, and G4 chromatin immunoprecipitation sequencing (G4 ChIP-seq) to detect G4s in in situ fixed chromatin (in vivo) using the G4-specific antibody BG4. We recently reported on G4-RNA precipitation and sequencing (G4RP-seq) to assess the in vivo prevalence of RNA G4 landscapes transcriptome wide using the small molecule BioTASQ. Here, we apply this technique for mapping DNA G4s in plants (rice) and compare the efficiency of this new technique, G4-DNA precipitation and sequencing, G4DP-seq, to that of BG4-DNA-IP-seq that we developed for mapping of DNA G4s in rice using BG4. By doing so, we compare the G4 capture ability of small-sized ligands (BioTASQ and BioCyTASQ) versus the antibody BG4.

Trehalose-Guanosine Glycopolymer Hydrogels Direct Adaptive Glia Responses in CNS Injury

Neural tissue damaged after central nervous system (CNS) injury does not naturally regenerate but is instead replaced by non-neural fibrotic scar tissue that serves no neurological function. Scar-free repair to create a more permissive environment for regeneration requires altering the natural injury responses of glial cells. In this work, glycopolymer-based supramolecular hydrogels are synthesized to direct adaptive glia repair after CNS injury. Combining poly(trehalose-co-guanosine) (pTreGuo) glycopolymers with free guanosine (fGuo) generates shear-thinning hydrogels through stabilized formation of long-range G-quadruplex secondary structures. Hydrogels with smooth or granular microstructures and mechanical properties spanning three orders of magnitude are produced through facile control of pTreGuo hydrogel composition. Injection of pTreGuo hydrogels into healthy mouse brains elicits minimal stromal cell infiltration and peripherally derived inflammation that is comparable to a bioinert methyl cellulose benchmarking material. pTreGuo hydrogels alter astrocyte borders and recruit microglia to infiltrate and resorb the hydrogel bulk over 7 d. Injections of pTreGuo hydrogels into ischemic stroke alter the natural responses of glial cells after injury to reduce the size of lesions and increase axon regrowth into lesion core environments. These results support the use of pTreGuo hydrogels as part of neural regeneration strategies to activate endogenous glia repair mechanisms.

Dynameric G-quadruplex-dextran hydrogels for cell growth applications

Hybrid dextran-G-quartet produces tunable biocompatible three-dimensional thixotropic hydrogels, able to support cell growth.

Self-assembly of guanosine into carbon-based multilayer materials

We report the utilization of guanosine as a supramolecular precursor that unprecedentedly renders the formation of carbon-based multilayer materials with naturally high-level nitrogen doping. As a proof-of-concept, the porous carbon multilayers after anchoring 0.5 wt% Rh electrocatalysts displayed an excellent hydrogen evolution reaction activity.

Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology

Biomimetics is defined as a "practice of making technological design that copies natural processes", with the idea that "nature has already solved the challenges we are trying to solve" (Cambridge Dictionary). The challenge we decided to address several years ago was the selective targeting of G quadruplexes (G4s) by small molecules (G4 ligands). Why? Because G4s, which are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences, are suspected to play key biological roles in human cells and diseases. Selective G4 ligands can thus be used as small-molecule modulators to gain a deep understanding of cell circuitry where G4s are involved, thus complying with the very definition of chemical biology (Stuart Schreiber) applied here to G4 biology. How? Following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G quartets, and then of G quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G quartet as a G4 ligand represents a unique example of biomimetic recognition of G4s.We formulated this hypothesis more than a decade ago, stepping on years of research on Gs, G4s, and G4 ligands. Our approach led to the design, synthesis, and use of a broad family of synthetic G quartets, also referred to as TASQs for template-assembled synthetic G quartets (John Sherman). This quest led us across various chemical lands (organic and supramolecular chemistry, chemical biology, and genetics), along a route on which every new generation of TASQ was a milestone in the growing portfolio of ever smarter molecular tools to decipher G4 biology. As discussed in this Account, we detail how and why we successively develop the very first prototypes of (i) biomimetic ligands, which interact with G4s according to a bioinspired, like-likes-like interaction between two G quartets, one from the ligand, the other from the G4; (ii) smart ligands, which adopt their active conformation only in the presence of their G4 targets; (iii) twice-as-smart ligands, which act as both smart ligands and smart fluorescent probes, whose fluorescence is triggered (turned on) upon interaction with their G4 targets; and (iv) multivalent ligands, which display additional functionalities enabling the detection, isolation, and identification of G4s both in vitro and in vivo. This quest led us to gather a panel of 14 molecular tools which were used to investigate the biology of G4s at a cellular level, from basic optical imaging to multiomics studies.

