i-Motif Quadruplex DNA-Based Biosensor for Distinguishing Single- and Multiwalled Carbon Nanotubes

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.

Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.

Subcellular localization of DNA nanodevices and their applications

The application of nanodevices based on DNA self-assembly in the field of cell biology has made significant progress in the past decade. In this study, the development of DNA nanotechnology is briefly reviewed. The subcellular localization of DNA nanodevices, and their new progress and applications in the fields of biological detection, subcellular and organ pathology, biological imaging, and other fields are reviewed. The future of subcellular localization and biological applications of DNA nanodevices is also discussed.

Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene

The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.

Recent Advances in DNA Nanotechnology for Plasmonic Biosensor Construction

Since 2010, DNA nanotechnology has advanced rapidly, helping overcome limitations in the use of DNA solely as genetic material. DNA nanotechnology has thus helped develop a new method for the construction of biosensors. Among bioprobe materials for biosensors, nucleic acids have shown several advantages. First, it has a complementary sequence for hybridizing the target gene. Second, DNA has various functionalities, such as DNAzymes, DNA junctions or aptamers, because of its unique folded structures with specific sequences. Third, functional groups, such as thiols, amines, or other fluorophores, can easily be introduced into DNA at the 5′ or 3′ end. Finally, DNA can easily be tailored by making junctions or origami structures; these unique structures extend the DNA arm and create a multi-functional bioprobe. Meanwhile, nanomaterials have also been used to advance plasmonic biosensor technologies. Nanomaterials provide various biosensing platforms with high sensitivity and selectivity. Several plasmonic biosensor types have been fabricated, such as surface plasmons, and Raman-based or metal-enhanced biosensors. Introducing DNA nanotechnology to plasmonic biosensors has brought in sight new horizons in the fields of biosensors and nanobiotechnology. This review discusses the recent progress of DNA nanotechnology-based plasmonic biosensors.

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

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

The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome

G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.

Exploring the Thermodynamics of 7-Amino Actinomycin D-Induced Single-Stranded DNA Hairpin by Spectroscopic Techniques and Computational Simulations

NMR studies have indicated that the anti-tumor therapeutic agent actinomycin D (ACTD) can induce seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT₃GTGG-3' to form a hairpin structure with tandem GT mismatches at the stem region next to a loop of three stacked thymine bases. In an effort to uncover the preference of binding sequence and to elucidate the thermodynamics properties of the binding, a combination of spectroscopic techniques and computational simulation studies was performed with d(CCGTT_nGTGG) and d(CCGAA_nGAGG) (denoted as GTT_n and GAA_n, respectively; n = 3, 5, and 7) sequences. In the presence of 7-amino actinomycin D (7AACTD), all the six oligomers formed stable hairpin structures. The GTT₅-7AACTD/GAA₅-7AACTD hairpin structure was more stable than the corresponding GTT_n-7AACTD and GAA_n-7AACTD (n = 3, 7). No significant ΔG difference was observed between GTT_n-7AACTD and GAA_n-7AACTD complexes with the same loop length. In agreement with the 7AACTD-induced hairpin stability results, the binding affinity of GTT_n and GAA_n with 7AACTD increased from n = 3 to n = 5 and then decreased when n is 7. Moreover, GTT_n and GAA_n with the same loop length showed comparable binding affinities to 7AACTD. Furthermore, molecular dynamics simulations found that van der Waals interactions between GTT_n/GAA_n and 7AACTD were the primary attractive forces for 7AACTD binding, and the electrostatic interactions between the carbonyl groups of 7AACTD and bases in the hairpin were the major unfavorable forces. These findings furthered our understanding that 7AACTD is sensitive to the loop size and sequence as well as tandem GT/GA mismatches of their deoxyribonucleic acid (DNA) targets. A deep understanding of the thermodynamics and the molecular recognition mechanism of 7AACTD with ssDNAs would further the development of ACTD-like antitumor agents.

G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection

G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.

