Effect of Molecular Crowding on the Stability of RNA G-Quadruplexes with Various Numbers of Quartets and Lengths of Loops

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

Elucidating the Quenching Mechanism of Tris(2,2'-bipyridyl)ruthenium(II) Complex in the Water-Glycerol Binary System Based on the Microscopic Structure of the Media

Kinetic studies on the photochemical quenching reaction of the tris(2,2'-bipyridyl) ruthenium(II) complex ([Ru(bpy)3]2+) in water-glycerol binary media were conducted based on the Einstein-Smoluchowski (E-S) theory. Dynamic and static quenching behaviors were analyzed by comparing results from time-resolved spectroscopy and emission spectroscopy. While the dynamic quenching reaction aligns well with the E-S theory, static quenching was observed, leading to a notable increase in the overall photoquenching reaction rate constant. Employing chromatography and infrared spectroscopy, we correlated the microscopic molecular structure of the binary solvent system and the solvation environment around the emitters with the reaction mechanism. This correlation was found to correspond to ion pair formation and the confinement effect of the emitter, respectively.

Effects of Molecular Crowding on the Structure, Stability, and Interaction with Ligands of G-quadruplexes

G-quadruplexes (G4s) are widely found in cells and have significant biological functions, which makes them a target for screening antitumor and antiviral drugs. Most of the previous research on G4s has been conducted mainly in diluted solutions. However, cells are filled with organelles and many biomolecules, resulting in a constant state of a crowded molecular environment. The conformation and stability of some G4s were found to change significantly in the molecularly crowded environment, and interactions with ligands were disturbed to some extent. The structure of the G4s and their biological functions are correlated, and the effect of the molecularly crowded environment on G4 conformational transitions and interactions with ligands should be considered in drug design targeting G4s. This review discusses the changes in the conformation and stability of G4s in a physiological environment. Moreover, the mechanism of action of the molecularly crowded environment affecting the G4 has been further reviewed based on previous studies. Furthermore, current challenges and future research directions are put forward. This review has implications for the design of drugs targeting G4s.

G-quadruplexes from non-coding RNAs

Non-coding RNAs (ncRNAs) are significant regulators of gene expression in a wide range of biological processes, such as transcription, RNA maturation, or translation. ncRNAs interplay with proteins or other RNAs through not only classical sequence-based mechanisms but also unique higher-order structures such as RNA G-quadruplexes (rG4s). rG4s are predictably formed in guanine-rich sequences and are closely related to various human diseases, such as tumors, neurodegenerative diseases, and infections. This review focuses on the vital role of rG4s in ncRNAs, particularly lncRNAs and miRNAs. We outline the dynamic balance between rG4s and RNA stem-loop/hairpin structures and the interplay between ncRNAs and interactors, thereby modulating gene expression and disease progression. A complete understanding of the biological regulatory role and mechanism of rG4s in ncRNAs affirms the critical importance of folding into the appropriate three-dimensional structure in maintaining or modulating the functions of ncRNAs. It makes them novel therapeutic targets for adjusting potential-G4-containing-ncRNAs-associated diseases.

Molecular crowding promotes the aggregation of parallel structured G-quadruplexes