In Vitro Antiproliferative Activity and Phytochemicals Screening of Extracts of the Freshwater Microalgae, Chlorochromonas danica

The present study was focused on the screening of phytochemicals, their quantitative estimation and analysis by LC-MS profile, and antiproliferative efficacy of the aqueous-ethanolic extracts of the microalgae, Chlorochromonas danica isolated from the freshwater body Tavanampalli. The aqueous-ethanol extract of Chlorochromonas danica showed the presence of flavonoids, phenols, and proteins. The total flavonoid content, total phenol content, and total protein content were determined to be 158.65 mg of quercetin equivalent, 15.75 mg of gallic acid equivalent, and 134.65 mg/g dry weight of the extract, respectively. The LC-MS analysis confirmed the presence of several major bioactive molecules including L-Histidine, D-glutamine, L-aspartic acid, adenine, adenosine, cotinine, guanine hypoxanthine, L-glutamic acid, nicotinamide, 4-Hydroxycoumarin, and Stearamide. The aqueous-ethanol extract of Chlorochromonas danica exhibited an IC₅₀ values of 63.34 µg, 279.29 µg, 125.42 µg, 90.56 µg, and 95.58 µg against A375, A549, HeLa, HepG2, and HT29 cell lines respectively, compared to the positive control cisplatin with IC₅₀ values of 3.56 µg, 4.65 µg, 3.88 µg, 4.87 µg, and 7.23 µg respectively. These data suggest that Chlorochromonas danica remains a promising drug candidate for the treatment of cancers, particularly melanoma (A375 cell line) that can be considered for purification of antiproliferative compound and further clinical trials for the discovery of novel antiproliferative drugs from cost-effective sources.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

Ion slippage through Li+-centered G-quadruplex

Single-ion conductors have garnered attention in energy storage systems as a promising alternative to currently widespread electrolytes that allow migration of cations and anions. However, ion transport phenomena of most single-ion conductors are affected by strong ion (e.g., Li⁺)-ion (immobilized anionic domains) interactions and tortuous paths, which pose an obstacle to achieving performance breakthroughs. Here, we present a Li⁺-centered G-quadruplex (LiGQ) as a class of single-ion conductor based on directional Li⁺ slippage at the microscopic level. A guanine derivative with liquid crystalline moieties is self-assembled to form a hexagonal ordered columnar structure in the LiGQ, thereby yielding one-dimensional central channels that provide weak ion-dipole interaction and straightforward ionic pathways. The LiGQ exhibits weak Li⁺ binding energy and low activation energy for ion conduction, verifying its viability as a new electrolyte design.

Click-Chemistry-Based Biomimetic Ligands Efficiently Capture G-Quadruplexes In Vitro and Help Localize Them at DNA Damage Sites in Human Cells

Interrogating G-quadruplex (G4) biology at its deepest roots in human cells relies on the design, synthesis, and use of ever smarter molecular tools. Here, we demonstrate the versatility of biomimetic G4 ligands referred to as TASQ (template assembled synthetic G-quartet) in which a biotin handle was incorporated for G4-focused chemical biology investigations. We have rethought the biotinylated TASQ design to make it readily chemically accessible via an efficient click-chemistry-based strategy. The resulting biotinylated, triazole-assembled TASQ, or BioTriazoTASQ, was thus shown to efficiently isolate both DNA and RNA G4s from solution by affinity purification protocols, for identification purposes. Its versatility was then further demonstrated by optical imaging that provided unique mechanistic insights into the actual strategic relevance of G4-targeting strategies, showing that ligand-stabilized G4 sites colocalize with and, thus, are responsible for DNA damage foci in human cells.

