DNA Quadruple Helices in Nanotechnology

Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study

Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca²⁺, Sr²⁺ and Ba²⁺). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca²⁺ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.

Engineering DNA G-quadruplex assembly for label-free detection of Ochratoxin A in colorimetric and fluorescent dual modes

Colorimetric and fluorescent methods for Ochratoxin A (OTA) detection are convenient and well received. However, the pigments and autofluorescence originated from food matrices often interfere with detection signals. We have developed a strategy with colorimetric and fluorescent dual modes to solve this challenge. In the colorimetric mode, OTA aptamer (AP9) was assembled into a DNA triple-helix switch with a specially designed signal-amplifying sequence. The OTA-induced G-quadruplex (G4) of AP9 would open the switch and release the signal-amplifying sequence for colorimetric signal amplification. The G4 structures of AP9 were further utilized to combine with the fluorogenic dye ThT for fluorescent mode. By skillfully engineering DNA G4 assembly for signal amplification, there was no need for any DNA amplification or nanomaterials labeling. Detections could be carried out in a wide temperature range (22-37 ℃) and finished rapidly (colorimetric mode, 60 min; fluorescent mode, 15 min). Broad linear ranges (colorimetric mode, 10-1.5 ×10³ μg/kg; fluorescent mode, 0.05-1.0 ×10³ μg/kg) were achieved. The limit of detection for colorimetric and fluorescent modes were 4 μg/kg and 0.01 μg/kg, respectively. The two modes have been successfully applied to detect OTA in samples with intrinsic pigments and autofluorescence, showing their applicability and reliability.

A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K+ or Sr2+ . TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.

Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures

Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.

Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold

A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Three-level hierarchical self-assembly of azobenzene conjugated phenylalanines into superhelical nanostructures with light-switchable helicity

Photosensitive azobenzene conjugated phenylalanines can self-assemble into a series of hierarchical superhelices, which can reversibly transform into achiral nanorods via light stimuli.

Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine

Guanine radical cation (G^•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)₃ (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G^•+ (Tel21⁺). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21⁺ systems, differing in the position of G^•+ in the sequence. When G^•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na⁺ ions and increase the solvent exposed surface of G^•+. Analysis of solvation patterns of G^•+ provides new insights on the main reactions of G^•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.

Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups

The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G⁺)^● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)^● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.

Engineering DNA quadruplexes in DNA nanostructures for biosensor construction

DNA quadruplexes are nucleic acid conformations comprised of four strands. They are prevalent in human genomes and increasing efforts are being directed toward their engineering. Taking advantage of the programmability of Watson-Crick base-pairing and conjugation methodology of DNA with other molecules, DNA nanostructures of increasing complexity and diversified geometries have been artificially constructed since 1980s. In this review, we investigate the interweaving of natural DNA quadruplexes and artificial DNA nanostructures in the development of the ever-prosperous field of biosensing, highlighting their specific roles in the construction of biosensor, including recognition probe, signal probe, signal amplifier and support platform. Their implementation in various sensing scenes was surveyed. And finally, general conclusion and future perspective are discussed for further developments.

Recent Advances in Polyallenes: Preparation, Self-Assembly, and Stimuli-Responsiveness

Polyallenes, as a typical type of reactive polymers, are of great significance and have aroused widespread interest because they contain double bonds that can be post-modified into other functionalities to afford varieties of functional materials. This Minireview firstly highlights the recent advances in the preparation of polyallenes, including preparation of helical polyallenes through directly polymerization of chiral allene monomers or helix-sense-selective polymerization (HSSP) of achiral allene monomers, synthesis of 1,2-regulated polyallenes and 2,3-regulated polyallenes via selective polymerization of allene monomers, polymerization of allene monomers catalyzed by Ni(II)-terminated poly(3-hexylthiophene) (P3HT), and so on. Then, latest progress on the self-assembly and stimuli-responses of polyallene-based diblock, ABA and ABC triblock copolymers is summarized. We hope this Minireview will inspire more interest in developing polyallenes and encourage further advances in functional materials.

Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

Stimuli-Responsive and Reversible Nanoassemblies of G-Triplexes

G-triplex (G3) structures formed with three consecutive G-tracts have recently been identified as a new emerging guanine-rich DNA fold. There could likely be a wide range of biological functions for G3s as occurring for G-quadruplex (G4) structures formed with four consecutive G-tracts. However, in comparison to the many reports on G4 nanoassemblies that organize monomers together in a controllable manner, G3-favored nanoassemblies have yet to be explored. In this work, we found that a natural alkaloid of sanguinarine can serve as a dynamic ligand glue to reversibly switch the dimeric nanoassemblies of the thrombin binding aptamer G3 (TBA-G3). The glue planarity was considered to be a crucial factor for realizing this switching. More importantly, external stimuli including pH, sulfite, O₂ and H₂ O₂ can be employed as common regulators to easily modulate the glue's adhesivity for constructing and destructing the G3 nanoassemblies as a result of the ligand converting between isoforms. However, this assembly behavior does not occur with the counterpart TBA-G4. Our work demonstrates that higher-order G3 nanoassemblies can be reversibly operated by manipulating ligand adhesivity. This provides an alternative understanding of the unique behavior of guanine-rich sequences and focuses attention on the G3 fold since the nanoassembly event investigated herein might occur in living cells.

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.

Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes

Recently, a Na+-binding aptamer was reported to be embedded in a few RNA-cleaving DNAzymes, including NaA43, Ce13d, and NaH1. The Na+ aptamer consists of multiple GG stretches, which is a prerequisite for the formation of G-quadruplex (G4) structures. These DNAzymes require Na+ for activity but show no activity in the presence of K+ or other metal ions. Given that DNA can selectively bind K+ by forming a G4 structure, this work aims to answer whether this Na+ aptamer also uses a G4 to bind Na+. Through comparative ThT fluorescence spectrometry studies, while a control G4 DNA exhibited notable fluorescence enhancement up to 5 mM K+ with a Kd of 0.28 ± 0.06 mM, the Ce13d DNAzyme fluorescence was negligibly perturbed with similar concentrations of K+. Opposed to this, Ce13d displayed specific remarkable fluorescence decrease with low millimolar concentrations of Na+. NMR experiments at two different pH values suggest that Ce13d adopts a significantly different conformation or equilibrium of conformations in the presence of Na+ versus K+ and has a more stable structure in the presence of Na+. Additionally, absence of characteristic G4 peaks in one-dimensional 1H NMR suggest that G4 is not responsible for the Na+ binding. This hypothesis is confirmed by the absence of characteristic peaks in the CD spectra of this sequence. Therefore, we concluded that the aptamer must be selective for Na+ and that it binds Na+ using a structural element that does not contain G4.

Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy

A robust understanding of the sequence-dependent thermodynamics of DNA hybridization has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the sequence-dependent kinetics and mechanisms of hybridization and dehybridization remains comparatively underdeveloped. In this work, we establish new understanding of the sequence-dependent hybridization/dehybridization kinetics and mechanism within a family of self-complementary pairs of 10-mer DNA oligomers by integrating coarse-grained molecular simulation, machine learning of the slow dynamical modes, data-driven inference of long-time kinetic models, and experimental temperature-jump infrared spectroscopy. For a repetitive ATATATATAT sequence, we resolve a rugged dynamical landscape comprising multiple metastable states, numerous competing hybridization/dehybridization pathways, and a spectrum of dynamical relaxations. Introduction of a G:C pair at the terminus (GATATATATC) or center (ATATGCATAT) of the sequence reduces the ruggedness of the dynamics landscape by eliminating a number of metastable states and reducing the number of competing dynamical pathways. Only by introducing a G:C pair midway between the terminus and the center to maximally disrupt the repetitive nature of the sequence (ATGATATCAT) do we recover a canonical "all-or-nothing" two-state model of hybridization/dehybridization with no intermediate metastable states. Our results establish new understanding of the dynamical richness of sequence-dependent kinetics and mechanisms of DNA hybridization/dehybridization by furnishing quantitative and predictive kinetic models of the dynamical transition network between metastable states, present a molecular basis with which to understand experimental temperature jump data, and furnish foundational design rules by which to rationally engineer the kinetics and pathways of DNA association and dissociation for DNA nanotechnology applications.

Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters

Transient, dissipative, aggregation and deaggregation of Au nanoparticles (NPs) or semiconductor quantum dots (QDs) leading to control over their transient optical properties are introduced. The systems consist of nucleic acid-modified pairs of Au NPs or pairs of CdSe/ZnS QDs, an auxiliary duplex L₁/T₁, and the nicking enzyme Nt.BbvCI as functional modules yielding transient aggregation/deaggregation of the NPs and dynamically controlling over their optical properties. In the presence of a fuel strand L₁', the duplex L₁/T₁ is separated, leading to the release of T₁ and the formation of duplex L₁/L₁'. The released T₁ leads to aggregation of the Au NPs or to the T₁-induced G-quadruplex bridged aggregated CdSe/ZnS QDs. Biocatalytic nicking of the L₁/L₁' duplex fragments L₁' and the released L₁ displaces T₁ bridging the aggregated NPs or QDs, resulting in the dynamic recovery of the original NPs or QDs modules. The dynamic aggregation/deaggregation of the Au NPs is followed by the transient interparticle plasmon coupling spectral changes. The dynamic aggregation/deaggregation of the CdSe/ZnS QDs is probed by following the transient chemiluminescence generated by the hemin/G-quadruplexes bridging the QDs and by the accompanying transient chemiluminescence resonance energy transfer proceeding in the dynamically formed QDs aggregates. A third system demonstrating transient, dissipative, luminescence properties of a reaction module consisting of nucleic acid-stabilized Ag nanoclusters (NCs) is introduced. Transient dynamic formation and depletion of the supramolecular luminescent Ag NCs system via strand displacement accompanied by a nicking process are demonstrated.

A pH and Mg2+-Responsive Molecular Switch Based on a Stable DNA Minidumbbell Bearing 5' and 3'-Overhangs

Minidumbbell (MDB) is a non-B DNA structure of which the thermodynamic stability is sensitive to a chemical environment such as pH, serving as a potential structural motif in constructing DNA-based molecular switches. This work aims to design thermodynamically stable MDB structures bearing 5' and 3'-overhanging deoxyribonucleotides in order to examine the possibility of MDB to be functionalized. Via making use of 5-methylcytosine and adjusting the pH of solution to be acidic, MDBs bearing 1-nucleotide (nt) or 2-nt overhanging residues at the 5' and 3'-ends have been obtained. Based on one of the new MDB sequences, we have designed a molecular switch that could respond to dual inputs of pH and Mg²⁺. The MDB strand and its partner strand formed a duplex (the "ON" state) upon inputting pH 7 and Mg²⁺, whereas the duplex dissociated to restore the MDB structure (the "OFF" state) upon inputting pH 5 and EDTA. The demonstration on the ability of MDB to sustain 5' and 3'-overhanging residues and the construction of a pH and Mg²⁺-responsive molecular switch will extend the application of MDB structures in dynamic DNA nanotechnology.

Photoresponsive Control of G-Quadruplex DNA Systems

G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.

Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy

G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.

On-Strand Knoevenagel Insertion of a Hemicyanine Molecular Rotor Loop Residue for Turn-On Fluorescence Detection of Pb-Induced G-Quadruplex Rigidity

We demonstrate the ability to distinguish Pb2+ from K+ within the central cavity of the antiparallel G-quadruplex (GQ) DNA produced by the thrombin binding aptamer (TBA) using an internal molecular rotor fluorescent probe. An indole-aldehyde containing an acyclic N-glycol group was first employed in the on-strand Knoevenagel condensation with five different heterocyclic quaternary cationic acceptors to assess the molecular rotor character of the resulting cyanine-styryl dyes within duplex DNA. An indole-pyridinium (4PI) nucleobase surrogate displayed the greatest turn-on emission response to duplex formation and was thus inserted into the loop residues of TBA to monitor GQ-folding in the presence of Pb2+ versus K+. TBA-4PI exhibits turn-on emission upon Pb2+-binding with a brightness (ε·Φfl) of 9000 cm-1 M-1 compared to K+-binding (ε·Φfl ∼ 2000 cm-1 M-1) due to Pb2+-induced GQ rigidity with 4PI-G-tetrad stacking interactions. The Pb2+-bound TBA-4PI GQ also provides energy-transfer (ET) fluorescence with a diagnostic excitation at 310 nm for distinguishing Pb2+ from K+ within the antiparallel GQ. The TBA-4PI GQ affords the desired turn-on fluorescence response for detecting Pb2+ ions with an apparent dissociation constant (Kd) of 63 nM and a limit of detection (LOD) of 19 nM in an aqueous buffer. It can also distinguish Pb2+ (230 nM) from K+ (1.5 mM, 6500-fold excess) in an antiparallel GQ recognition motif without topology twitching.

Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs

The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem-loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem-loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA-mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment

G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Redox manipulation of enzyme activity through physiologically active molecule

The effective utility of physiologically active molecules is crucial in numerous biological processes. However, the regulation of enzyme functions through active substances remains challenging at present. Here, glutathione (GSH), produced in cells, was used to modulate the catalytic activity of thrombin without external stimulus. It was found that high concentrations of GSH was more conducive to initiate the cleavage of compound AzoDiTAB in the range of concentration used to mimic the difference between cancer and normal cells, which has practical implications for targeting cancel cells since GSH is overexpressed in cancer cells. Importantly, GSH treatment caused the deformation of G4 structure by cleaving AzoDiTAB and thus triggered the transition of thrombin from being free to be inhibited in complex biological systems. This work would open up a new route for the specific manipulation of enzyme-catalyzed systems in cancer cells.

•

The transition of telomere DNA structures based on redox switch

•

Achieving redox manipulation of thrombin activity through active substance

•

This switch can be specifically used for enzyme regulation in cancer cells

The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology

Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the 'flanking effect' in this work. This 'flanking effect' was more pronounced when nucleotides were added at the 5'-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5'-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.

The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization

Guanine quadruplexes are four-stranded DNA/RNA structures composed of a guanine core (vertically stacked guanine tetrads) and peripheral groups (dangling ends and/or loops). Such a dual structural arrangement of the nucleobases favors their photoionization at energies significantly lower than the guanine ionization potential. This effect is important with respect to the oxidative DNA damage and for applications in the field of optoelectronics. Photoionization quantum yields, determined at 266 nm by nanosecond transient absorption spectroscopy, strongly depend on both the type and position of the peripheral nucleobases. The highest value (1.5 × 10-2) is found for the tetramolecular structure (AG4A)4 in which adenines are intermittently stacked on the adjacent guanine tetrads, as determined by nuclear magnetic resonance spectroscopy. Quantum chemistry calculations show that peripheral nucleobases interfere in a key step preceding electron ejection: charge separation, initiated by the population of charge transfer states during the relaxation of electronic excited states.

Metal-dependent electrochemical discrimination of DNA quadruplex sequences

Films of four different DNA quadruplex-forming (G4) sequences (c-KIT, c-MYC, HTelo, and BCL2) on gold surfaces were investigated by electrochemical impedance spectroscopy (EIS) to evaluate whether they evoke unique electrochemical responses that can be used for their identification. This could render EIS an alternative means for the determination of G4 sequences of unknown structure. Towards, this end, cation-dependent topology changes in the presence of either K+, K+ in combination with Li+, or Pb2+ in the presence of Li+ were first evaluated by circular dichroism (CD) spectroscopy, and electrochemical studies were performed subsequently. As a result, G4-sequence specific charge transfer resistance (RCT) patterns were in fact observed for each G4 sequence, allowing their discrimination by EIS.

A world beyond double-helical nucleic acids: the structural diversity of tetra-stranded G-quadruplexes

Nucleic acids can adopt various secondary structures including double-, triple-, and tetra-stranded helices that differ by the specific hydrogen bond mediated pairing pattern between their nucleobase constituents. Whereas double-helical DNA relies on Watson–Crick base pairing to play a prominent role in storing genetic information, G-quadruplexes are tetra-stranded structures that are formed by the association of guanine bases from G-rich DNA and RNA sequences. During the last few decades, G-quadruplexes have attracted considerable interest after the realization that they form and exert regulatory functions in vivo. In addition, quadruplex architectures have also been recognized as versatile and powerful tools in a growing number of technological applications. To appreciate the astonishing structural diversity of these tetra-stranded structures and to give some insight into basic interactions that govern their folding, this article gives an overview of quadruplex structures and rules associated with the formation of different topologies. A brief discussion will also focus on nonconventional quadruplexes as well as on general principles when targeting quadruplexes with ligands.