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

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

I-motif Formed at Physiological pH Triggered by Spatial Confinement of Nanochannels: An Electrochemical Platform for pH Monitoring in Brain Microdialysates

The development of switches responding to specific pH changes was particularly useful in wide application fields. Owing to flexible switches simulated by pH, i-motif DNAs are widely used as a pH sensor. But its character of structure transition strongly dependent on acidic pH severely hampers the application of i-motif DNA in physiological media. Herein, we report the stable i-motif structure formed at a physiological pH triggered by spatial confinement of silica nanochannels. Three classic DNA chains containing 21-mer i-motif domain base-pairs and a single-stranded multiply (T)_n spacer, 5'-COOH-(T)_n-CCCTAACCCTAACCCTAACCC-3', were employed to evaluate the enhanced stability of i-motif structure. Compared to their free states in a dilute solution, the transition pH of all i-motif DNAs decorated in nanochannels remarkably shifts toward a neutral pH. Moreover, the transition midpoint can be tuned sensitively over the physiologically relevant pH range through slightly varying the length of T base spacer. Density functional theory (DFT) calculations validate that the increased proton density in a nanochannel triggers the formation of an i-motif structure under a neutral pH. Finally, this i-motif DNA based nanochannels electrode was successfully employed to monitor pH in brain microdialysates followed by cerebral ischemia. The present approach is not limited by fundamental investigation for DNA conformation but may extend toward the manipulation of i-motif based structures for artificial molecular machines and signaling systems.

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

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

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene

In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.

Nucleic Acid-Based Functional Nanomaterials as Advanced Cancer Therapeutics

Nucleic acid-based functional nanomaterials (NAFN) have been widely used as emerging drug delivery nanocarriers for cancer therapeutics. Considerable works have demonstrated that NAFN can effectively load and protect therapeutic agents, and particularly enable targeting delivery to the tumor site and stimuli-responsive release. These outstanding performances are due to NAFN's unique properties including inherent biological functions and sequence programmability as well as biocompatibility and biodegradability. In this Review, the recent progress on NAFN as advanced cancer therapeutics is highlighted. Three main cancer therapy approaches are categorized including chemo-, immuno-, and gene-therapy. Examples are presented to show how NAFN are rationally and exquisitely designed to address problems in cancer therapy. The challenges and future development of NAFN are also discussed toward future more practical biomedical applications.

Cationic porphyrins with large side arm substituents as resonance light scattering ratiometric probes for specific recognition of nucleic acid G-quadruplexes

Specific G-quadruplex-probing is crucial for both biological sciences and biosensing applications. Most reported probes are focused on fluorescent or colorimetric recognition of G-quadruplexes. Herein, for the first time, we reported a new specific G-quadruplex-probing technique-resonance light scattering (RLS)-based ratiometric recognition. To achieve the RLS probing of G-quadruplexes in the important physiological pH range of 7.4-6.0, four water soluble cationic porphyrin derivatives, including an unreported octa-cationic porphyrin, with large side arm substituents were synthesized and developed as RLS probes. These RLS probes were demonstrated to work well for ratiometric recognition of G-quadruplexes with high specificity against single- and double-stranded DNAs, including long double-stranded ones. The working mechanism was speculated to be based on the RLS signal changes caused by porphyrin protonation that was promoted by the end-stacking of porphyrins on G-quadruplexes. This work adds an important member in G-quadruplex probe family, thus providing a useful tool for studies on G-quadruplex-related events concerning G-quadruplex formation, destruction and changes in size, shape and aggregation. As a proof-of-concept example of applications, the RLS probes were demonstrated to work well for label-free and sequence-specific sensing of microRNA. This work also provides a simple and useful way for the preparation of cationic porphyrins with high charges.

DNA conformational polymorphism for biosensing applications

In this mini review, we will briefly introduce the rapid development of DNA conformational polymorphism in biosensing field, including canonical DNA duplex, triplex, quadruplex, DNA origami, as well as more functionalized DNAs (aptamer, DNAzyme etc.). Various DNA structures are adopted to play important roles in sensor construction, through working as recognition receptor, signal reporter or linking staple for signal motifs, etc. We will mainly summarize their recent developments in DNA-based electrochemical and fluorescent sensors. For the electrochemical sensors, several types will be included, e.g. the amperometric, electrochemical impedance, electrochemiluminescence, as well as field-effect transistor sensors. For the fluorescent sensors, DNA is usually modified with fluorescent molecules or novel nanomaterials as report probes, excepting its core recognition function. Finally, general conclusion and future perspectives will be discussed for further developments.