G-quadruplexes are widely distributed in cells and are usually essential in mediating biological processes. The intracellular environment is often in a state of molecular crowding, and the current research considerably focuses on the effect of molecular crowding on the conformation of telomeric G-quadruplexes. However, G-quadruplex-forming oligonucleotides are primarily located in the promoter region of the proto-oncogene and on mRNA inside the cell and are reported to fold into parallel structures. Thus, studying the interaction mechanism between ligands and parallel structured G-quadruplexes under crowding conditions is crucial for the design of drugs targeting G-quadruplexes. In our study, molecular crowding was simulated through polyethylene glycol with an average molecular weight of 200 (PEG200) to investigate the parallel structure of the canonical G-quadruplexes c-KIT1, c-MYC, and 32KRAS and their interactions with ligands. Circular dichroism (CD) spectral scanning, fluorescence resonance energy transfer (FRET), and native polyacrylamide gel electrophoresis (PAGE) analysis revealed that molecular crowding failed to induce oligonucleotides to form parallel G-quadruplex structures in the explored model sequences while induced telomeric G-rich sequences to form antiparallel G-quadruplexes in solution without K⁺. Molecular crowding did not induce changes in their parallel structures but promoted the formation of G-quadruplex aggregates. Moreover, to some extent, molecular crowding also induced a looser structure of the monomer G-quadruplexes. Further studies showed that molecular crowding did not alter the binding stoichiometry of the ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino [4,3,2-kl] acridinium methosulfate (RHPS4) to c-KIT1, while it inhibited its interaction with parallel structured G-quadruplexes. This work provides new insights into developing anticancer drugs targeting parallel structured G-quadruplexes.

G-quadruplex from precursor miR-1587 modulated its maturation and function

A certain proportion of pre-miRNAs, which contained potential G-quadruplex forming sequences, was found to act as a mediator to Dicer-mediated cleavage, and that the regulation of miRNA production and function may be achieved through the G-quadruplex structure. In this study, human precursor miR-1587 sequence was transfected after the incubation with different solution conditions (K⁺, TMPyP4, etc.). Firstly, the formation of G-quadruplex from precursor miR-1587 sequences was confirmed by CD and UV melting. The expression of miR-1587 level was then evaluated by Q-RT-PCR, and the results showed that the formation of G-quadruplex inhibited the miR-1587 maturation process, resulting in a reduced miR-1587 expression. Meanwhile the destabilization of G-quadruplex led to an increased miR-1587 expression by contrast. Then, the weakened inhibition of miR-1587 towards its target genes, such as TAGLN or NCOR1, was presented confirming by Q-RT-PCR and western blot. Molecular mechanism by dual-luciferase assays showed that the modulations of miR-1587 expression and function were due to the G-quadruplex structure transformation, but not the simple change of solution conditions. This study highlighted the importance of maintaining specific structures during miRNA biosynthesis and provided a way to alter the function of G-rich precursor miRNAs by modulating molecular conformation using ionic solutions or ligands.

Understanding the Interactions of Guanine Quadruplexes with Peptides as Novel Strategies for Diagnosis or Tuning Biological Functions

Guanine quadruplexes (G4s) are nucleic acid structures exhibiting a complex structural behavior and exerting crucial biological functions in both cells and viruses. The specific interactions of peptides with G4s, as well as an understanding of the factors driving the specific recognition are important for the rational design of both therapeutic and diagnostic agents. In this review, we examine the most important studies dealing with the interactions between G4s and peptides, highlighting the strengths and limitations of current analytic approaches. We also show how the combined use of high-level molecular simulation techniques and experimental spectroscopy is the best avenue to design specifically tuned and selective peptides, thus leading to the control of important biological functions.

Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase

Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.

Physicochemical and antiproliferative characteristics of RNA and DNA sequence-related G-quadruplexes

In this article the physicochemical and biological properties of sequence-related G-quadruplex forming oligonucleotides in RNA and DNA series are analyzed and compared. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads and homogeneity of the core. Our studies show that even slight variations in sequence initiate certain changes of G-quadruplex properties. DNA G-quadruplexes are less thermally stable than their RNA counterparts, more topologically diversified and are better candidates as inhibitors of cancer cells proliferation. The most efficient antiproliferative activity within the studied group of molecules was observed for two DNA G-quadruplexes with unperturbed core and lower content of thymidine residues within the loops leading to reduction of cells viability up to 65% and 33% for HeLa and MCF-7 cell lines, respectively.

rG4detector, a novel RNA G-quadruplex predictor, uncovers their impact on stress granule formation