Graphic abstract

G-Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly

Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that are frequently found in genomes. The stability of G4s depends, among other factors, on the number of G-tetrads. Three- or four-tetrad G4s and antiparallel two-tetrad G4s have been characterized experimentally; however, the existence of an intramolecular (i. e., not dimeric or multimeric) two-tetrad parallel-stranded DNA G4 has never been experimentally observed. Many sequences compatible with two-tetrad G4 can be found in important genomic regions, such as promoters, for which parallel G4s predominate. Using experimental and theoretical approaches, the propensity of the model sequence AATGGGTGGGTTTGGGTGGGTAA to form an intramolecular parallel-stranded G4 upon increasing the number of GGG-to-GG substitutions has been studied. Deletion of a single G leads to the formation of intramolecular G4s with a stacked G-triad, whose topology depends on the location of the deletion. Removal of another guanine from another G-tract leads to di- or multimeric G4s. Further deletions mostly prevent the formation of any stable G4. Thus, a solitary two-tetrad parallel DNA G4 is not thermodynamically stable and requires additional interactions through capping residues. However, transiently populated metastable two-tetrad species can associate to form stable dimers, the dynamic formation of which might play additional delicate roles in gene regulation. These findings provide essential information for bioinformatics studies searching for potential G4s in genomes.

DNAzyme Sensor Uses Chemiluminescence Resonance Energy Transfer for Rapid, Portable, and Ratiometric Detection of Metal Ions

DNAzymes have emerged as an important class of sensors for a wide variety of metal ions, with florescence DNAzyme sensors as the most widely used in different sensing and imaging applications because of their fast response time, high signal intensity, and high sensitivity. However, the requirements of an external excitation light source and its associated power increase the cost and size of the fluorometer, making it difficult to be used for portable detections. To overcome these limitations, we report herein a DNAzyme sensor that relies on chemiluminescence resonance energy transfer (CRET) without the need for external light. The sensor is constructed by combining the functional motifs from both Pb2+-dependent 8-17 DNAzyme conjugated to fluorescein (FAM) and hemin/G-quadruplex that mimics horseradish peroxidase to catalyze the oxidation of luminol by H2O2 to yield chemiluminescence. In the absence of Pb2+, the hybridization between the enzyme and substrate strands bring the FAM and hemin/G-quadruplex in close proximity, resulting in CRET. The presence of Pb2+ ions can drive the cleavage on the substrate strand, resulting in a sharp decrease in the melting temperature of hybridization and thus separation of the FAM from hemin/G-quadruplex. The liberated CRET pair causes a ratiometric increase in the donor's fluorescent signal and a decrease in the acceptor signal. Using this method, Pb2+ ions have been measured rapidly (<15 min) with a low limit of detection at 5 nM. By removing the requirement of exogenous light excitation, we have demonstrated a simple and portable detection using a smartphone, making the DNAzyme-CRET system suitable for field tests of lake water. Since DNAzymes selective for other metal ions or targets, such as bacteria, can be obtained using in vitro selection, the method reported here opens a new avenue for rapid, portable, and ratiometric detection of many targets in environmental monitoring, food safety, and medical diagnostics.

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5′TGGGTGGGTGGGTGGG3′), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.