Modulating Aptamer Specificity with pH-Responsive DNA Bonds

Aptamers that recognize specific cells in a complex environment have emerged as invaluable molecular tools in bioanalysis and in the development of targeted therapeutics. The selective recognition of aptamers, however, can be compromised by the coexistence of target receptors on both target cells and other cells. To address this problem, we constructed a structure-switchable aptamer (SW-Apt) with reconfigurable binding affinity in accordance with the microenvironment of target cells. The SW-Apt makes use of i-motifs, which are quadruplex structures that form in sequences rich in cytosine. More specifically, we report the design of single-stranded, pH-responsive i-motif-modified aptamers able to bind specifically with target cells by exploiting their pH. Here, the i-motif serves as a structural domain to either facilitate the binding ability of aptamers to target cells or suppress the binding ability of aptamers to nontarget cell based on the pH of the cellular microenvironment. SW-Apt exhibited high binding ability with target cells at acidic pH, while no obvious binding was observed at physiological pH. The i-motif-induced structure-switching was verified with Förster resonance energy transfer and circular dichroism spectroscopy. Notably, SW-Apt exhibits high specificity in serum and excellent stability, likely attributed to the folded quadruplex i-motif structure. This study provides a simple and efficient strategy to chemically modulate aptamer binding ability and thus improve aptamer binding specificity to target cells, irrespective of the coexistence of identical receptors on target and nontarget cells.

Coupling oligonucleotides possessing a poly-cytosine tag with magnetic ionic liquids for sequence-specific DNA analysis

Oligonucleotide probes were designed with a poly-cytosine region that facilitates stable anchoring to a magnetic ionic liquid support. By tethering a recognition sequence to the poly-C tag, the resulting diblock oligonucleotides distinguished single-nucleotide variants and captured DNA targets from interfering genomic DNA and cell lysate for qPCR amplification.

Improved i-motif thermal stability by insertion of anthraquinone monomers

In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone. The insertion of anthraquinone was found to stabilize the i-motif structure when replacing any one of the positions of the central TAA loop and the thermal stabilities were typically higher than those previously found for i-motifs containing pyrene-modified uracilyl unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T₁₀ enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A₆ and T₁₆ were modified with a double replacement by the 2,6-isomer into the TAA loops in the outer regions. The largest destabilization is observed for the 1,5-disubstituted anthraquinone linker upon the replacement of A₁₈. CD curves of anthraquinone-modified variants imply no structural changes in all cases under potassium buffer conditions compared with those of the native i-motif. Molecular modeling studies explained the increased thermal stabilities of anthraquinone-modified i-motifs.

Length-Dependent Diblock DNA with Poly-cytosine (Poly-C) as High-Affinity Anchors on Graphene Oxide

DNA-functionalized graphene oxide (GO) is a popular system for biosensor development and directed materials assembly. Compared to covalent attachment, simple physisorption of DNA has been more popular, and a DNA sequence with a strong affinity on GO is highly desirable. Recently, we found that poly-cytosine (poly-C) DNA can strongly adsorb on many common nanomaterials, including GO. To identify an optimal length of poly-C DNA, we herein designed a series of diblock DNA sequences containing between 0 and 30 cytosines. The displacement of a random sequenced DNA by poly-C DNA was demonstrated, confirming the desired diblock structure on GO with the poly-C block anchoring on the surface and the other block available for hybridization. The adsorption density of poly-C containing DNA did not vary much as the length of the poly-C block increased, suggesting the conformation of the anchoring DNA on the GO was quite independent of the DNA length. With a longer poly-C block, the efficiency of surface hybridization of the other block increased, while nonspecific adsorption of noncomplementary DNA was inhibited more. Compared to poly-adenine (poly-A)-containing DNAs, which were previously used for the same purpose, poly-C DNA adsorption is more stable. Using four types of 15-mer DNA homopolymers as the intended anchoring sequences, the C₁₅ DNA had the best hybridization efficiency. This work has suggested the optimal length for the poly-C block to be 15-mer or longer, and it has provided interesting insights into the DNA/GO biointerface.

Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH

i-Motifs are alternative DNA secondary structures formed in cytosine-rich sequences. Particular examples of these structures, traditionally assumed to be stable only at acidic pH, have been found to form under near-physiological conditions. To determine the potential impact of these structures on physiological processes, investigation of sequences with the capacity to fold under physiological conditions is required. Here we describe a systematic study of cytosine-rich DNA sequences, with varying numbers of consecutive cytosines, to gain insights into i-motif DNA sequence and structure stability. i-Motif formation was assessed using ultraviolet spectroscopy, circular dichroism and native gel electrophoresis. We found that increasing cytosine tract lengths resulted in increased thermal stability; sequences with at least five cytosines per tract folded into i-motif at room temperature and neutral pH. Using these results, we postulated a folding rule for i-motif formation, analogous to (but different from) that for G-quadruplexes. This indicated that thousands of cytosine-rich sequences in the human genome may fold into i-motif structures under physiological conditions. Many of these were found in locations where structure formation is likely to influence gene expression. Characterization of a selection of these identified i-motif forming sequences uncovered 17 genomic i-motif forming sequence examples which were stable at neutral pH.

Dynamic Nanoparticle Assemblies for Biomedical Applications

Designed synthesis and assembly of nanoparticles assisted by their surface ligands can create "smart" materials with programmed responses to external stimuli for biomedical applications. These assemblies can be designed to respond either exogenously (for example, to magnetic field, temperature, ultrasound, light, or electric pulses) or endogenously (to pH, enzymatic activity, or redox gradients) and play an increasingly important role in a diverse range of biomedical applications, such as biosensors, drug delivery, molecular imaging, and novel theranostic systems. In this review, the recent advances and challenges in the development of stimuli-responsive nanoparticle assemblies are summarized; in particular, the application-driven design of surface ligands for stimuli-responsive nanoparticle assemblies that are capable of sensing small changes in the disease microenvironment, which induce the related changes in their physico-chemical properties, is described. Finally, possible future research directions and problems that have to be addressed are briefly discussed.

Luminescence switch-on assay of interferon-gamma using a G-quadruplex-selective iridium(III) complex

In this study, we synthesized a series of 9 luminescent iridium(III) complexes and studied their ability to function as luminescent probes for G-quadruplex DNA. The iridium(III) complex 8 [Ir(pbtz)2(dtbpy)]PF6 (where pbtz = 2-phenylbenzo[d]thiazole; dtbpy = 4,4'-di-tert-butyl-2,2'-bipyridine) showed high selectivity for G-quadruplex DNA over single-stranded and double-stranded DNA, and was subsequently utilized for the development of a label-free oligonucleotide-based assay for interferon-gamma (IFN-γ), an important biomarker for a range of immune and infectious diseases, in aqueous solution. We further demonstrated that this assay could monitor IFN-γ levels even in the presence of cellular debris. This assay represents the first G-quadruplex-based assay for IFN-γ detection described in the literature.

Carbon Nanomaterials and DNA: from Molecular Recognition to Applications

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

Conformational switch-mediated accelerated release of drug from cytosine-rich nucleic acid-capped magnetic nanovehicles

A novel concept that the conformational switch of cytosine-rich DNA can accelerate the release of drug from DNA-capped nanovehicles is rationally devised.

Cobalt disulfide nanowires as an effective fluorescent sensing platform for DNA detection

Cobalt disulfide nanowires are synthesized in solution using a facile two-step hydrothermal method for the first time and applied as an effective sensing platform for nucleic acid detection.

A label-free G-quadruplex-based mercury detection assay employing the exonuclease III-mediated cleavage of T-Hg2+-T mismatched DNA

We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg2+. Unlike common DNA-based Hg2+ detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This 'mix-and-detect' methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM of Hg2+.