Solution structure of a thrombin binding aptamer complex with a non-planar platinum(ii) compound

Thrombin Binding Aptamer (TBA) is a monomolecular well-defined two G-tetrad antiparallel G-quadruplex DNA that inhibits the activity of human α-thrombin. In this report, we synthesized a quasi-cross-shaped platinum(ii) compound (L'2LPt) with one cyclometalated and two carbene ligands. We found L'2LPt has selective affinity to bind the TBA G-quadruplex. A fibrinogen clotting assay revealed that L'2LPt can abrogate the inhibitory activity of TBA against thrombin. We solved the 1 : 1 L'2LPt-TBA complex structure by NMR, which revealed a unique self-adaptive property of L'2LPt upon binding to TBA. In the complex, a carbene ligand of L'2LPt rotates to pair with the cyclometalated ligand to form a plane stacking over half of the TBA G-tetrad and covered by lateral TT loops. It is notable that the heavy atom Pt stays out of the G-tetrad. Meanwhile, the other carbene ligand remains relatively perpendicular and forms a hydrogen bond with a guanine to anchor the L'2LPt position. This structure exhibits a quasi-cross-shaped Pt(ii) compound bound to the G-quadruplex with an unusual "wall-mounted" binding mode. Our structures provide insights into the specific recognition of antiparallel G-quadruplex DNA by a self-adaptive Pt(ii) compound and useful information for the design of selective G-quadruplex targeting non-planar molecules.

Analytical study to determine the optical properties of gold nanoparticles in the visible solar spectrum

In this work the optical properties of the formed gold nanoparticles, that obtained upon reducing the gold(I):6-thioguanosine hydrogel by dimethylamine borane (DMAB) have been studied. The analytical measurements to calculate the optical band gap showed a significant narrowing in the optical band gap value (Eg). Tauc plot was used to estimate the optical band gap (Eg) with the direct and indirect allowed transitions, before and after the reducing process. Narrowing the band gap is very important to increase the efficiency of the semiconductor material as it leads to absorbing in the visible region of the solar spectrum.

DNA G-quadruplexes are uniquely stable in the presence of denaturants and monovalent cations

Ions in the Hofmeister series exhibit varied effects on biopolymers. Those classed as kosmotropes generally stabilize secondary structure, and those classed as chaotropes generally destabilize secondary structure. Here, we report that several anionic chaotropes exhibit unique effects on one DNA secondary structure - a G quadruplex. These chaotropes exhibit the expected behaviour (destabilization of secondary structure) in two other structural contexts: a DNA duplex and i-Motifs. Uniquely among secondary structures, we observe that G quadruplexes are comparatively insensitive to the presence of anionic chaotropes, but not other denaturants. Further, the presence of equimolar NaCl provided greater mitigation of the destabilization caused by other non-anionic denaturants. These results are consistent with the presence of monovalent cations providing an especially pronounced stabilizing effect to G quadruplexes when studied in denaturing solution conditions.

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G-quadruplexes exhibit the lowest sensitivity to denaturation by anionic chaotropes among several DNA secondary structures.

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In G-quadruplexes, the destabilizing effect of other denaturants is uniquely well-mitigated by the presence of sodium ions.

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This phenomenon affords a structure-specific means of modulating nucleic acid folding.

Feedback-controlled topological reconfiguration of molecular assemblies for programming supramolecular structures

In biology, nonequilibrium assembly is characterized by fuel-driven switching between associating and nonassociating states of biomolecules. This dynamic assembly model has been used routinely to describe the nonequilibrium processes in synthetic systems. Here, we present a G-quartet-based nonequilibrium system based on fuel-driven co-assembly of guanosine 5'-monophosphate disodium salt hydrate and urease. Addition of lanthanum(III) ions to the system caused macroscopic dynamic switching between precipitates and hydrogels. Interestingly, combined analyses of the nonequilibrium systems demonstrated that molecules could switch between two distinct associating states without undergoing a nonassociating state. This finding suggested a nonequilibrium assembly mechanism of topological reconfiguration of molecular assemblies. We detailed quantitatively the nonequilibrium assembly mechanism to precisely control the phase behaviors of the active materials; thus, we were able to use the materials for transient-gel-templated polymerization and transient circuit connection. This work presents a new nonequilibrium system with unusual phase behaviors, and the resultant active hydrogels hold promise in applications such as fluid confinements and transient electronics.

Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives

Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.

Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq

Guanine-rich RNAs can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), and participate in a wide range of biological processes. Here we describe in detail a G4-RNA-specific precipitation (G4RP) protocol, which enables the transcriptomic profiling of G4-RNAs. The G4RP protocol consists of a chemical cross-linking step, followed by affinity capture with a G4-specific probe, BioTASQ. G4RP can be coupled with sequencing to capture a comprehensive global snapshot of folded G4-RNAs. This method can also be used to profile induced changes (i.e., through G4 ligand treatments) within the G4-RNA transcriptome. The entire protocol can be completed in 1-2 weeks and can be scaled up or down depending on the specific experimental goals. In addition to the protocol details, we also provide here a guide for optimization in different laboratory setups.

A novel chemosensor for sensitive and facile detection of strontium ions based on ion-imprinted hydrogels modified with guanosine derivatives

A novel chemosensor is developed for the sensitive and facile detection of trace strontium ions (Sr²⁺) based on the ion-imprinted hydrogels. With Sr²⁺ as the templates, the ion-imprinted hydrogels are synthesized by copolymerizing the ion-responsive units 5'-O-acryloyl-2',3'-O-isopropylidene guanosine (APG) and the thermo-responsive units N-isopropylacrylamide (NIPAM). In the presence of Sr²⁺, APG units can self-assemble to form planar G-quartets via the complexation with Sr²⁺, which are introduced into the gel network during polymerization. Then Sr²⁺ templates can be removed by multiple repeated washing. When re-exposed to Sr²⁺, the relaxed G-quartets can recognize Sr²⁺, leading to the weakening of electrostatic repulsion between the four oxygen atoms in the G-quartets and inducing the shrinkage of the hydrogels. In this work, the Sr²⁺-imprinted chemosensors are designed as the grating systems for detecting trace Sr²⁺. Based on the array of hydrogel strings synthesized on a nano-scale, the smart grating systems thus constructed can convert and amplify the Sr²⁺ concentration signals to the easily-measurable optical signals. With the Sr²⁺-imprinted hydrogel gratings, trace Sr²⁺ (10^-11 M) in an aqueous solution can be detected sensitively. Moreover, the proposed Sr²⁺-imprinted chemosensors can be integrated with other smart systems for developing various detectors with high performance.

Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil

An idea of employing an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was examined in this work by analyzing structural features for singular and bimolecular models. Density functional theory (DFT) calculations were performed for optimizing the structures and evaluating molecular and atomic descriptors for analyzing the models systems. Two bimolecular models were obtained assigning by S-FeC and O-FeC models, in which each of S and O atom of 2TU was relaxed towards the Fe region of FeC surface in the mentioned models, respectively. The results indicated that both models were achievable with slightly more favorability for formation of S-FeC model. The obtained molecular orbital properties revealed the dominant role of FeC monolayer for managing future interactions of attached 2TU, which is indeed a major role for employing nanomaterials for targeted drug delivery purposes. In addition to energies and molecular orbital features, atomic quadrupole coupling constants indicated the benefit of employing FeC monolayer for drug delivery of 2TU.

Programmable Transient Supramolecular Chiral G-quadruplex Hydrogels via a Chemically Fueled Non-Equilibrium Self-assembly Strategy