Dynamic nanoassembly-based drug delivery system (DNDDS): Learning from nature

Dynamic nanoassembly-based drug delivery system (DNDDS) has evolved from being a mere curiosity to emerging as a promising strategy for high-performance diagnosis and/or therapy of various diseases. However, dynamic nano-bio interaction between DNDDS and biological systems remains poorly understood, which can be critical for precise spatiotemporal and functional control of DNDDS in vivo. To deepen the understanding for fine control over DNDDS, we aim to explore natural systems as the root of inspiration for researchers from various fields. This review highlights ingenious designs, nano-bio interactions, and controllable functionalities of state-of-the-art DNDDS under endogenous or exogenous stimuli, by learning from nature at the molecular, subcellular, and cellular levels. Furthermore, the assembly strategies and response mechanisms of tailor-made DNDDS based on the characteristics of various diseased microenvironments are intensively discussed. Finally, the current challenges and future perspectives of DNDDS are briefly commented.

Programmable DNA Circuits for Flexible and Robust Exciton-Plasmon Interaction-Based Photoelectrochemical Biosensing

DNA circuits as one of the dynamic nanostructures can be rationally designed and show amazing geometrical complexity and nanoscale accuracy, which are becoming increasingly attractive for DNA entropy-driven amplifier design. Herein, a novel and elegant exciton-plasmon interaction (EPI)-based photoelectrochemical (PEC) biosensor was developed with the assistance of a programmable entropy-driven DNA amplifier and superparamagnetic nanostructures. Low-abundance miRNA-let-7a as a model can efficiently initiate the operation of the entropy-driven DNA amplifier, and the released output DNAs can open the partially hybridized double-stranded DNA anchored on Fe₃O₄@SiO₂ particles. The liberated Au nanoparticles (NPs)-cDNA can completely hybridize with CdSe/ZnS quantum dots (QDs)-cDNA-1 and result in proportionally decreased photocurrent of CdSe/ZnS QDs-cDNA-1. This unique entropy-driven amplification strategy is beneficial for reducing the reversibility of each step reaction, enables the base sequence invariant and the reaction efficiency improvement, and exhibits high thermal stability and specificity as well as flexible design. These features grant the PEC biosensor with ultrasensitivity and high selectivity. Also, instead of solid-liquid interface assembly for conventional EPI-based PEC biosensors, herein, DNA hybridization in the solution phase enables the improved hybridization efficiency and sensitivity. In addition, superparamagnetic Fe₃O₄@SiO₂ particles further ensure the enhancement of the selectivity and reliability of the as-designed PEC biosensor. Particularly, this single-step electrode modification procedure evidently improves the electrode fabrication efficiency, reproducibility, and stability.

G-quadruplex binders as cytostatic modulators of innate immune genes in cancer cells

G-quadruplexes (G4s) are non-canonical nucleic acid structures involved in fundamental biological processes. As G4s are promising anticancer targets, in past decades the search for effective anticancer G4 binders aimed at the discovery of more cytotoxic ligands interfering with specific G4 structures at oncogenes or telomeres. Here, we have instead observed a significant activation of innate immune genes by two unrelated ligands at non-cytotoxic concentrations. The studied G4 binders (pyridostatin and PhenDC3) can induce an increase of micronuclei triggering the activation of the cytoplasmic STING (stimulator of interferon response cGAMP interactor 1) signaling pathway in human and murine cancer cells. Ligand activity can then lead to type I interferon production and innate immune gene activation. Moreover, specific gene expression patterns mediated by a G4 binder in cancer cells correlate with immunological hot features and better survival in human TCGA (The Cancer Genome Atlas) breast tumors. The findings open to the development of cytostatic G4 binders as effective immunomodulators for combination immunotherapies in unresponsive tumors.

Quadruplex World

The RNA world hypothesis relies on the double-helix complementarity principle for both replication and catalytic activity of RNA. However, the de novo appearance of the complementarity rules, without previous evolution steps, is doubtful. Another major problem of the RNA world is its isolated nature, making it almost impossible to accommodate the genetic code and transform it into modern biochemistry. These and many other unanswered questions of the RNA world led to suggestions that some simpler molecules must have preceded RNA. Most of these alternative hypotheses proposed the double-helical polymers with different backbones but used the same complementarity principle. The current paper describes a fundamentally different idea: the de novo appearance of a nucleic acid polymer without any preexisting rules or requirements. This approach, coined as the quadruplex world hypothesis, is based on (i) the ability of guanines to form stable G-tetrads that facilitate polymerization; and (ii) the unique property of polyguanines to fold into a monomolecular tetrahelix with a strictly defined building pattern and tertiary structure. The tetrahelix is capable of high-affinity intermolecular interactions and catalytic activities. The quadruplex world hypothesis has the potential to address almost all the shortcomings of the RNA world.