Development of an Aptamer-Based Sensing Platform for Metal Ions, Proteins, and Small Molecules through Terminal Deoxynucleotidyl Transferase Induced G-Quadruplex Formation

We report a label-free, structure-independent luminescent-sensing platform for metal ions, proteins, and small molecules utilizing an Ir(III) complex, terminal deoxynucleotidyl transferase (TdT), and a structure-folding aptamer. A novel G-quadruplex-selective Ir(III) complex was identified to detect the nascent G-quadruplex motifs with an enhanced luminescence response. Unlike most label-free DNA-based assays reported in the literature, this sensing platform does not require a specific secondary structure of aptamer, thus greatly simplifying DNA design. The detection platform was demonstrated by the detection of K(+) ions, thrombin, and cocaine as representative examples of metal ions, proteins, and small molecules.

A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe

Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications.

A Luminescent Cocaine Detection Platform Using a Split G-Quadruplex-Selective Iridium(III) Complex and a Three-Way DNA Junction Architecture

In this study, a series of 10 in-house cyclometalated iridium(III) complexes bearing different auxiliary ligands were tested for their selectivity toward split G-quadruplex in order to construct a label-free switch-on cocaine detection platform employing a three-way junction architecture and a G-quadruplex motif as a signal output unit. Through two rounds of screening, we discovered that the iridium(III) complex 7 exhibited excellent selectivity toward the intermolecular G-quadruplex motif. A detection limit as low as 30 nM for cocaine can be achieved by this sensing approach with a linear relationship between luminescence intensity and cocaine concentration established from 30 to 300 nM. Furthermore, this sensing approach could detect cocaine in diluted oral fluid. We hope that our simple, signal-on, label-free oligonucleotide-based sensing method for cocaine using a three-way DNA junction architecture could act as a useful platform in bioanalytical research.

Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe

A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)2(5,5-dmbpy)]PF6 (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5'-dimethyl-2,2'-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na(+) /K(+) ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased π-π stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.

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

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

Active biopolymers in green non-conventional media: a sustainable tool for developing clean chemical processes

By understanding structure–function relationships of active biopolymers (e.g. enzymes and nucleic acids) in green non-conventional media, sustainable chemical processes may be developed.

G-quadruplex-based logic gates for HgII and AgI ions employing a luminescent iridium(iii) complex and extension of metal-mediated base pairs by polymerase

We report herein the synthesis of a series of cyclometallated iridium(iii) complexes as luminescent G-quadruplex-selective probes to construct AND, OR and INHIBIT logic gates for the detection of Hg^II and Ag^I ions.

Chemiluminescence excited paper-based photoelectrochemical competitive immunosensing based on porous ZnO spheres and CdS nanorods

A chemiluminescence excited photoelectrochemical (PEC) competitive immunosensor for sensitive and specific detection of the prostate specific antigen (PSA) is firstly developed by combining a microfluidic paper-based device. Firstly, porous ZnO spheres with large surface area and good biocompatibility are attached onto the Au nanoparticle modified paper working electrode, which serve as an effective matrix for antigens. CdS nanorods (NRs) are selected as the photoactive materials due to their excellent fast and long distance electron transport capability, which allow the binding of the horseradish peroxidase-labeled signal antibody onto CdS NRs (CdS NR-Ab-HRP). After a competitive immunoassay format, the CdS NR-Ab-HRP labels are captured onto the electrode surface. The chemiluminescent excitation is produced from the oxidation of luminol by H₂O₂ in the presence of HRP. The more antigens in solution can bind to CdS NR-Ab-HRP the less CdS NR-Ab-HRP can bind to antigens immobilized on the electrode, which result in the decrease of chemiluminescence emission and light absorption, leading to the decrease of photocurrent intensity. The PEC response from CdS NR-Ab-HRP successfully fulfilled the sensitive detection of PSA in the linear range from 0.005 to 150 ng mL^-1 with a detection limit of 2.3 pg mL^-1. The proposed immunosensor shows excellent analytical performance with high reproducibility and stability, and can become a promising platform for other protein detection.