RNA G-quadruplexes (rG4s) are RNA secondary structures, which are formed by guanine-rich sequences and have important cellular functions. Existing computational tools for rG4 prediction rely on specific sequence features and/or were trained on small datasets, without considering rG4 stability information, and are therefore sub-optimal. Here, we developed rG4detector, a convolutional neural network to identify potential rG4s in transcriptomics data. rG4detector outperforms existing methods in both predicting rG4 stability and in detecting rG4-forming sequences. To demonstrate the biological-relevance of rG4detector, we employed it to study RNAs that are bound by the RNA-binding protein G3BP1. G3BP1 is central to the induction of stress granules (SGs), which are cytoplasmic biomolecular condensates that form in response to a variety of cellular stresses. Unexpectedly, rG4detector revealed a dynamic enrichment of rG4s bound by G3BP1 in response to cellular stress. In addition, we experimentally characterized G3BP1 cross-talk with rG4s, demonstrating that G3BP1 is a bona fide rG4-binding protein and that endogenous rG4s are enriched within SGs. Furthermore, we found that reduced rG4 availability impairs SG formation. Hence, we conclude that rG4s play a direct role in SG biology via their interactions with RNA-binding proteins and that rG4detector is a novel useful tool for rG4 transcriptomics data analyses.

The Pressure Dependence of the Stability of the G-quadruplex Formed by d(TGGGGT)

The G-quadruplex (GQ), a tetrahelix formed by guanine-rich nucleic acid sequences, is a potential drug target for several diseases. Monomolecular GQs are stabilized by guanine tetrads and non-guanine regions that form loops. Hydrostatic pressure destabilizes the folded, monomolecular GQ structures. In this communication, we present data on the effect of pressure on the conformational stability of the tetramolecular GQ, d[5′-TGGGGT-3′]₄. This molecule does not have loops linking the tetrads; thus, its physical properties presumably reflect those of the tetrads alone. Understanding the properties of the tetrads will aid in understanding the contribution of the other structural components to the stability of GQ DNA. By measuring UV light absorption, we have studied the effect of hydrostatic pressure on the thermal stability of the tetramolecular d[5′-TGGGGT-3′]₄ in the presence of sodium ions. Our data show that, unlike monomolecular GQ, the temperature at which d[5′-TGGGGT-3′]₄ dissociates to form the constituent monomers is nearly independent of pressure up to 200 MPa. This implies that there is no net molar volume difference (∆V) between the GQ and the unfolded random-coil states. This finding further suggests that the large negative ∆V values for the unfolding of monomolecular GQ are due to the presence of the loop regions in those structures.

Volumetric Strategy for Quantitatively Elucidating a Local Hydration Network around a G-Quadruplex

Hydration around nucleic acids, such as DNA and RNA, is an important factor not only for the stability of nucleic acids but also for their interaction with binding molecules. Thus, it is necessary to quantitatively elucidate the hydration properties of nucleic acids around a certain structure. In this study, volumetric changes in G-quadruplex (G4) RNA formation were investigated by systematically changing the number of G-quartet stacks under high pressure. The volumetric contribution at the level of each G4 structural unit revealed that the core G4 helix was significantly more dehydrated than the other parts, including the edges of G-quartets and loops. These findings will help in predicting the binding of G4 ligands on the surface of G4, depending on the chemical structure of the ligand and solution environment. Therefore, the preset volumetric parameter provides information that can predict molecular interactions in G4 formations during molecular crowding in cells.

Enzyme kinetics in confined geometries at the single enzyme level

Different confinement, femtoliter chambers and molecular crowders revealed the effects on the catalytic rates of β-galactosidase at the single molecule level.