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.

Selectivity and Targeting of G-Quadruplex Binders Activated by Adaptive Binding and Controlled by Chemical Kinetics

G-quadruplexes (G4s) are prevalent in oncogenes and are potential antitumor drug targets. However, binding selectivity of compounds to G4s still faces challenges. Herein, we report a platinum(II) complex (Pt1), whose affinity to G4-DNA is activated by adaptive binding and selectivity controlled by binding kinetics. The resolved structure of Pt1/VEGF-G4 (a promoter G4) shows that Pt1 matches 3'-G-tetrad of VEGF-G4 through Cl^- -dissociation and loop rearrangement of VEGF-G4. Binding rate constants are determined by coordination bond breakage/formation, correlating fully with affinities. The selective rate-determining binding step, Cl^- -dissociation upon G4-binding, is 2-3 orders of magnitude higher than dsDNA. Pt1 potently targets G4 in living cells, effectively represses VEGF expression, and inhibits vascular growth in zebrafish. We show adaptive G4-binding activation and controlled by kinetics, providing a complementary design principle for compounds targeting G4 or similar biomolecules.

Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes

Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.

Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing

i-DNA is a four-stranded, pH-sensitive structure formed by cytosine-rich DNA sequences. Previous reports have addressed the conditions for formation of this motif in DNA in vitro and validated its existence in human cells. Unfortunately, these in vitro studies have often been performed under different experimental conditions, making comparisons difficult. To overcome this, we developed a four-dimensional UV melting and annealing (4DUVMA) approach to analyze i-DNA formation under a variety of conditions (e.g., pH, temperature, salt, crowding). Analysis of 25 sequences provided a global understanding of i-DNA formation under disparate conditions, which should ultimately allow the design of accurate prediction tools. For example, we found reliable linear correlations between the midpoint of pH transition and temperature (-0.04 ± 0.003 pH unit per 1.0 °C temperature increment) and between the melting temperature and pH (-23.8 ± 1.1 °C per pH unit increment). In addition, by analyzing the hysteresis between denaturing and renaturing profiles in both pH and thermal transitions, we found that loop length, nature of the C-tracts, pH, temperature, and crowding agents all play roles in i-DNA folding kinetics. Interestingly, our data indicate which conformer is more favorable for the sequences with an odd number of cytosine base pairs. Then the thermal and pH stabilities of "native" i-DNAs from human promoter genes were measured under near physiological conditions (pH 7.0, 37 °C). The 4DUVMA method can become a universal resource to analyze the properties of any i-DNA-prone sequence.

Ultrafast excited state dynamics and light-switching of [Ru(phen)2(dppz)]2+ in G-quadruplex DNA

The triplet metal to ligand charge transfer (³MLCT) luminescence of ruthenium (II) polypyridyl complexes offers attractive imaging properties, specifically towards the development of sensitive and structure-specific DNA probes. However, rapidly-deactivating dark state formation may compete with ³MLCT luminescence depending on different DNA structures. In this work, by combining femtosecond and nanosecond pump-probe spectroscopy, the ³MLCT relaxation dynamics of [Ru(phen)₂(dppz)]²⁺ (phen = 1,10-phenanthroline, dppz = dipyridophenazine) in two iconic G-quadruplexes has been scrutinized. The binding modes of stacking of dppz ligand on the terminal G-quartet fully and partially are clearly identified based on the biexponential decay dynamics of the ³MLCT luminescence at 620 nm. Interestingly, the inhibited dark state channel in ds-DNA is open in G-quadruplex, featuring an ultrafast picosecond depopulation process from ³MLCT to a dark state. The dark state formation rates are found to be sensitive to the content of water molecules in local G-quadruplex structures, indicating different patterns of bound water. The unique excited state dynamics of [Ru(phen)₂(dppz)]²⁺ in G-quadruplex is deciphered, providing mechanistic basis for the rational design of photoactive ruthenium metal complexes in biological applications.