The temporal and spatial control of natural systems has aroused great interest in the creation of synthetic mimics. Operating with boronic ester-based dynamic covalent chemistry and coupling it with an internal pH feedback system, herein, we developed a new chemically fueled reaction network to design non-equilibrium supramolecular chiral G-quadruplex hydrogels with programmable lifetime from minutes, to hours, to days, as well as high transparency and conductivity, excellent injectability and rapid self-healability. The cycle system can be controlled via in-situ kinetically-controlled formation and dissociation of dynamic boronic ester bonds between cis-diols of guanosine (G) and 5-fluorobenzoxaborole (B) under chemical fuels (KOH and 1,3-propanesultone), leading to the formation of a precipitate-solution-gel-precipitate cycle under non-equilibrium conditions. A combined experimental-computational approach revealed that the underlying mechanism of the non-equilibrium self-assembly involves aggregation and disaggregation of right-handed helical G-quadruplex superstructure. With consecutive cycles of fuel addition, the non-equilibrium system can be easily refueled at least 6 cycles without obvious loss in the rheological moduli of the transient hydrogels. The proposed dynamic boronic ester-based non-equilibrium self-assembly strategy offers a new option to design next-generation adaptive and interactive smart materials.

Heterocycle-modified 2'-Deoxyguanosine Nucleolipid Analogs Stabilize Guanosine Gels and Self-assemble to Form Green Fluorescent Gels

Nucleoside-lipid conjugates are very useful supramolecular building blocks to construct self-assembled architectures suited for biomedical and material applications. Such nucleoside derivatives can be further synthetically manipulated to endow additional functionalities that could augment the assembling process and impart interesting properties. Here, we report the design, synthesis and self-assembling process of multifunctional supramolecular nucleolipid synthons containing an environment-sensitive fluorescent guanine. The amphiphilic synthons are composed of an 8-(2-(benzofuran-2-yl)vinyl)-guanine core and alkyl chains attached to 3'-O and 5'-O-positions of 2'-deoxyguanosine. The 2-(benzofuran-2-yl)vinyl (BFV) moiety attached at the C8 position of the nucleobase adopted a syn conformation about the glycosidic bond, which facilitated the self-assembly process through the formation of a G-tetrad as the basic unit. While 3',5'-diacylated BFV-modified dG analog stabilized the guanosine hydrogel by hampering the crystallization process and imparted fluorescence, BFV-modified dGs containing longer alkyl chains formed a green fluorescent organogel, which transformed into a yellow fluorescent gel in the presence of a complementary non-fluorescent cytidine nucleolipid. The ability of the dG analog containing short alkyl chains to modulate the mechanical property of a gel, and interesting fluorescence properties and self-assembling behavior exhibited by the dG analogs containing long alkyl chains in response to heat and complementary base underscore the potential use of these new supramolecular synthons in material applications.

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+ , Ca2+ , Sr2+ , and Ba2+ ), and (post-)transition metal (Zn2+ , Cd2+ , Hg2+ , and Pb2+ ) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+ ). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations' unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.

Manipulating the Assembly of DNA Nanostructures and Their Enzymatic Properties by Incorporating a 5'-5' Polarity of Inversion Site in the G-Tract

Supramolecular DNA complexes consisting of both DNA duplexes and tetrameric G-quadruplexes are fabricated successfully by utilizing a single short DNA strand that contains one 5'-5' polarity of inversion site in the middle of G-tract. The resulting DNA supramolecules exhibit significantly high peroxidase activities after interaction with hemin due to the presence of various G-quadruplex-duplex (G4-duplex) interfaces. Significantly, we find that the addition of a C-rich fragment to the designed sequence not only allows the self-assembly of two-dimensional porous DNA nanostructures via the formation of dimeric i-motif structures but also could act as a control element to facilitate the generation of pH-sensitive G4-based DNAzymes. The enhanced catalytic activity obtained from specific sequence modifications as well as the controllable feature of these DNA nanostructures can significantly benefit further applications of DNA functional materials in complex biological systems.

Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.

Self-Assembly of Functionalized Lipophilic Guanosines into Cation-Free Stacked Guanine-Quartets

The hierarchical self-assembly of various lipophilic guanosines exposing either a phenyl or a ferrocenyl group in the C(8) position was investigated. In a solution, all the derivatives were found to self-assemble primarily into isolated guanine (G)-quartets. In spite of the apparent similar bulkiness of the two substituents, most of the derivatives form disordered structures in the solid state, whereas a specific 8-phenyl derivative self-assembles into an unprecedented, cation-free stacked G-quartet architecture.

Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface

Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.