RHPS4 shifted the conformation ensemble equilibrium of Tel24 by preferentially stabilizing the (3 + 1) hybrid-2 conformation

Telomeric G-quadruplexes have been a promising target for developing antitumor drugs with fewer side effects. The intracellular environment is usually in a state of molecular crowding. Studying the interaction mechanism among ligands and telomeric G-quadruplexes under crowded conditions is important for designing drugs that target telomeric G-quadruplexes. In the present study, the telomeric G-quadruplex Tel24 (TTAGGG)₄ was found to fold into a conformational ensemble of parallel and (3 + 1) hybrid-2 conformations in solution with molecular crowding conditions created by PEG200. G-quadruplex-ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl] acridinium methosulfate (RHPS4) preferentially stabilized the (3 + 1) hybrid-2 conformation and shifted the conformational ensemble equilibrium of Tel24 towards the hybrid conformation. We also found that the (3 + 1) hybrid-2 conformation of Tel24 was more likely to form as compared to the parallel conformation in the conformational ensemble of Tel24. Overall, this study provides new insights into the conformation of telomere G-quadruplexes and their interactions with ligands in a physiological environment.

Tel24 G-quadruplex can form a conformational ensemble consisting of parallel and (3 + 1) hybrid-2 conformations. RHPS4 preferentially stabilized the hybrid-2 conformation and shifted the conformational ensemble equilibrium.

Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP

Given the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which particularly threatens older people with comorbidities such as diabetes mellitus and dementia, understanding the relationship between Covid-19 and other diseases is an important factor for treatment. Possible targets for medical intervention include G-quadruplexes (G4Qs) and their protein interaction partners. We investigated the stability and conformational space of the RG-1 RNA-G-quadruplex of the SARS-CoV-2 N-gene in the presence of salts, cosolutes, crowders and intrinsically disordered peptides, focusing on α-Synuclein and the human islet amyloid polypeptide, which are involved in Parkinson's disease (PD) and type-II diabetes mellitus (T2DM), respectively. We found that the conformational dynamics of the RG-1 G4Q is strongly affected by the various solution conditions. Further, the amyloidogenic peptides were found to strongly modulate the conformational equilibrium of the RG-1. Considerable changes are observed with respect to their interaction with human telomeric G4Qs, which adopt different topologies. These results may therefore shed more light on the relationship between PD as well as T2DM and the SARS-CoV-2 disease and their molecular underpinnings. Since dysregulation of G4Q formation by rationally designed targeting compounds affects the control of cellular processes, this study should contribute to the development of specific ligands for intervention.

Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3

Specific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K⁺, but Na⁺, Li⁺, and Rb⁺ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na⁺ has stronger stabilizing effect on HepB than K⁺, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na⁺, K⁺, Li⁺, and Rb⁺ respectively. Binding constants for Na⁺ and K⁺ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.

RNA G-quadruplexes (rG4s): genomics and biological functions

G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.

Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation

Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher's fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life.

Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation

Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.

Watson-Crick versus Hoogsteen Base Pairs: Chemical Strategy to Encode and Express Genetic Information in Life

Nucleic acids typically form a double helix structure through Watson-Crick base-pairing. In contrast, non-Watson-Crick base pairs can form other three-dimensional structures. Although it is well-known that Watson-Crick base pairs may be more unstable than non-Watson-Crick base pairs under some conditions, the importance of non-Watson-Crick base pairs has not been widely examined. Hoogsteen base pairs, the non-Watson-Crick base pairs, contain important hydrogen-bond patterns that form the helices of nucleic acids, such as in Watson-Crick base pairs, and can form non-double helix structures such as triplexes and quadruplexes. In recent years, non-double helix structures have been discovered in cells and were reported to considerably influence gene expression. The complex behavior of these nucleic acids in cells is gradually being revealed, but the underlying mechanisms remain almost unknown.Quantitatively analyzing the structural stability of nucleic acids is important for understanding their behavior. A nucleic acid is an anionic biopolymer composed of a sugar, base, and phosphoric acid. The physicochemical factors that determine the stability of nucleic acid structures include those derived from the interactions of nucleic acid structures and those derived from the environments surrounding nucleic acids. The Gibbs free energy change (ΔG) of structure formation is the most commonly used physicochemical parameter for analyzing quantitative stability. Quantitatively understanding the intracellular behavior of nucleic acids involves describing the formation of nucleic acid structures and related reactions as ΔG. Based on this concept, we quantitatively analyzed the stability of double helix and non-double helix structures and found that decreased water activity, an important factor in crowded cellular conditions, significantly destabilize the formation of Watson-Crick base pairs but stabilizes Hoogsteen base pairs.Here, we describe a physicochemical approach to understand the regulation of gene expressions based on the stability of nucleic acid structures. We developed new methods for predicting the stability of double and non-double helices in various molecular environments by mimicking intracellular environments. Furthermore, the physicochemical approach used for analyzing gene expression regulated by non-double helix structures is useful for not only determining how gene expression is controlled by cellular environments but also for developing new technologies to chemically regulate gene expression by targeting non-double helix structures. We discuss the roles of Watson-Crick and Hoogsteen base pairs in cells based on our results and why both types of base pairing are required for life. Finally, a new concept in nucleic acid science beyond that of Watson and Crick base pairing is introduced.

New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments

The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.

Porphyrins ameliorate spinocerebellar ataxia type 36 GGCCTG repeat expansion-mediated cytotoxicity

Spinocerebellar ataxia type 36 (SCA36) is a noncoding repeat expansion disorder caused by an expanded GGCCTG hexanucleotide repeat (HNR) in the first intron of the nucleolar protein 56 (NOP56) gene. Another disease-causing HNR expansion derived from C9orf72-linked GGGGCC repeats that form G-quadruplexes (GQs) affects genetic stability, RNA splicing, and mRNA localization within neurites. The porphyrin derivative TMPyP4 was shown to ameliorate RNA toxicity caused by GGGGCC HNR expansion by binding and distorting RNA GQ structures. SCA36 GGCCTG HNRs can potentially form RNA GQs; therefore, we investigated whether several porphyrin derivatives could reduce RNA toxicity in SCA36 cell models. Among these, sodium copper chlorophyllin and hemin chloride, which have already been used in clinical practice, reduced SCA36 GGCCTG expansion-mediated cytotoxicity and improved cell viability. These data suggest that porphyrins are potential therapeutic candidates against SCA36 pathogenesis.

Reversible photo-regulation on the folding/unfolding of telomere G-quadruplexes with solid-state nanopores

The formation of G-quadruplexes (G4) in human telomere and other important biological regions inhibits the replication and transcription of DNA, thereby influencing further cell proliferation. The investigation of G4 formation and unfolding is vital for understanding their modulation in biological processes and life science. Photo regulation is a facile and sensitive approach for monitoring the structures of biomacromolecules and material surface properties. The nanopore-based technique is also prevalent for label-free single-molecule characterization with high accuracy. This study provides a combination of solid-state nanopore technology with light-switch as a platform for the modulation of human telomere G4 formation and splitting under switchable light exposure. The introduction of molecular switch, namely azobenzene moiety at different positions of the DNA sequence influences the formation and stability of G4. Three azobenzenes immobilized on each of the G-quartet plane (hTelo-3azo-p) or four azobenzenes on the same plane (hTelo-4azo-4p) of the human telomere G4 sequence realized the reversible control of G4 folding/unfolding at the temporal scale upon photo regulation, and the formation and splitting of G4 with hTelo-4azo-4p is slower and not thorough compared to that with hTelo-3azo-p due to the coplanar steric hindrance. Moreover, the G4 formation recorded with the combined nanopore and photo-responsive approach was also characterized with fluorescence, and the variation in the fluorescence intensity of the NMM and G4 complex exhibited a different tendency under reverse light irradiation due to the distinct interactions of NMM with the azobenzene-modified G4. Our study demonstrated a controllable and sensitive way for the manipulation of G4 structures, which will be inspiring for the intervention of G4-related cell senescence, cancer diagnosis and drug exploration.

Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells

This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.